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Sample records for calculating complete evolutionary

  1. Completely integrable operator evolutionary equations

    International Nuclear Information System (INIS)

    Chudnovsky, D.V.

    1979-01-01

    The authors present natural generalizations of classical completely integrable equations where the functions are replaced by arbitrary operators. Among these equations are the non-linear Schroedinger, the Korteweg-de Vries, and the modified KdV equations. The Lax representation and the Baecklund transformations are presented. (Auth.)

  2. Calculating evolutionary dynamics in structured populations.

    Directory of Open Access Journals (Sweden)

    Charles G Nathanson

    2009-12-01

    Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.

  3. Mueller Navelet jets at LHC - complete NLL BFKL calculation

    Energy Technology Data Exchange (ETDEWEB)

    Colferai, Dimitri [Firenze Univ. (Italy). Dipt. di Fisica; INFN, Florence (Italy); Schwennsen, Florian [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Szymanowski, Lech [Soltan Inst. for Nuclear Studies, Warsaw (Poland); Ecole Polytechnique, CNRS, Palaiseau (France). CPHT; Wallon, Samuel [Paris-Sud Univ., CNRS, Orsay (France). LPT; UPMC Univ. Paris 06 (France). Faculte de Physique

    2010-03-15

    We calculate cross section and azimuthal decorrelation of Mueller Navelet jets at the LHC in the complete next-lo-leading order BFKL framework, i.e. including next-to-leading corrections to the Green's function as well as next-to-leading corrections to the Mueller Navelet vertices. The obtained results for standard observables proposed for studies of Mueller Navelet jets show that both sources of corrections are of equal, big importance for final magnitude and final behavior of observables. The astonishing conclusion of our analysis is that the observables obtained within the complete next-lo-leading order BFKL framework of the present paper are quite similar to the same observables obtained within next-to-leading logarithm DGLAP type treatment. This fact sheds doubts on general belief that the studies of Mueller Navelet jets at the LHC will lead to clear discrimination between the BFKL and the DGLAP dynamics. (orig.)

  4. Mueller Navelet jets at LHC - complete NLL BFKL calculation

    International Nuclear Information System (INIS)

    Colferai, Dimitri; Schwennsen, Florian; Szymanowski, Lech; Ecole Polytechnique, CNRS, Palaiseau; Wallon, Samuel; UPMC Univ. Paris 06

    2010-03-01

    We calculate cross section and azimuthal decorrelation of Mueller Navelet jets at the LHC in the complete next-lo-leading order BFKL framework, i.e. including next-to-leading corrections to the Green's function as well as next-to-leading corrections to the Mueller Navelet vertices. The obtained results for standard observables proposed for studies of Mueller Navelet jets show that both sources of corrections are of equal, big importance for final magnitude and final behavior of observables. The astonishing conclusion of our analysis is that the observables obtained within the complete next-lo-leading order BFKL framework of the present paper are quite similar to the same observables obtained within next-to-leading logarithm DGLAP type treatment. This fact sheds doubts on general belief that the studies of Mueller Navelet jets at the LHC will lead to clear discrimination between the BFKL and the DGLAP dynamics. (orig.)

  5. Evolutionary calculations for planetary nebula nuclei with continuing mass loss and realistic starting conditions

    International Nuclear Information System (INIS)

    Faulkner, D.J.; Wood, P.R.

    1984-01-01

    Evolutionary calculations for nuclei of planetary nebulae are described. They were made using assumptions regarding mass of the NPN, phase in the He shell flash cycle at which the NPN leaves the AGB, and time variation of the mass loss rate. Comparison of the evolutionary tracks with the observational Harman-Seaton sequence indicates that some recently published NPN luminosities may be too low by a factor of three. Comparison of the calculated timescales with the observed properties of NPN and of white dwarfs provides marginal evidence for the PN ejection being initiated by the helium shell flash itself

  6. New developments in multireference and complete configuration interaction calculations

    International Nuclear Information System (INIS)

    Knowles, P.J.; Werner, H.J.

    1987-01-01

    Some recently developed techniques for the calculation of Hamiltonian matrix elements in molecular electronic structure calculations are described. These techniques allow the very rapid calculation, in any desired order, of one particle coupling coefficients between spin symmetry adapted basis functions of arbitrary structure. The matrix elements that are required, for either internally contracted multireference CI calculations, or full CI calculations, are then obtainable from suitable summations over resolutions of the identity, which has been shown previously to be rather efficient; this is especially true on vector computers, since all arithmetic can be formulated as matrix multiplications. These ideas have culminated in the preparation of a new multireference CI program which is capable of handling very large numbers of reference configurations. Application of the new techniques to full CI calculations are also presented

  7. Complete mitochondrial genomes reveal phylogeny relationship and evolutionary history of the family Felidae.

    Science.gov (United States)

    Zhang, W Q; Zhang, M H

    2013-09-03

    Many mitochondrial DNA sequences are used to estimate phylogenetic relationships among animal taxa and perform molecular phylogenetic evolution analysis. With the continuous development of sequencing technology, numerous mitochondrial sequences have been released in public databases, especially complete mitochondrial DNA sequences. Using multiple sequences is better than using single sequences for phylogenetic analysis of animals because multiple sequences have sufficient information for evolutionary process reconstruction. Therefore, we performed phylogenetic analyses of 14 species of Felidae based on complete mitochondrial genome sequences, with Canis familiaris as an outgroup, using neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods. The consensus phylogenetic trees supported the monophyly of Felidae, and the family could be divided into 2 subfamilies, Felinae and Pantherinae. The genus Panthera and species tigris were also studied in detail. Meanwhile, the divergence of this family was estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock, and the results shown were consistent with previous studies. In summary, the evolution of Felidae was reconstructed by phylogenetic analysis based on mitochondrial genome sequences. The described method may be broadly applicable for phylogenetic analyses of anima taxa.

  8. The complete mitochondrial genome of Gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes.

    Science.gov (United States)

    Liu, Guozheng; Cao, Dandan; Li, Shuangshuang; Su, Aiguo; Geng, Jianing; Grover, Corrinne E; Hu, Songnian; Hua, Jinping

    2013-01-01

    Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes. We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.

  9. Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications.

    Science.gov (United States)

    Kim, Young-Kyu; Park, Chong-wook; Kim, Ki-Joong

    2009-03-31

    The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast matK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our

  10. Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio

    Directory of Open Access Journals (Sweden)

    Gillings Michael R

    2006-01-01

    Full Text Available Abstract Background Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be. Multiple insertion events can lead to the assembly of large integron-associated cassette arrays. The most striking examples are found in Vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains. Results The complete Vibrio sp. DAT722 integron cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene cassette encoded genes. It differs extensively in terms of genomic context as well as gene cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene cassette pool suggests frequent transfer of cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene cassettes and others where cassettes have been inserted into chromosomal locations outside integrons. Conclusion Our systematic approach greatly facilitates the isolation and annotation of large integrons gene cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene

  11. Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

    OpenAIRE

    Nakamura, Yoji; Mori, Kazuki; Saitoh, Kenji; Oshima, Kenshiro; Mekuchi, Miyuki; Sugaya, Takuma; Shigenobu, Yuya; Ojima, Nobuhiko; Muta, Shigeru; Fujiwara, Atushi; Yasuike, Motoshige; Oohara, Ichiro; Hirakawa, Hideki; Chowdhury, Vishwajit Sur; Kobayashi, Takanori

    2013-01-01

    Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing tec...

  12. Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.

    Science.gov (United States)

    Nakamura, Yoji; Mori, Kazuki; Saitoh, Kenji; Oshima, Kenshiro; Mekuchi, Miyuki; Sugaya, Takuma; Shigenobu, Yuya; Ojima, Nobuhiko; Muta, Shigeru; Fujiwara, Atushi; Yasuike, Motoshige; Oohara, Ichiro; Hirakawa, Hideki; Chowdhury, Vishwajit Sur; Kobayashi, Takanori; Nakajima, Kazuhiro; Sano, Motohiko; Wada, Tokio; Tashiro, Kosuke; Ikeo, Kazuho; Hattori, Masahira; Kuhara, Satoru; Gojobori, Takashi; Inouye, Kiyoshi

    2013-07-02

    Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.

  13. Automated calculation of complete Pxy and Txy diagrams for binary systems

    DEFF Research Database (Denmark)

    Cismondi, Martin; Michelsen, Michael Locht

    2007-01-01

    phase equilibrium calculations in binary systems, in: Proceedings of the CD-ROM EQUIFASE 2006, Morelia, Michoacan, Mexico, October 21-25, 2006; www.gpec.plapiqui.edu.ar]. In this work we present the methods and computational strategy for the automated calculation of complete Pxy and Txy diagrams...

  14. Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2

    Energy Technology Data Exchange (ETDEWEB)

    Dash, Paban Kumar, E-mail: pabandash@rediffmail.com; Sharma, Shashi; Soni, Manisha; Agarwal, Ankita; Parida, Manmohan; Rao, P.V.Lakshmana

    2013-07-05

    Highlights: •Complete genome of Indian DENV-2 was deciphered for the first time in this study. •The recent Indian DENV-2 revealed presence of many unique amino acid residues. •Genotype shift (American to Cosmopolitan) characterizes evolution of DENV-2 in India. •Circulation of a unique clade of DENV-2 in South Asia was identified. -- Abstract: Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a

  15. Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2

    International Nuclear Information System (INIS)

    Dash, Paban Kumar; Sharma, Shashi; Soni, Manisha; Agarwal, Ankita; Parida, Manmohan; Rao, P.V.Lakshmana

    2013-01-01

    Highlights: •Complete genome of Indian DENV-2 was deciphered for the first time in this study. •The recent Indian DENV-2 revealed presence of many unique amino acid residues. •Genotype shift (American to Cosmopolitan) characterizes evolution of DENV-2 in India. •Circulation of a unique clade of DENV-2 in South Asia was identified. -- Abstract: Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a

  16. Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History

    Science.gov (United States)

    He, Yang; Deng, Cao; Fan, Gang; Qin, Shishang

    2017-01-01

    The Coptis chinensis Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of C. chinensis. This genome is 155,484 bp long with 38.17% GC content. Two 26,758 bp long inverted repeats separated the genome into a typical quadripartite structure. The C. chinensis chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in C. chinensis are poly-A/T. The numbers of mononucleotide SSRs in C. chinensis and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae. C. chinensis diverged from other Ranunculaceae species an estimated 81 million years ago (Mya). The divergence between Ranunculaceae and Berberidaceae was ~111 Mya, while the Ranunculales and Magnoliaceae shared a common ancestor during the Jurassic, ~153 Mya. Position 104 of the C. chinensis ndhG protein was identified as a positively selected site, indicating possible selection for the photosystem-chlororespiration system in C. chinensis. In summary, the complete sequencing and annotation of the C. chinensis chloroplast genome will facilitate future studies on this important medicinal species. PMID:28698879

  17. Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History

    Directory of Open Access Journals (Sweden)

    Yang He

    2017-01-01

    Full Text Available The Coptis chinensis Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of C. chinensis. This genome is 155,484 bp long with 38.17% GC content. Two 26,758 bp long inverted repeats separated the genome into a typical quadripartite structure. The C. chinensis chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in C. chinensis are poly-A/T. The numbers of mononucleotide SSRs in C. chinensis and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae. C. chinensis diverged from other Ranunculaceae species an estimated 81 million years ago (Mya. The divergence between Ranunculaceae and Berberidaceae was ~111 Mya, while the Ranunculales and Magnoliaceae shared a common ancestor during the Jurassic, ~153 Mya. Position 104 of the C. chinensis ndhG protein was identified as a positively selected site, indicating possible selection for the photosystem-chlororespiration system in C. chinensis. In summary, the complete sequencing and annotation of the C. chinensis chloroplast genome will facilitate future studies on this important medicinal species.

  18. A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus: an evolutionary history of camelidae

    Directory of Open Access Journals (Sweden)

    Meng He

    2007-07-01

    Full Text Available Abstract Background The family Camelidae that evolved in North America during the Eocene survived with two distinct tribes, Camelini and Lamini. To investigate the evolutionary relationship between them and to further understand the evolutionary history of this family, we determined the complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus, the only wild survivor of the Old World camel. Results The mitochondrial genome sequence (16,680 bp from C. bactrianus ferus contains 13 protein-coding, two rRNA, and 22 tRNA genes as well as a typical control region; this basic structure is shared by all metazoan mitochondrial genomes. Its protein-coding region exhibits codon usage common to all mammals and possesses the three cryptic stop codons shared by all vertebrates. C. bactrianus ferus together with the rest of mammalian species do not share a triplet nucleotide insertion (GCC that encodes a proline residue found only in the nd1 gene of the New World camelid Lama pacos. This lineage-specific insertion in the L. pacos mtDNA occurred after the split between the Old and New World camelids suggests that it may have functional implication since a proline insertion in a protein backbone usually alters protein conformation significantly, and nd1 gene has not been seen as polymorphic as the rest of ND family genes among camelids. Our phylogenetic study based on complete mitochondrial genomes excluding the control region suggested that the divergence of the two tribes may occur in the early Miocene; it is much earlier than what was deduced from the fossil record (11 million years. An evolutionary history reconstructed for the family Camelidae based on cytb sequences suggested that the split of bactrian camel and dromedary may have occurred in North America before the tribe Camelini migrated from North America to Asia. Conclusion Molecular clock analysis of complete mitochondrial genomes from C. bactrianus ferus and L

  19. Tracking the Obscured Star Formation Along the Complete Evolutionary Merger Sequence of LIRGs

    Science.gov (United States)

    Diaz-Santos, Tanio

    2014-10-01

    We propose to obtain WFC3 narrow-band Pa-beta imaging of a sample of 24 nearby luminous infrared (IR) galaxies (LIRGs) from the Great Observatories All-sky LIRG survey (GOALS) selected to be in advanced stages of interaction. LIRGs account for half of the obscured star formation of the Universe at z ~ 1-2, and they represent a key population in galaxy formation and evolution. We will use the Pa-beta images to trace the ionized gas in LIRGs and study its spatial distribution from scales of ~ 100 pc to up to several kpc, probing the youngest, massive stars formed in the most buried environments of LIRGs due to the interaction process. This will allow us to measure how the gas in the center of mergers is converted into stars, which eventually leads to the build-up of a nuclear stellar cusp and the "inside-out" growth of bulges. We will also create spatially-resolved Pa-beta equivalent width maps to search for age gradients across the galaxies and correlate the distribution of Pa-beta emission with that of un-obscured star clusters detected in the UV and optical with HST on the same spatial scales. Finally, we will combine our data with previous studies mainly focused on isolated and early-stage interacting LIRG systems to analyze the size and compactness of the starburst along the complete merger sequence of LIRGs. The requested data represent a critical missing piece of information that will allow us to understand both the physics of merger-induced star formation and the applicability of local LIRGs as templates for high-z interacting starburst galaxies.

  20. Calculation of complete or incomplete elliptic integrals of the first and second kind

    International Nuclear Information System (INIS)

    Guillermin, J.M.; Guerin, M.

    1968-01-01

    The structure of the article is as following: inversion of the Jacobi function Sn (U, K), definition of the functions F (PHI, K) and E (PHI, K), Landen transformation, calculation of elliptic integrals F (PHI, K) and E (PHI, K), particular case of complete elliptic integrals, realised programs [fr

  1. A representation-theoretic approach to the calculation of evolutionary distance in bacteria

    Science.gov (United States)

    Sumner, Jeremy G.; Jarvis, Peter D.; Francis, Andrew R.

    2017-08-01

    In the context of bacteria and models of their evolution under genome rearrangement, we explore a novel application of group representation theory to the inference of evolutionary history. Our contribution is to show, in a very general maximum likelihood setting, how to use elementary matrix algebra to sidestep intractable combinatorial computations and convert the problem into one of eigenvalue estimation amenable to standard numerical approximation techniques.

  2. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Gary [Los Alamos National Laboratory; Detter, Chris [Los Alamos National Laboratory; Bruce, David [Los Alamos National Laboratory; Challacome, Jean F [Los Alamos National Laboratory; Brettin, Thomas S [Los Alamos National Laboratory; Barabote, Ravi D [UC DAVIS; Leu, David [UC DAVIS; Normand, Philippe [CNRS, UNIV LYON; Necsula, Anamaria [CNRS, UNIV LYON; Daubin, Vincent [CNRS, UNIV LYON; Medigue, Claudine [CNRS/GENOSCOPE; Adney, William S [NREL; Xu, Xin C [UC DAVIS; Lapidus, Alla [DOE JOINT GENOME INST.; Pujic, Pierre [CNRS, UNIV LYON; Richardson, Paul [DOE JOINT GENOME INST; Berry, Alison M [UC DAVIS

    2008-01-01

    We present here the complete 2.4 MB genome of the actinobacterial thermophile, Acidothermus cellulolyticus lIB, that surprisingly reveals thermophilic amino acid usage in only the cytosolic subproteome rather than its whole proteome. Thermophilic amino acid usage in the partial proteome implies a recent, ongoing evolution of the A. cellulolyticus genome since its divergence about 200-250 million years ago from its closest phylogenetic neighbor Frankia, a mesophilic plant symbiont. Differential amino acid usage in the predicted subproteomes of A. cellulolyticus likely reflects a stepwise evolutionary process of modern thermophiles in general. An unusual occurrence of higher G+C in the non-coding DNA than in the transcribed genome reinforces a late evolution from a higher G+C common ancestor. Comparative analyses of the A. cellulolyticus genome with those of Frankia and other closely-related actinobacteria revealed that A. cellulolyticus genes exhibit reciprocal purine preferences at the first and third codon positions, perhaps reflecting a subtle preference for the dinucleotide AG in its mRNAs, a possible adaptation to a thermophilic environment. Other interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote reveal streamlining for adaptation to its specialized ecological niche. These include a low occurrence of pseudogenes or mobile genetic elements, a flagellar gene complement previously unknown in this organism, and presence of laterally-acquired genomic islands of likely ecophysiological value. New glycoside hydrolases relevant for lignocellulosic biomass deconstruction were identified in the genome, indicating a diverse biomass-degrading enzyme repertoire several-fold greater than previously characterized, and significantly elevating the industrial value of this organism.

  3. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

    Science.gov (United States)

    Barabote, Ravi D.; Xie, Gary; Leu, David H.; Normand, Philippe; Necsulea, Anamaria; Daubin, Vincent; Médigue, Claudine; Adney, William S.; Xu, Xin Clare; Lapidus, Alla; Parales, Rebecca E.; Detter, Chris; Pujic, Petar; Bruce, David; Lavire, Celine; Challacombe, Jean F.; Brettin, Thomas S.; Berry, Alison M.

    2009-01-01

    We present here the complete 2.4-Mb genome of the cellulolytic actinobacterial thermophile Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized and elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls, and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. Several of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and noncoding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs-dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and the presence of three laterally acquired genomic islands of likely ecophysiological value. PMID:19270083

  4. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Gary [Los Alamos National Laboratory; Detter, John C [Los Alamos National Laboratory; Bruce, David C [Los Alamos National Laboratory; Challacombe, Jean F [Los Alamos National Laboratory; Brettin, Thomas S [Los Alamos National Laboratory; Necsulea, Anamaria [UNIV LYON; Daubin, Vincent [UNIV LYON; Medigue, Claudine [GENOSCOPE; Adney, William S [NREL; Xu, Xin C [UC DAVIS; Lapidus, Alla [JGI; Pujic, Pierre [UNIV LYON; Berry, Alison M [UC DAVIS; Barabote, Ravi D [UC DAVIS; Leu, David [UC DAVIS; Normand, Phillipe [UNIV LYON

    2009-01-01

    We present here the complete 2.4 MB genome of the actinobacterial thermophile, Acidothermus cellulolyticus 11B, that surprisingly reveals thermophilic amino acid usage in only the cytosolic subproteome rather than its whole proteome. Thermophilic amino acid usage in the partial proteome implies a recent, ongoing evolution of the A. cellulolyticus genome since its divergence about 200-250 million years ago from its closest phylogenetic neighbor Frankia, a mesophilic plant symbiont. Differential amino acid usage in the predicted subproteomes of A. cellulolyticus likely reflects a stepwise evolutionary process of modern thermophiles in general. An unusual occurrence of higher G+C in the non-coding DNA than in the transcribed genome reinforces a late evolution from a higher G+C common ancestor. Comparative analyses of the A. cellulolyticus genome with those of Frankia and other closely-related actinobacteria revealed that A. cellulolyticus genes exhibit reciprocal purine preferences at the first and third codon positions, perhaps reflecting a subtle preference for the dinucleotide AG in its mRNAs, a possible adaptation to a thermophilic environment. Other interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote reveal streamlining for adaptation to its specialized ecological niche. These include a low occurrence of pseudo genes or mobile genetic elements, a flagellar gene complement previously unknown in this organism, and presence of laterally-acquired genomic islands of likely ecophysiological value. New glycoside hydrolases relevant for lignocellulosic biomass deconstruction were identified in the genome, indicating a diverse biomass-degrading enzyme repertoire several-fold greater than previously characterized, and significantly elevating the industrial value of this organism.

  5. First complete NLL BFKL calculation of Mueller Navelet jets at LHC

    Energy Technology Data Exchange (ETDEWEB)

    Wallon, Samuel [Laboratoire de Physique Theorique d' Orsay - LPT, Bat. 210, Univ. Paris-Sud 11, 91405 Orsay Cedex (France); UPMC Univ. Paris 06 (France); Colferai, Dimitri [Dipartimento di Fisica, Universita di Firenze, Via G. Sansone 1, IT-50019 Firenze (Italy); Istituto Nazionale di Fisica Nucleare - INFN, Sezione di Firenze, Via G.Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Schwennsen, Florian [Deutsches Elektronen-Synchrotron - DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Szymanowski, Lech [Soltan Institute for Nuclear Studies, Hoza 69, 00691, Warsaw (Poland)

    2010-07-01

    We calculate cross section and azimuthal de-correlation of Mueller Navelet jets at the LHC in the complete next-lo-leading order BFKL framework, i.e. including next-to-leading corrections to the Green's function as well as next-to-leading corrections to the Mueller Navelet vertices. The obtained results for standard observables proposed for studies of Mueller Navelet jets show that both sources of corrections are of equal, big importance for final magnitude and final behavior of observables. The astonishing conclusion of our analysis is that the observables obtained within the complete next-lo-leading order BFKL framework of the present work are quite similar to the same observables obtained within next-to-leading logarithm DGLAP type treatment. This fact sheds doubts on general belief that the studies of Mueller Navelet jets at the LHC will lead to clear discrimination between the BFKL and the DGLAP dynamics. (author)

  6. Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes.

    Science.gov (United States)

    Gao, Lei; Yi, Xuan; Yang, Yong-Xia; Su, Ying-Juan; Wang, Ting

    2009-06-11

    Ferns have generally been neglected in studies of chloroplast genomics. Before this study, only one polypod and two basal ferns had their complete chloroplast (cp) genome reported. Tree ferns represent an ancient fern lineage that first occurred in the Late Triassic. In recent phylogenetic analyses, tree ferns were shown to be the sister group of polypods, the most diverse group of living ferns. Availability of cp genome sequence from a tree fern will facilitate interpretation of the evolutionary changes of fern cp genomes. Here we have sequenced the complete cp genome of a scaly tree fern Alsophila spinulosa (Cyatheaceae). The Alsophila cp genome is 156,661 base pairs (bp) in size, and has a typical quadripartite structure with the large (LSC, 86,308 bp) and small single copy (SSC, 21,623 bp) regions separated by two copies of an inverted repeat (IRs, 24,365 bp each). This genome contains 117 different genes encoding 85 proteins, 4 rRNAs and 28 tRNAs. Pseudogenes of ycf66 and trnT-UGU are also detected in this genome. A unique trnR-UCG gene (derived from trnR-CCG) is found between rbcL and accD. The Alsophila cp genome shares some unusual characteristics with the previously sequenced cp genome of the polypod fern Adiantum capillus-veneris, including the absence of 5 tRNA genes that exist in most other cp genomes. The genome shows a high degree of synteny with that of Adiantum, but differs considerably from two basal ferns (Angiopteris evecta and Psilotum nudum). At one endpoint of an ancient inversion we detected a highly repeated 565-bp-region that is absent from the Adiantum cp genome. An additional minor inversion of the trnD-GUC, which is possibly shared by all ferns, was identified by comparison between the fern and other land plant cp genomes. By comparing four fern cp genome sequences it was confirmed that two major rearrangements distinguish higher leptosporangiate ferns from basal fern lineages. The Alsophila cp genome is very similar to that of the

  7. Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes

    Directory of Open Access Journals (Sweden)

    Yang Yong-Xia

    2009-06-01

    Full Text Available Abstract Background Ferns have generally been neglected in studies of chloroplast genomics. Before this study, only one polypod and two basal ferns had their complete chloroplast (cp genome reported. Tree ferns represent an ancient fern lineage that first occurred in the Late Triassic. In recent phylogenetic analyses, tree ferns were shown to be the sister group of polypods, the most diverse group of living ferns. Availability of cp genome sequence from a tree fern will facilitate interpretation of the evolutionary changes of fern cp genomes. Here we have sequenced the complete cp genome of a scaly tree fern Alsophila spinulosa (Cyatheaceae. Results The Alsophila cp genome is 156,661 base pairs (bp in size, and has a typical quadripartite structure with the large (LSC, 86,308 bp and small single copy (SSC, 21,623 bp regions separated by two copies of an inverted repeat (IRs, 24,365 bp each. This genome contains 117 different genes encoding 85 proteins, 4 rRNAs and 28 tRNAs. Pseudogenes of ycf66 and trnT-UGU are also detected in this genome. A unique trnR-UCG gene (derived from trnR-CCG is found between rbcL and accD. The Alsophila cp genome shares some unusual characteristics with the previously sequenced cp genome of the polypod fern Adiantum capillus-veneris, including the absence of 5 tRNA genes that exist in most other cp genomes. The genome shows a high degree of synteny with that of Adiantum, but differs considerably from two basal ferns (Angiopteris evecta and Psilotum nudum. At one endpoint of an ancient inversion we detected a highly repeated 565-bp-region that is absent from the Adiantum cp genome. An additional minor inversion of the trnD-GUC, which is possibly shared by all ferns, was identified by comparison between the fern and other land plant cp genomes. Conclusion By comparing four fern cp genome sequences it was confirmed that two major rearrangements distinguish higher leptosporangiate ferns from basal fern lineages. The

  8. Calculating complete and exact Pareto front for multiobjective optimization: a new deterministic approach for discrete problems.

    Science.gov (United States)

    Hu, Xiao-Bing; Wang, Ming; Di Paolo, Ezequiel

    2013-06-01

    Searching the Pareto front for multiobjective optimization problems usually involves the use of a population-based search algorithm or of a deterministic method with a set of different single aggregate objective functions. The results are, in fact, only approximations of the real Pareto front. In this paper, we propose a new deterministic approach capable of fully determining the real Pareto front for those discrete problems for which it is possible to construct optimization algorithms to find the k best solutions to each of the single-objective problems. To this end, two theoretical conditions are given to guarantee the finding of the actual Pareto front rather than its approximation. Then, a general methodology for designing a deterministic search procedure is proposed. A case study is conducted, where by following the general methodology, a ripple-spreading algorithm is designed to calculate the complete exact Pareto front for multiobjective route optimization. When compared with traditional Pareto front search methods, the obvious advantage of the proposed approach is its unique capability of finding the complete Pareto front. This is illustrated by the simulation results in terms of both solution quality and computational efficiency.

  9. Theoretical calculation and evaluation of complete neutron data for natural niobium

    International Nuclear Information System (INIS)

    Ma Gonggui; Zou Yiming; Wang Shiming

    1990-07-01

    An evaluation of a complete neutron nuclear data for natural niobium has been finished on the data measured by experiments up to 1989 and theoretical calculations with program MUP2 and AUJP. The purpose of present work is to build CENDL-2 databank (Chinese Evaluation Nuclear Data Library, second version) which replaces the CENDL-1 (first version of CENDL). The neutron energy for niobium is in the range of 10 -5 eV to 20 MeV. Data of cross section include total, elastic, nonelastic, total elastic, inelastic cross section to 13 discrete levels, inelastic continuum, (n,2n), (n,3n), (n,n ' α) + (n,αn ' ), (n,n ' p) + (n,pn ' ), (n,n ' d) + (n,dn ' ), (n,p), (n,d), (n,t), (n,α) and capture cross sections. Data for MT 251,252 and 253 as well as angular distributions and energy spectra of secondary neutrons are also given

  10. Many-body calculations of molecular electric polarizabilities in asymptotically complete basis sets

    Science.gov (United States)

    Monten, Ruben; Hajgató, Balázs; Deleuze, Michael S.

    2011-10-01

    The static dipole polarizabilities of Ne, CO, N2, F2, HF, H2O, HCN, and C2H2 (acetylene) have been determined close to the Full-CI limit along with an asymptotically complete basis set (CBS), according to the principles of a Focal Point Analysis. For this purpose the results of Finite Field calculations up to the level of Coupled Cluster theory including Single, Double, Triple, Quadruple and perturbative Pentuple excitations [CCSDTQ(P)] were used, in conjunction with suited extrapolations of energies obtained using augmented and doubly-augmented Dunning's correlation consistent polarized valence basis sets of improving quality. The polarizability characteristics of C2H4 (ethylene) and C2H6 (ethane) have been determined on the same grounds at the CCSDTQ level in the CBS limit. Comparison is made with results obtained using lower levels in electronic correlation, or taking into account the relaxation of the molecular structure due to an adiabatic polarization process. Vibrational corrections to electronic polarizabilities have been empirically estimated according to Born-Oppenheimer Molecular Dynamical simulations employing Density Functional Theory. Confrontation with experiment ultimately indicates relative accuracies of the order of 1 to 2%.

  11. CALCULATION OF REACTION COMPLETENESS AND SUBSTANCE TRANSFORMATION AT WATER-COAL GASIFICATION

    Directory of Open Access Journals (Sweden)

    N. S. Nazarov

    2007-01-01

    Full Text Available Process of water-coal gasification is satisfactorily described by three thermal and chemical equations; using these equations composition of gasification product (water carbon monoxide gas has been calculated in accordance with a temperature. Results of the calculations are presented in the form of charts. 

  12. Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae).

    Science.gov (United States)

    Botero-Castro, Fidel; Tilak, Marie-ka; Justy, Fabienne; Catzeflis, François; Delsuc, Frédéric; Douzery, Emmanuel J P

    2013-12-01

    Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of

  13. Statistical calculation of complete events in medium-energy nuclear collisions

    International Nuclear Information System (INIS)

    Randrup, J.

    1984-01-01

    Several heavy-ion accelerators throughout the world are presently able to deliver beams of heavy nuclei with kinetic energies in the range from tens to hundreds of MeV per nucleon, the so-called medium or intermediate energy range. At such energies a large number of final channels are open, each consisting of many nuclear fragments. The disassembly of the collision system is expected to be a very complicated process and a detailed dynamical description is beyond their present capability. However, by virtue of the complexity of the process, statistical considerations may be useful. A statistical description of the disassembly yields the least biased expectations about the outcome of a collision process and provides a meaningful reference against which more specific dynamical models, as well as the data, can be discussed. This lecture presents the essential tools for formulating a statistical model for the nuclear disassembly process. The authors consider the quick disassembly (explosion) of a hot nuclear system, a so-called source, into multifragment final states, which complete according to their statistical weight. First some useful notation is introduced. Then the expressions for exclusive and inclusive distributions are given and the factorization of an exclusive distribution into inclusive ones is carried out. In turn, the grand canonical approximation for one-fragment inclusive distributions is introduced. Finally, it is outlined how to generate a statistical sample of complete final states. On this basis, a model for statistical simulation of complete events in medium-energy nuclear collisions has been developed

  14. 41 CFR 102-34.70 - What do we do with completed calculations of our fleet vehicle acquisitions?

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What do we do with completed calculations of our fleet vehicle acquisitions? 102-34.70 Section 102-34.70 Public Contracts and Property Management Federal Property Management Regulations System (Continued) FEDERAL MANAGEMENT...

  15. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

    Directory of Open Access Journals (Sweden)

    Leila do Nascimento Vieira

    Full Text Available BACKGROUND: Podocarpus lambertii (Podocarpaceae is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR. It contains 118 unique genes and one duplicated tRNA (trnN-GUU, which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi and Araucariaceae (Agathis dammara. Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of

  16. Contrasting population-level responses to Pleistocene climatic oscillations in an alpine bat revealed by complete mitochondrial genomes and evolutionary history inference

    DEFF Research Database (Denmark)

    Alberdi, Antton; Gilbert, M. Thomas P; Razgour, Orly

    2015-01-01

    Aim: We used an integrative approach to reconstruct the evolutionary history of the alpine long-eared bat, Plecotus macrobullaris, to test whether the variable effects of Pleistocene climatic oscillations across geographical regions led to contrasting population-level demographic histories within...... a single species. Location: The Western Palaearctic. Methods: We sequenced the complete mitochondrial genomes of 57 individuals from across the distribution of the species. The analysis integrated ecological niche modelling (ENM), approximate Bayesian computation (ABC), measures of genetic diversity...... and Bayesian phylogenetic methods. Results: We identified two deep lineages: a western lineage, restricted to the Pyrenees and the Alps, and an eastern lineage, which expanded across the mountain ranges east of the Dinarides (Croatia). ENM projections of past conditions predicted that climatic suitability...

  17. On the calculation of complete dissociation curves of closed-shell pseudo-onedimensional systems via the complete active space method of increments

    Energy Technology Data Exchange (ETDEWEB)

    Fertitta, E.; Paulus, B. [Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin (Germany); Barcza, G.; Legeza, Ö. [Strongly Correlated Systems “Lendület” Research Group, Wigner Research Centre for Physics, P.O. Box 49, Budapest (Hungary)

    2015-09-21

    The method of increments (MoI) has been employed using the complete active space formalism in order to calculate the dissociation curve of beryllium ring-shaped clusters Be{sub n} of different sizes. Benchmarks obtained through different quantum chemical methods including the ab initio density matrix renormalization group were used to verify the validity of the MoI truncation which showed a reliable behavior for the whole dissociation curve. Moreover we investigated the size dependence of the correlation energy at different interatomic distances in order to extrapolate the values for the periodic chain and to discuss the transition from a metal-like to an insulator-like behavior of the wave function through quantum chemical considerations.

  18. Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions.

    Science.gov (United States)

    Liu, Maoyan; Liu, Xiangning; Li, Xun; Zhang, Deyong; Dai, Liangyin; Tang, Qianjun

    2016-03-01

    The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92% sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.

  19. Calculation of evolutionary correlation between individual genes and full-length genome: a method useful for choosing phylogenetic markers for molecular epidemiology.

    Directory of Open Access Journals (Sweden)

    Shuai Wang

    Full Text Available Individual genes or regions are still commonly used to estimate the phylogenetic relationships among viral isolates. The genomic regions that can faithfully provide assessments consistent with those predicted with full-length genome sequences would be preferable to serve as good candidates of the phylogenetic markers for molecular epidemiological studies of many viruses. Here we employed a statistical method to evaluate the evolutionary relationships between individual viral genes and full-length genomes without tree construction as a way to determine which gene can match the genome well in phylogenetic analyses. This method was performed by calculation of linear correlations between the genetic distance matrices of aligned individual gene sequences and aligned genome sequences. We applied this method to the phylogenetic analyses of porcine circovirus 2 (PCV2, measles virus (MV, hepatitis E virus (HEV and Japanese encephalitis virus (JEV. Phylogenetic trees were constructed for comparisons and the possible factors affecting the method accuracy were also discussed in the calculations. The results revealed that this method could produce results consistent with those of previous studies about the proper consensus sequences that could be successfully used as phylogenetic markers. And our results also suggested that these evolutionary correlations could provide useful information for identifying genes that could be used effectively to infer the genetic relationships.

  20. Neutronic study of nuclear reactors. Complete calculation of TRIGA MARKII reactor and calculations of fuel temperature coefficients. (Qualification of WIMS code)

    International Nuclear Information System (INIS)

    Benmansour, L.

    1992-01-01

    The present work shows a group of results, obtained by a neutronic study, concerning the TRIGA MARK II reactor and LIGHT WATER reactors. These studies aim to make cell and diffusion calculations. WIMS D-4 with extended library and DIXY programs are used and tested for those purposes. We also have proceeded to a qualification of WIMS code based on the fuel temperature coefficient calculations. 33 refs.; 23 figs.; 30 tabs. (author)

  1. Calculations of complete data for n + 89Y in the energy region 0.001∼20 MeV

    International Nuclear Information System (INIS)

    Cai Chonghai

    1998-01-01

    All reaction cross sections, secondary neutron spectra and elastic scattering angular distributions of n + 89 Y in E n = 0.001 ∼20 MeV are calculated. Pretty good results in accordance with experimental data are obtained. And the data results are given in ENDF/B-6 format

  2. Calculation of a complete data set for n + 83Kr, 84Kr, 85Kr and 86Kr in the energy region 0.001-20 MeV

    International Nuclear Information System (INIS)

    Cai Chonghai

    1999-01-01

    Complete reaction cross sections, secondary neutron spectra and elastic scattering angular distributions of 83 Kr, 84 Kr, 85 Kr and 86 Kr in the energy region 0.001-20 MeV are calculated, theoretical results are in ENDF/B-6 in pretty good accordance with experimental data

  3. X-ray Reflected Spectra from Accretion Disk Models. III. A Complete Grid of Ionized Reflection Calculations

    Science.gov (United States)

    Garcia, J.; Dauser, T.; Reynolds, C. S.; Kallman, T. R.; McClintock, J. E.; Wilms, J.; Ekmann, W.

    2013-01-01

    We present a new and complete library of synthetic spectra for modeling the component of emission that is reflected from an illuminated accretion disk. The spectra were computed using an updated version of our code xillver that incorporates new routines and a richer atomic data base. We offer in the form of a table model an extensive grid of reflection models that cover a wide range of parameters. Each individual model is characterized by the photon index Gamma of the illuminating radiation, the ionization parameter zeta at the surface of the disk (i.e., the ratio of the X-ray flux to the gas density), and the iron abundance A(sub Fe) relative to the solar value. The ranges of the parameters covered are: 1.2 <= Gamma <= 3.4, 1 <= zeta <= 104, and 0.5 <= A(sub Fe) <= 10. These ranges capture the physical conditions typically inferred from observations of active galactic nuclei, and also stellar-mass black holes in the hard state. This library is intended for use when the thermal disk flux is faint compared to the incident power-law flux. The models are expected to provide an accurate description of the Fe K emission line, which is the crucial spectral feature used to measure black hole spin. A total of 720 reflection spectra are provided in a single FITS file suitable for the analysis of X-ray observations via the atable model in xspec. Detailed comparisons with previous reflection models illustrate the improvements incorporated in this version of xillver.

  4. Evolutionary Nephrology.

    Science.gov (United States)

    Chevalier, Robert L

    2017-05-01

    Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  5. Genomic sequences of murine gamma B- and gamma C-crystallin-encoding genes: promoter analysis and complete evolutionary pattern of mouse, rat and human gamma-crystallins.

    Science.gov (United States)

    Graw, J; Liebstein, A; Pietrowski, D; Schmitt-John, T; Werner, T

    1993-12-22

    The murine genes, gamma B-cry and gamma C-cry, encoding the gamma B- and gamma C-crystallins, were isolated from a genomic DNA library. The complete nucleotide (nt) sequences of both genes were determined from 661 and 711 bp, respectively, upstream from the first exon to the corresponding polyadenylation sites, comprising more than 2650 and 2890 bp, respectively. The new sequences were compared to the partial cDNA sequences available for the murine gamma B-cry and gamma C-cry, as well as to the corresponding genomic sequences from rat and man, at both the nt and predicted amino acid (aa) sequence levels. In the gamma B-cry promoter region, a canonical CCAAT-box, a TATA-box, putative NF-I and C/EBP sites were detected. An R-repeat is inserted 366 bp upstream from the transcription start point. In contrast, the gamma C-cry promoter does not contain a CCAAT-box, but some other putative binding sites for transcription factors (AP-2, UBP-1, LBP-1) were located by computer analysis. The promoter regions of all six gamma-cry from mouse, rat and human, except human psi gamma F-cry, were analyzed for common sequence elements. A complex sequence element of about 70-80 bp was found in the proximal promoter, which contains a gamma-cry-specific and almost invariant sequence (crygpel) of 14 nt, and ends with the also invariant TATA-box. Within the complex sequence element, a minimum of three further features specific for the gamma A-, gamma B- and gamma D/E/F-cry genes can be defined, at least two of which were recently shown to be functional. In addition to these four sequence elements, a subtype-specific structure of inverted repeats with different-sized spacers can be deduced from the multiple sequence alignment. A phylogenetic analysis based on the promoter region, as well as the complete exon 3 of all gamma-cry from mouse, rat and man, suggests separation of only five gamma-cry subtypes (gamma A-, gamma B-, gamma C-, gamma D- and gamma E/F-cry) prior to species separation.

  6. Evolutionary Nephrology

    Directory of Open Access Journals (Sweden)

    Robert L. Chevalier

    2017-05-01

    Full Text Available Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as “maladaptive.” In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or from evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ∼40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons, evolutionary selection for APOL1 mutations (which provide resistance to trypanosome infection, a tradeoff, and modern life experience (Western diet mismatch leading to diabetes and hypertension. Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout the life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo, developmental programming, and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  7. Estimation of isotropic nuclear magnetic shieldings in the CCSD(T) and MP2 complete basis set limit using affordable correlation calculations

    DEFF Research Database (Denmark)

    Kupka, Teobald; Stachów, Michal; Kaminsky, Jakub

    2013-01-01

    , estimated from calculations with the family of polarizationconsistent pcS-n basis sets is reported. This dependence was also supported by inspection of profiles of deviation between CBS estimated nuclear shieldings and obtained with significantly smaller basis sets pcS-2 and aug-cc-pVTZ-J for the selected......A linear correlation between isotropic nuclear magnetic shielding constants for seven model molecules (CH2O, H2O, HF, F2, HCN, SiH4 and H2S) calculated with 37 methods (34 density functionals, RHF, MP2 and CCSD(T) ), with affordable pcS-2 basis set and corresponding complete basis set results...... set of 37 calculation methods. It was possible to formulate a practical approach of estimating the values of isotropic nuclear magnetic shielding constants at the CCSD(T)/CBS and MP2/CBS levels from affordable CCSD(T)/pcS-2, MP2/pcS-2 and DFT/CBS calculations with pcS-n basis sets. The proposed method...

  8. Self-consistent Green’s-function technique for bulk and surface impurity calculations: Surface core-level shifts by complete screening

    DEFF Research Database (Denmark)

    Aldén, M.; Abrikosov, I. A.; Johansson, B.

    1994-01-01

    of the frozen-core and atomic-sphere approximation but, in addition, includes the dipole contribution to the intersphere potential. Within the concept of complete screening, we identify the surface core-level binding-energy shift with the surface segregation energy of a core-ionized atom and use the Green......'s-function impurity technique in a comprehensive study of the surface core-level shifts (SCLS) of the 4d and 5d transition metals. In those cases, where observed data refer to single crystals, we obtain good agreement with experiment, whereas the calculations typically underestimate the measured shift obtained from...

  9. Evolutionary thinking

    Science.gov (United States)

    Hunt, Tam

    2014-01-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766

  10. Evolutionary Demography

    DEFF Research Database (Denmark)

    Levitis, Daniel

    2015-01-01

    of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness......Demography is the quantitative study of population processes, while evolution is a population process that influences all aspects of biological organisms, including their demography. Demographic traits common to all human populations are the products of biological evolution or the interaction...

  11. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    , they are correlated among people who share environments because these individuals satisfice within their cognitive bounds by using cues in order of validity, as opposed to using cues arbitrarily. Any difference in expectations thereby arise from differences in cognitive ability, because two individuals with identical...... cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary......The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover...

  12. [Evolutionary medicine].

    Science.gov (United States)

    Wjst, M

    2013-12-01

    Evolutionary medicine allows new insights into long standing medical problems. Are we "really stoneagers on the fast lane"? This insight might have enormous consequences and will allow new answers that could never been provided by traditional anthropology. Only now this is made possible using data from molecular medicine and systems biology. Thereby evolutionary medicine takes a leap from a merely theoretical discipline to practical fields - reproductive, nutritional and preventive medicine, as well as microbiology, immunology and psychiatry. Evolutionary medicine is not another "just so story" but a serious candidate for the medical curriculum providing a universal understanding of health and disease based on our biological origin. © Georg Thieme Verlag KG Stuttgart · New York.

  13. Evolutionary Awareness

    Directory of Open Access Journals (Sweden)

    Gregory Gorelik

    2014-10-01

    Full Text Available In this article, we advance the concept of “evolutionary awareness,” a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities—which we refer to as “intergenerational extended phenotypes”—by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  14. Complete tree-level calculation of the reaction e+e-→μ+μ-b anti b and the Higgs boson signal at LEP200 and NLC energies

    International Nuclear Information System (INIS)

    Boos, E.

    1993-07-01

    A complete tree-level calculation of the reaction e + e - →μ + μ - b anti b in the electroweak standard theory for the energy range of LEP200 and the Next Linear Collider is presented. The matrix elements have been calculated by employing the computer program CompHEP, the phase space integrals by the Monte Carlo integrator and event generator BASES/SPRING. The dependence of the 4-fermion cross section on energy, Higgs boson mass and Higgs width is studied in detail. Interference contributions between the various diagrams are found not to alter significantly the production and decay distributions of the Higgs boson. It is shown that already the counting rate of the reaction e + e - →μ + μ - b anti b at LEP200 can provide evidence for the existence of the Higgs boson. The dependence of the μ + μ - b anti b cross section on the Higgs width will allow to extract information on this width in particular at LEP200 energies. (orig.)

  15. Evolutionary robotics

    Indian Academy of Sciences (India)

    In evolutionary robotics, a suitable robot control system is developed automatically through evolution due to the interactions between the robot and its environment. It is a complicated task, as the robot and the environment constitute a highly dynamical system. Several methods have been tried by various investigators to ...

  16. Evolutionary institutionalism.

    Science.gov (United States)

    Fürstenberg, Dr Kai

    Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

  17. Methanol to olefin Conversion on HSAPO-34 zeolite from periodic density functional theory calculations: a complete cycle of side chain hydrocarbon pool mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Wang, C.M.; Wang, Y.D.; Xie, Z.K.; Liu, Z.P. [SINOPEC, Shanghai (China)

    2009-03-15

    For its unique position in the coal chemical industry, the methanol to olefin (MTO) reaction has been a hot topic in zeolite catalysis. Due to the complexities of catalyst structure and reaction networks, many questions such as how the olefin chain is built from methanol remain elusive. On the basis of periodic density functional theory calculations, this work establishes the first complete catalytic cycle for MTO reaction via hexamethylbenzene (HMB) trapped in HSAPO-34 zeolite based on the so-called side chain hydrocarbon pool mechanism. The cycle starts from the methylation of HMB that leads to heptamethylbenzenium ion (heptaMB{sup +}) intermediate. This is then followed by the growth of side chain via repeated deprotonation of benzenium ions and methylation of the exocyclic double bond. Ethene and propene can finally be released from the side ethyl and isopropyl groups of benzenium ions by deprotonation and subsequent protonation steps. We demonstrate that (i) HMB/HSAPO-34 only yields propene as the primary product based on the side chain hydrocarbon pool mechanism and (ii) an indirect proton-shift step mediated by water that is always available in the system is energetically more favorable than the traditionally regarded internal hydrogen-shift step. Finally, the implications of our results toward understanding the effect of acidity of zeolite on MTO activity are also discussed.

  18. Industrial Applications of Evolutionary Algorithms

    CERN Document Server

    Sanchez, Ernesto; Tonda, Alberto

    2012-01-01

    This book is intended as a reference both for experienced users of evolutionary algorithms and for researchers that are beginning to approach these fascinating optimization techniques. Experienced users will find interesting details of real-world problems, and advice on solving issues related to fitness computation, modeling and setting appropriate parameters to reach optimal solutions. Beginners will find a thorough introduction to evolutionary computation, and a complete presentation of all evolutionary algorithms exploited to solve different problems. The book could fill the gap between the

  19. Structural dynamics of phenylisothiocyanate in the light-absorbing excited states: Resonance Raman and complete active space self-consistent field calculation study

    International Nuclear Information System (INIS)

    Ouyang, Bing; Xue, Jia-Dan; Zheng, Xuming; Fang, Wei-Hai

    2014-01-01

    The excited state structural dynamics of phenyl isothiocyanate (PITC) after excitation to the light absorbing S 2 (A′), S 6 (A′), and S 7 (A′) excited states were studied by using the resonance Raman spectroscopy and complete active space self-consistent field method calculations. The UV absorption bands of PITC were assigned. The vibrational assignments were done on the basis of the Fourier transform (FT)-Raman and FT-infrared measurements, the density-functional theory computations, and the normal mode analysis. The A-, B-, and C-bands resonance Raman spectra in cyclohexane, acetonitrile, and methanol solvents were, respectively, obtained at 299.1, 282.4, 266.0, 252.7, 228.7, 217.8, and 208.8 nm excitation wavelengths to probe the corresponding structural dynamics of PITC. The results indicated that the structural dynamics in the S 2 (A′), S 6 (A′), and S 7 (A′) excited states were very different. The conical intersection point CI(S 2 /S 1 ) were predicted to play important role in the low-lying excited state decay dynamics. Two major decay channels were predicted for PITC upon excitation to the S 2 (A′) state: the radiative S 2,min → S 0 transition and the nonradiative S 2 → S 1 internal conversion via CI(S 2 /S 1 ). The differences in the decay dynamics between methyl isothiocyanate and PITC in the first light absorbing excited state were discussed. The role of the intersystem crossing point ISC(S 1 /T 1 ) in the excited state decay dynamics of PITC is evaluated

  20. Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory

    Czech Academy of Sciences Publication Activity Database

    Mládek, Arnošt; Krepl, Miroslav; Svozil, Daniel; Čech, P.; Otyepka, M.; Banáš, P.; Zgarbová, M.; Jurečka, P.; Šponer, Jiří

    2013-01-01

    Roč. 15, č. 19 (2013), s. 7295-7310 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GAP208/11/1822 Grant - others:GA MŠk(CZ) ED1.1.00/02.0068 Program:ED Institutional research plan: CEZ:AV0Z50040702 Institutional support: RVO:68081707 Keywords : GAUSSIAN-BASIS SETS * GENERALIZED GRADIENT APPROXIMATION * CORRELATED MOLECULAR CALCULATIONS Subject RIV: BO - Biophysics Impact factor: 4.198, year: 2013

  1. Completion of a simulation model for calculation of static and dynamic behaviour of steam generators and its use for a pilot steam generator

    Energy Technology Data Exchange (ETDEWEB)

    Seybold, M

    1979-07-20

    In the present paper, first of all the model concept reported in detail by Schittke is applied to the steady-state predictive calculation of an arbitrarily nested steam generator based on the design data and empirical values on heat discharge and heat transfer. The dynamics of the system are precalculated on the basis of the known steady-state behaviour and with the construction data, that is without experimental identification, according to the Schittke concept. The object for the calculation is a steam generator with once-through forced flow (VDE) which was put at the disposal of the Institute for Process Engineering and Steamboiler Studies. Data for the computer programs were taken only from the construction documents (geometries, nesting etc.) or from design data (thermic parameters). Parallel with the program preparation and the calculation measurements on the experimental plant were planned, adaptations and tests were carried out. The correctness of precalculating a steam generator could then be checked with the experimental plant and by comparison with the results of the measurements.

  2. Attractive evolutionary equilibria

    NARCIS (Netherlands)

    Joosten, Reinoud A.M.G.; Roorda, Berend

    2011-01-01

    We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary

  3. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General Article Volume 21 Issue 9 September 2016 pp 803- ... Keywords. Evolutionary game theory, evolutionary stable state, conflict, cooperation, biological games.

  4. Evolutionary molecular medicine.

    Science.gov (United States)

    Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

    2012-05-01

    Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

  5. A complete vibrational study on a potential environmental toxicant agent, the 3,3',4,4'-tetrachloroazobenzene combining the FTIR, FTRaman, UV-Visible and NMR spectroscopies with DFT calculations.

    Science.gov (United States)

    Castillo, María V; Pergomet, Jorgelina L; Carnavale, Gustavo A; Davies, Lilian; Zinczuk, Juan; Brandán, Silvia A

    2015-01-05

    In this study 3,3',4,4'-tetrachloroazobenzene (TCAB) was prepared and then characterized by infrared, Raman, multidimensional nuclear magnetic resonance (NMR) and ultraviolet-visible spectroscopies. The density functional theory (DFT) together with the 6-31G(*) and 6-311++G(**) basis sets were used to study the structures and vibrational properties of the two cis and trans isomers of TCAB. The harmonic vibrational wavenumbers for the optimized geometries were calculated at the same theory levels. A complete assignment of all the observed bands in the vibrational spectra of TCAB was performed combining the DFT calculations with the scaled quantum mechanical force field (SQMFF) methodology. The molecular electrostatic potentials, atomic charges, bond orders and frontier orbitals for the two isomers of TCAB were compared and analyzed. The comparison of the theoretical ultraviolet-visible spectrum with the corresponding experimental demonstrates a good concordance while the calculated (1)H and (13)C chemicals shifts are in good conformity with the corresponding experimental NMR spectra of TCAB in solution. The npp(*) transitions for both forms were studied by natural bond orbital (NBO) while the topological properties were calculated by employing Bader's Atoms in the Molecules (AIM) theory. This study shows that the cis and trans isomers exhibit different structural and vibrational properties and absorption bands. Copyright © 2014. Published by Elsevier B.V.

  6. Remembering the evolutionary Freud.

    Science.gov (United States)

    Young, Allan

    2006-03-01

    Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.

  7. Preventive evolutionary medicine of cancers.

    Science.gov (United States)

    Hochberg, Michael E; Thomas, Frédéric; Assenat, Eric; Hibner, Urszula

    2013-01-01

    Evolutionary theory predicts that once an individual reaches an age of sufficiently low Darwinian fitness, (s)he will have reduced chances of keeping cancerous lesions in check. While we clearly need to better understand the emergence of precursor states and early malignancies as well as their mitigation by the microenvironment and tissue architecture, we argue that lifestyle changes and preventive therapies based in an evolutionary framework, applied to identified high-risk populations before incipient neoplasms become clinically detectable and chemoresistant lineages emerge, are currently the most reliable way to control or eliminate early tumours. Specifically, the relatively low levels of (epi)genetic heterogeneity characteristic of many if not most incipient lesions will mean a relatively limited set of possible adaptive traits and associated costs compared to more advanced cancers, and thus a more complete and predictable understanding of treatment options and outcomes. We propose a conceptual model for preventive treatments and discuss the many associated challenges.

  8. NEW EVOLUTIONARY SEQUENCES FOR HOT H-DEFICIENT WHITE DWARFS ON THE BASIS OF A FULL ACCOUNT OF PROGENITOR EVOLUTION

    International Nuclear Information System (INIS)

    Althaus, L. G.; Panei, J. A.; Miller Bertolami, M. M.; Corsico, A. H.; Romero, A. D.; Garcia-Berro, E.; Kepler, S. O.; Rohrmann, R. D.

    2009-01-01

    We present full evolutionary calculations appropriate for the study of hot hydrogen-deficient DO white dwarfs, PG 1159 stars, and DB white dwarfs. White dwarf sequences are computed for a wide range of stellar masses and helium envelopes on the basis of a complete treatment of the evolutionary history of progenitors stars, including the core hydrogen and helium burning phases, the thermally pulsing asymptotic giant branch phase, and the born-again episode that is responsible for the hydrogen deficiency. We also provide colors and magnitudes for the new sequences for T eff < 40,000 K, where the NLTE effects are not dominant. These new calculations provide a homogeneous set of evolutionary tracks appropriate for mass and age determinations for both PG 1159 stars and DO white dwarfs. The calculations are extended down to an effective temperature of 7000 K. We applied these new tracks to redetermine stellar masses and ages of all known DO white dwarfs with spectroscopically determined effective temperatures and gravities, and compare them with previous results. We also compare for the first time consistent mass determinations for both DO and PG 1159 stars, and find a considerably higher mean mass for the DO white dwarfs. We discuss as well the chemical profile expected in the envelope of variable DB white dwarfs from the consideration of the evolutionary history of progenitor stars. Finally, we present tentative evidence for a different evolutionary channel, other than that involving the PG 1159 stars, for the formation of hot, hydrogen-deficient white dwarfs.

  9. Attractive evolutionary equilibria

    OpenAIRE

    Roorda, Berend; Joosten, Reinoud

    2011-01-01

    We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary dynamics. For instance, each attractive evolutionarily stable strategy is an attractive evolutionarily stable equilibrium for certain barycentric ray-projection dynamics, and vice versa.

  10. Polymorphic Evolutionary Games.

    Science.gov (United States)

    Fishman, Michael A

    2016-06-07

    In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Evolutionary relevance facilitates visual information processing.

    Science.gov (United States)

    Jackson, Russell E; Calvillo, Dusti P

    2013-11-03

    Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

  12. Evolutionary Relevance Facilitates Visual Information Processing

    Directory of Open Access Journals (Sweden)

    Russell E. Jackson

    2013-07-01

    Full Text Available Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

  13. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

    Science.gov (United States)

    Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

    2012-01-01

    Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.

  14. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    2014-03-15

    Mar 15, 2014 ... ... of events: 'Entities that were capable of independent replication ... There have been many major evolutionary events that this definition of .... selection at level x to exclusive selection at x – will probably require a multiplicity ...

  15. Evolutionary relationships among Astroviridae

    NARCIS (Netherlands)

    Lukashov, Vladimir V.; Goudsmit, Jaap

    2002-01-01

    To study the evolutionary relationships among astroviruses, all available sequences for members of the family Astroviridae were collected. Phylogenetic analysis distinguished two deep-rooted groups: one comprising mammalian astroviruses, with ovine astrovirus being an outlier, and the other

  16. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  17. Evolutionary Multiplayer Games

    OpenAIRE

    Gokhale, Chaitanya S.; Traulsen, Arne

    2014-01-01

    Evolutionary game theory has become one of the most diverse and far reaching theories in biology. Applications of this theory range from cell dynamics to social evolution. However, many applications make it clear that inherent non-linearities of natural systems need to be taken into account. One way of introducing such non-linearities into evolutionary games is by the inclusion of multiple players. An example is of social dilemmas, where group benefits could e.g.\\ increase less than linear wi...

  18. Extracting the evolutionary signal from genomes.

    NARCIS (Netherlands)

    Dutilh, B.E.

    2007-01-01

    Several methods to analyze aspects of evolution are developed, that depend on the availability of complete genomes. While I consistently find a phylogenetic signal using many approaches, a question that is winning concern is how these evolutionary relationships should be interpreted. Since Darwin’s

  19. Proteomics in evolutionary ecology.

    Science.gov (United States)

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  20. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  1. Applying evolutionary anthropology.

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. © 2015 Wiley Periodicals, Inc.

  2. Applying Evolutionary Anthropology

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561

  3. Archaeogenetics in evolutionary medicine.

    Science.gov (United States)

    Bouwman, Abigail; Rühli, Frank

    2016-09-01

    Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.

  4. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    of Computational Intelligence. First, comprehensive surveys of genetic algorithms, genetic programming, evolution strategies, parallel evolutionary algorithms are presented, which are readable and constructive so that a large audience might find them useful and – to some extent – ready to use. Some more general...... kinds of evolutionary algorithms, have been prudently analyzed. This analysis was followed by a thorough analysis of various issues involved in stochastic local search algorithms. An interesting survey of various technological and industrial applications in mechanical engineering and design has been...... topics like the estimation of distribution algorithms, indicator-based selection, etc., are also discussed. An important problem, from a theoretical and practical point of view, of learning classifier systems is presented in depth. Multiobjective evolutionary algorithms, which constitute one of the most...

  5. Evolutionary Statistical Procedures

    CERN Document Server

    Baragona, Roberto; Poli, Irene

    2011-01-01

    This proposed text appears to be a good introduction to evolutionary computation for use in applied statistics research. The authors draw from a vast base of knowledge about the current literature in both the design of evolutionary algorithms and statistical techniques. Modern statistical research is on the threshold of solving increasingly complex problems in high dimensions, and the generalization of its methodology to parameters whose estimators do not follow mathematically simple distributions is underway. Many of these challenges involve optimizing functions for which analytic solutions a

  6. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    Science.gov (United States)

    Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

    2015-01-01

    Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

  7. The Evolutionary Puzzle of Suicide

    Directory of Open Access Journals (Sweden)

    Henri-Jean Aubin

    2013-12-01

    Full Text Available Mechanisms of self-destruction are difficult to reconcile with evolution’s first rule of thumb: survive and reproduce. However, evolutionary success ultimately depends on inclusive fitness. The altruistic suicide hypothesis posits that the presence of low reproductive potential and burdensomeness toward kin can increase the inclusive fitness payoff of self-removal. The bargaining hypothesis assumes that suicide attempts could function as an honest signal of need. The payoff may be positive if the suicidal person has a low reproductive potential. The parasite manipulation hypothesis is founded on the rodent—Toxoplasma gondii host-parasite model, in which the parasite induces a “suicidal” feline attraction that allows the parasite to complete its life cycle. Interestingly, latent infection by T. gondii has been shown to cause behavioral alterations in humans, including increased suicide attempts. Finally, we discuss how suicide risk factors can be understood as nonadaptive byproducts of evolved mechanisms that malfunction. Although most of the mechanisms proposed in this article are largely speculative, the hypotheses that we raise accept self-destructive behavior within the framework of evolutionary theory.

  8. Evolutionary trends in Heteroptera

    NARCIS (Netherlands)

    Cobben, R.H.

    1968-01-01

    1. This work, the first volume of a series dealing with evolutionary trends in Heteroptera, is concerned with the egg system of about 400 species. The data are presented systematically in chapters 1 and 2 with a critical review of the literature after each family.

    2. Chapter 3 evaluates facts

  9. Evolutionary mysteries in meiosis

    NARCIS (Netherlands)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E.; Wijnker, Erik; Haag, Christoph R.

    2016-01-01

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these

  10. Applications of Evolutionary Computation

    NARCIS (Netherlands)

    Mora, Antonio M.; Squillero, Giovanni; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Smith, Stephen L; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Mora, Antonio M.; Squillero, Giovanni; Jan, Mathieu; Matthias, M; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Esparcia-Alcazar, Anna I; Silva, Sara; Agapitos, Alexandros; Cotta, Carlos; De Falco, Ivanoe; Cioppa, Antonio Della; Diwold, Konrad; Ekart, Aniko; Tarantino, Ernesto; Vega, Francisco Fernandez De; Burelli, Paolo; Sim, Kevin; Cagnoni, Stefano; Simoes, Anabela; Merelo, J.J.; Urquhart, Neil; Haasdijk, Evert; Zhang, Mengjie; Squillero, Giovanni; Eiben, A E; Tettamanzi, Andrea G B; Glette, Kyrre; Rohlfshagen, Philipp; Schaefer, Robert; Caserta, Marco; Ramirez, Adriana; Voß, Stefan

    2015-01-01

    The application of genetic and evolutionary computation to problems in medicine has increased rapidly over the past five years, but there are specific issues and challenges that distinguish it from other real-world applications. Obtaining reliable and coherent patient data, establishing the clinical

  11. Evolutionary perspectives on ageing.

    Science.gov (United States)

    Reichard, Martin

    2017-10-01

    From an evolutionary perspective, ageing is a decrease in fitness with chronological age - expressed by an increase in mortality risk and/or decline in reproductive success and mediated by deterioration of functional performance. While this makes ageing intuitively paradoxical - detrimental to individual fitness - evolutionary theory offers answers as to why ageing has evolved. In this review, I first briefly examine the classic evolutionary theories of ageing and their empirical tests, and highlight recent findings that have advanced our understanding of the evolution of ageing (condition-dependent survival, positive pleiotropy). I then provide an overview of recent theoretical extensions and modifications that accommodate those new discoveries. I discuss the role of indeterminate (asymptotic) growth for lifetime increases in fecundity and ageing trajectories. I outline alternative views that challenge a universal existence of senescence - namely the lack of a germ-soma distinction and the ability of tissue replacement and retrogression to younger developmental stages in modular organisms. I argue that rejuvenation at the organismal level is plausible, but includes a return to a simple developmental stage. This may exempt a particular genotype from somatic defects but, correspondingly, removes any information acquired during development. A resolution of the question of whether a rejuvenated individual is the same entity is central to the recognition of whether current evolutionary theories of ageing, with their extensions and modifications, can explain the patterns of ageing across the Tree of Life. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Editorial overview: Evolutionary psychology

    NARCIS (Netherlands)

    Gangestad, S.W.; Tybur, J.M.

    2016-01-01

    Functional approaches in psychology - which ask what behavior is good for - are almost as old as scientific psychology itself. Yet sophisticated, generative functional theories were not possible until developments in evolutionary biology in the mid-20th century. Arising in the last three decades,

  13. Biochemistry and evolutionary biology

    Indian Academy of Sciences (India)

    Biochemical information has been crucial for the development of evolutionary biology. On the one hand, the sequence information now appearing is producing a huge increase in the amount of data available for phylogenetic analysis; on the other hand, and perhaps more fundamentally, it allows understanding of the ...

  14. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Hindi and English. Port 1. Resonance, Vo1.7 ... they use. Of course, many evolutionary biologists do work with fossils or DNA, or both, but there are also large numbers of ... The first major division that I like to make is between studies focussed ...

  15. Learning: An Evolutionary Analysis

    Science.gov (United States)

    Swann, Joanna

    2009-01-01

    This paper draws on the philosophy of Karl Popper to present a descriptive evolutionary epistemology that offers philosophical solutions to the following related problems: "What happens when learning takes place?" and "What happens in human learning?" It provides a detailed analysis of how learning takes place without any direct transfer of…

  16. Complex systems, evolutionary planning?

    NARCIS (Netherlands)

    Bertolini, L.; de Roo, G.; Silva, E.A.

    2010-01-01

    Coping with uncertainty is a defining challenge for spatial planners. Accordingly, most spatial planning theories and methods are aimed at reducing uncertainty. However, the question is what should be done when this seems impossible? This chapter proposes an evolutionary interpretation of spatial

  17. Molluscan Evolutionary Development

    DEFF Research Database (Denmark)

    Wanninger, Andreas Wilhelm Georg; Koop, Damien; Moshel-Lynch, Sharon

    2008-01-01

    Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable...

  18. Transfer Area Mechanical Handling Calculation

    International Nuclear Information System (INIS)

    Dianda, B.

    2004-01-01

    This calculation is intended to support the License Application (LA) submittal of December 2004, in accordance with the directive given by DOE correspondence received on the 27th of January 2004 entitled: ''Authorization for Bechtel SAX Company L.L. C. to Include a Bare Fuel Handling Facility and Increased Aging Capacity in the License Application, Contract Number DE-AC--28-01R W12101'' (Arthur, W.J., I11 2004). This correspondence was appended by further Correspondence received on the 19th of February 2004 entitled: ''Technical Direction to Bechtel SAIC Company L.L. C. for Surface Facility Improvements, Contract Number DE-AC--28-OIRW12101; TDL No. 04-024'' (BSC 2004a). These documents give the authorization for a Fuel Handling Facility to be included in the baseline. The purpose of this calculation is to establish preliminary bounding equipment envelopes and weights for the Fuel Handling Facility (FHF) transfer areas equipment. This calculation provides preliminary information only to support development of facility layouts and preliminary load calculations. The limitations of this preliminary calculation lie within the assumptions of section 5 , as this calculation is part of an evolutionary design process. It is intended that this calculation is superseded as the design advances to reflect information necessary to support License Application. The design choices outlined within this calculation represent a demonstration of feasibility and may or may not be included in the completed design. This calculation provides preliminary weight, dimensional envelope, and equipment position in building for the purposes of defining interface variables. This calculation identifies and sizes major equipment and assemblies that dictate overall equipment dimensions and facility interfaces. Sizing of components is based on the selection of commercially available products, where applicable. This is not a specific recommendation for the future use of these components or their

  19. Context dependent DNA evolutionary models

    DEFF Research Database (Denmark)

    Jensen, Jens Ledet

    This paper is about stochastic models for the evolution of DNA. For a set of aligned DNA sequences, connected in a phylogenetic tree, the models should be able to explain - in probabilistic terms - the differences seen in the sequences. From the estimates of the parameters in the model one can...... start to make biologically interpretations and conclusions concerning the evolutionary forces at work. In parallel with the increase in computing power, models have become more complex. Starting with Markov processes on a space with 4 states, and extended to Markov processes with 64 states, we are today...... studying models on spaces with 4n (or 64n) number of states with n well above one hundred, say. For such models it is no longer possible to calculate the transition probability analytically, and often Markov chain Monte Carlo is used in connection with likelihood analysis. This is also the approach taken...

  20. Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator-prey system.

    Science.gov (United States)

    Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

    2014-11-11

    Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.

  1. Evolutionary constrained optimization

    CERN Document Server

    Deb, Kalyanmoy

    2015-01-01

    This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

  2. Introduction to Evolutionary Algorithms

    CERN Document Server

    Yu, Xinjie

    2010-01-01

    Evolutionary algorithms (EAs) are becoming increasingly attractive for researchers from various disciplines, such as operations research, computer science, industrial engineering, electrical engineering, social science, economics, etc. This book presents an insightful, comprehensive, and up-to-date treatment of EAs, such as genetic algorithms, differential evolution, evolution strategy, constraint optimization, multimodal optimization, multiobjective optimization, combinatorial optimization, evolvable hardware, estimation of distribution algorithms, ant colony optimization, particle swarm opti

  3. Evolutionary games on graphs

    Science.gov (United States)

    Szabó, György; Fáth, Gábor

    2007-07-01

    Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.

  4. Evolutionary mysteries in meiosis.

    Science.gov (United States)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E; Wijnker, Erik; Haag, Christoph R

    2016-10-19

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

  5. Asymmetric Evolutionary Games

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-01-01

    Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

  6. Studies in evolutionary agroecology

    DEFF Research Database (Denmark)

    Wille, Wibke

    of population performance will increase in frequency. Yield, one of the fundamental agronomic variables, is not an individual, but a population characteristic. A farmer wants a high yield per hectare; he is not interested in the performance of individual plants. When individual selection and population...... of Evolutionary Agroecology that the highest yielding individuals do not necessarily perform best as a population. The investment of resources into strategies and structures increasing individual competitive ability carries a cost. If a whole population consists of individuals investing resources to compete...

  7. Towards Adaptive Evolutionary Architecture

    DEFF Research Database (Denmark)

    Bak, Sebastian HOlt; Rask, Nina; Risi, Sebastian

    2016-01-01

    This paper presents first results from an interdisciplinary project, in which the fields of architecture, philosophy and artificial life are combined to explore possible futures of architecture. Through an interactive evolutionary installation, called EvoCurtain, we investigate aspects of how...... to the development of designs tailored to the individual preferences of inhabitants, changing the roles of architects and designers entirely. Architecture-as-it-could-be is a philosophical approach conducted through artistic methods to anticipate the technological futures of human-centered development within...

  8. A hybrid method using the widely-used WIEN2k and VASP codes to calculate the complete set of XAS/EELS edges in a hundred-atoms system.

    Science.gov (United States)

    Donval, Gaël; Moreau, Philippe; Danet, Julien; Larbi, Séverine Jouanneau-Si; Bayle-Guillemaud, Pascale; Boucher, Florent

    2017-01-04

    Most of the recent developments in EELS modelling has been focused on getting a better agreement with measurements. Less work however has been dedicated to bringing EELS calculations to larger structures that can more realistically describe actual systems. The purpose of this paper is to present a hybrid approach well adapted to calculating the whole set of localised EELS core-loss edges (at the XAS level of theory) on larger systems using only standard tools, namely the WIEN2k and VASP codes. We illustrate the usefulness of this method by applying it to a set of amorphous silicon structures in order to explain the flattening of the silicon L 2,3 EELS edge peak at the onset. We show that the peak flattening is actually caused by the collective contribution of each of the atoms to the average spectrum, as opposed to a flattening occurring on each individual spectrum. This method allowed us to reduce the execution time by a factor of 3 compared to a usual-carefully optimised-WIEN2k calculation. It provided even greater speed-ups on more complex systems (interfaces, ∼300 atoms) that will be presented in a future paper. This method is suited to calculate all the localized edges of all the atoms of a structure in a single calculation for light atoms as long as the core-hole effects can be neglected.

  9. Core principles of evolutionary medicine

    Science.gov (United States)

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Abstract Background and objectives Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. Methodology The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Results Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. Conclusions and implications This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further. PMID:29493660

  10. Practical advantages of evolutionary computation

    Science.gov (United States)

    Fogel, David B.

    1997-10-01

    Evolutionary computation is becoming a common technique for solving difficult, real-world problems in industry, medicine, and defense. This paper reviews some of the practical advantages to using evolutionary algorithms as compared with classic methods of optimization or artificial intelligence. Specific advantages include the flexibility of the procedures, as well as their ability to self-adapt the search for optimum solutions on the fly. As desktop computers increase in speed, the application of evolutionary algorithms will become routine.

  11. Calculating the probability of multitaxon evolutionary trees: bootstrappers Gambit.

    OpenAIRE

    Lake, J A

    1995-01-01

    The reconstruction of multitaxon trees from molecular sequences is confounded by the variety of algorithms and criteria used to evaluate trees, making it difficult to compare the results of different analyses. A global method of multitaxon phylogenetic reconstruction described here, Bootstrappers Gambit, can be used with any four-taxon algorithm, including distance, maximum likelihood, and parsimony methods. It incorporates a Bayesian-Jeffreys'-bootstrap analysis to provide a uniform probabil...

  12. Complexity in Evolutionary Processes

    International Nuclear Information System (INIS)

    Schuster, P.

    2010-01-01

    Darwin's principle of evolution by natural selection is readily casted into a mathematical formalism. Molecular biology revealed the mechanism of mutation and provides the basis for a kinetic theory of evolution that models correct reproduction and mutation as parallel chemical reaction channels. A result of the kinetic theory is the existence of a phase transition in evolution occurring at a critical mutation rate, which represents a localization threshold for the population in sequence space. Occurrence and nature of such phase transitions depend critically on fitness landscapes. The fitness landscape being tantamount to a mapping from sequence or genotype space into phenotype space is identified as the true source of complexity in evolution. Modeling evolution as a stochastic process is discussed and neutrality with respect to selection is shown to provide a major challenge for understanding evolutionary processes (author)

  13. Spore: Spawning Evolutionary Misconceptions?

    Science.gov (United States)

    Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.

    2010-10-01

    The use of computer simulations as educational tools may afford the means to develop understanding of evolution as a natural, emergent, and decentralized process. However, special consideration of developmental constraints on learning may be necessary when using these technologies. Specifically, the essentialist (biological forms possess an immutable essence), teleological (assignment of purpose to living things and/or parts of living things that may not be purposeful), and intentionality (assumption that events are caused by an intelligent agent) biases may be reinforced through the use of computer simulations, rather than addressed with instruction. We examine the video game Spore for its depiction of evolutionary content and its potential to reinforce these cognitive biases. In particular, we discuss three pedagogical strategies to mitigate weaknesses of Spore and other computer simulations: directly targeting misconceptions through refutational approaches, targeting specific principles of scientific inquiry, and directly addressing issues related to models as cognitive tools.

  14. Evolutionary games under incompetence.

    Science.gov (United States)

    Kleshnina, Maria; Filar, Jerzy A; Ejov, Vladimir; McKerral, Jody C

    2018-02-26

    The adaptation process of a species to a new environment is a significant area of study in biology. As part of natural selection, adaptation is a mutation process which improves survival skills and reproductive functions of species. Here, we investigate this process by combining the idea of incompetence with evolutionary game theory. In the sense of evolution, incompetence and training can be interpreted as a special learning process. With focus on the social side of the problem, we analyze the influence of incompetence on behavior of species. We introduce an incompetence parameter into a learning function in a single-population game and analyze its effect on the outcome of the replicator dynamics. Incompetence can change the outcome of the game and its dynamics, indicating its significance within what are inherently imperfect natural systems.

  15. Open Issues in Evolutionary Robotics.

    Science.gov (United States)

    Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne

    2016-01-01

    One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots.

  16. Evolutionary economics and industry location

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.

    2003-01-01

    This paper aims to provide the outlines of an evolutionary economic geography of industry location. We discuss two evolutionary explanations of industry location, that is, one that concentrates on spin-offs, and one that focuses attention on knowledge and agglomeration economies. We claim that both

  17. Contemporary issues in evolutionary biology

    Indian Academy of Sciences (India)

    These discussions included, among others, the possible consequences of nonDNA-based inheritance—epigenetics and cultural evolution, niche construction, and developmental mechanisms on our understanding of the evolutionary process, speciation, complexity in biology, and constructing a formal evolutionary theory.

  18. Contemporary issues in evolutionary biology

    Indian Academy of Sciences (India)

    We are delighted to bring to the readers, a set of peer-reviewed papers on evolutionary biology, published as a special issue of the Journal of Genetics. These papers emanated from ruminations upon and discussions at the Foundations of. Evolutionary Theory: the Ongoing Synthesis meeting at Coorg, India, in February ...

  19. Fixation Time for Evolutionary Graphs

    Science.gov (United States)

    Nie, Pu-Yan; Zhang, Pei-Ai

    Evolutionary graph theory (EGT) is recently proposed by Lieberman et al. in 2005. EGT is successful for explaining biological evolution and some social phenomena. It is extremely important to consider the time of fixation for EGT in many practical problems, including evolutionary theory and the evolution of cooperation. This study characterizes the time to asymptotically reach fixation.

  20. Applications of evolutionary economic geography

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.; Puranam, Krishna Kishore; Ravi Kumar Jain B., xx

    2008-01-01

    This paper is written as the first chapter of an edited volume on evolutionary economics and economic geography (Frenken, K., editor, Applied Evolutionary Economics and Economic Geography, Cheltenham: Edward Elgar, expected publication date February 2007). The paper reviews empirical applications of

  1. Evolutionary Explanations of Eating Disorders

    Directory of Open Access Journals (Sweden)

    Igor Kardum

    2008-12-01

    Full Text Available This article reviews several most important evolutionary mechanisms that underlie eating disorders. The first part clarifies evolutionary foundations of mental disorders and various mechanisms leading to their development. In the second part selective pressures and evolved adaptations causing contemporary epidemic of obesity as well as differences in dietary regimes and life-style between modern humans and their ancestors are described. Concerning eating disorders, a number of current evolutionary explanations of anorexia nervosa are presented together with their main weaknesses. Evolutionary explanations of eating disorders based on the reproductive suppression hypothesis and its variants derived from kin selection theory and the model of parental manipulation were elaborated. The sexual competition hypothesis of eating disorder, adapted to flee famine hypothesis as well as explanation based on the concept of social attention holding power and the need to belonging were also explained. The importance of evolutionary theory in modern conceptualization and research of eating disorders is emphasized.

  2. Balance of attraction and repulsion in nucleic-acid base stacking: CCSD(T)/complete-basis-set-limit calculations on uracil dimer and a comparison with the force-field description

    Czech Academy of Sciences Publication Activity Database

    Morgado, C.A.; Jurečka, P.; Svozil, Daniel; Hobza, Pavel; Šponer, Jiří

    2009-01-01

    Roč. 5, č. 6 (2009), s. 1524-1544 ISSN 1549-9618 R&D Projects: GA AV ČR(CZ) IAA400040802; GA AV ČR(CZ) IAA400550701; GA MŠk(CZ) LC06030 Grant - others:GA ČR(CZ) GA203/09/1476 Program:GA Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : quantum chemical calculations * nucleic acids * force field Subject RIV: BO - Biophysics Impact factor: 4.804, year: 2009

  3. An evolutionary ecology of individual differences

    Science.gov (United States)

    Dall, Sasha R. X.; Bell, Alison M.; Bolnick, Daniel I.; Ratnieks, Francis L. W.

    2014-01-01

    Individuals often differ in what they do. This has been recognised since antiquity. Nevertheless, the ecological and evolutionary significance of such variation is attracting widespread interest, which is burgeoning to an extent that is fragmenting the literature. As a first attempt at synthesis, we focus on individual differences in behaviour within populations that exceed the day-to-day variation in individual behaviour (i.e. behavioural specialisation). Indeed, the factors promoting ecologically relevant behavioural specialisation within natural populations are likely to have far-reaching ecological and evolutionary consequences. We discuss such individual differences from three distinct perspectives: individual niche specialisations, the division of labour within insect societies and animal personality variation. In the process, while recognising that each area has its own unique motivations, we identify a number of opportunities for productive ‘crossfertilisation’ among the (largely independent) bodies of work. We conclude that a complete understanding of evolutionarily and ecologically relevant individual differences must specify how ecological interactions impact the basic biological process (e.g. Darwinian selection, development and information processing) that underpin the organismal features determining behavioural specialisations. Moreover, there is likely to be covariation amongst behavioural specialisations. Thus, we sketch the key elements of a general framework for studying the evolutionary ecology of individual differences. PMID:22897772

  4. An Angiotensin II type 1 receptor activation switch patch revealed through Evolutionary Trace analysis

    DEFF Research Database (Denmark)

    Bonde, Marie Mi; Yao, Rong; Ma, Jian-Nong

    2010-01-01

    to be completely resolved. Evolutionary Trace (ET) analysis is a computational method, which identifies clusters of functionally important residues by integrating information on evolutionary important residue variations with receptor structure. Combined with known mutational data, ET predicted a patch of residues......) displayed phenotypes associated with changed activation state, such as increased agonist affinity or basal activity, promiscuous activation, or constitutive internalization highlighting the importance of testing different signaling pathways. We conclude that this evolutionary important patch mediates...

  5. Chemical evolutionary games.

    Science.gov (United States)

    Aristotelous, Andreas C; Durrett, Richard

    2014-05-01

    Inspired by the use of hybrid cellular automata in modeling cancer, we introduce a generalization of evolutionary games in which cells produce and absorb chemicals, and the chemical concentrations dictate the death rates of cells and their fitnesses. Our long term aim is to understand how the details of the interactions in a system with n species and m chemicals translate into the qualitative behavior of the system. Here, we study two simple 2×2 games with two chemicals and revisit the two and three species versions of the one chemical colicin system studied earlier by Durrett and Levin (1997). We find that in the 2×2 examples, the behavior of our new spatial model can be predicted from that of the mean field differential equation using ideas of Durrett and Levin (1994). However, in the three species colicin model, the system with diffusion does not have the coexistence which occurs in the lattices model in which sites interact with only their nearest neighbors. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Evolutionary and developmental modules.

    Science.gov (United States)

    Lacquaniti, Francesco; Ivanenko, Yuri P; d'Avella, Andrea; Zelik, Karl E; Zago, Myrka

    2013-01-01

    The identification of biological modules at the systems level often follows top-down decomposition of a task goal, or bottom-up decomposition of multidimensional data arrays into basic elements or patterns representing shared features. These approaches traditionally have been applied to mature, fully developed systems. Here we review some results from two other perspectives on modularity, namely the developmental and evolutionary perspective. There is growing evidence that modular units of development were highly preserved and recombined during evolution. We first consider a few examples of modules well identifiable from morphology. Next we consider the more difficult issue of identifying functional developmental modules. We dwell especially on modular control of locomotion to argue that the building blocks used to construct different locomotor behaviors are similar across several animal species, presumably related to ancestral neural networks of command. A recurrent theme from comparative studies is that the developmental addition of new premotor modules underlies the postnatal acquisition and refinement of several different motor behaviors in vertebrates.

  7. Evolutionary disarmament in interspecific competition.

    Science.gov (United States)

    Kisdi, E; Geritz, S A

    2001-12-22

    Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

  8. Evolutionary computation for reinforcement learning

    NARCIS (Netherlands)

    Whiteson, S.; Wiering, M.; van Otterlo, M.

    2012-01-01

    Algorithms for evolutionary computation, which simulate the process of natural selection to solve optimization problems, are an effective tool for discovering high-performing reinforcement-learning policies. Because they can automatically find good representations, handle continuous action spaces,

  9. Evolutionary genetics: the Drosophila model

    Indian Academy of Sciences (India)

    Unknown

    Evolutionary genetics straddles the two fundamental processes of life, ... of the genus Drosophila have been used extensively as model systems in experimental ... issue will prove interesting, informative and thought-provoking for both estab-.

  10. Integrating genomics into evolutionary medicine.

    Science.gov (United States)

    Rodríguez, Juan Antonio; Marigorta, Urko M; Navarro, Arcadi

    2014-12-01

    The application of the principles of evolutionary biology into medicine was suggested long ago and is already providing insight into the ultimate causes of disease. However, a full systematic integration of medical genomics and evolutionary medicine is still missing. Here, we briefly review some cases where the combination of the two fields has proven profitable and highlight two of the main issues hindering the development of evolutionary genomic medicine as a mature field, namely the dissociation between fitness and health and the still considerable difficulties in predicting phenotypes from genotypes. We use publicly available data to illustrate both problems and conclude that new approaches are needed for evolutionary genomic medicine to overcome these obstacles. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Evolutionary robotics – A review

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    a need for a technique by which the robot is able to acquire new behaviours automatically .... Evolutionary robotics is a comparatively new field of robotics research, which seems to ..... Technical Report: PCIA-94-04, Institute of Psychology,.

  12. Using Evolutionary Theory to Guide Mental Health Research.

    Science.gov (United States)

    Durisko, Zachary; Mulsant, Benoit H; McKenzie, Kwame; Andrews, Paul W

    2016-03-01

    Evolutionary approaches to medicine can shed light on the origins and etiology of disease. Such an approach may be especially useful in psychiatry, which frequently addresses conditions with heterogeneous presentation and unknown causes. We review several previous applications of evolutionary theory that highlight the ways in which psychiatric conditions may persist despite and because of natural selection. One lesson from the evolutionary approach is that some conditions currently classified as disorders (because they cause distress and impairment) may actually be caused by functioning adaptations operating "normally" (as designed by natural selection). Such conditions suggest an alternative illness model that may generate alternative intervention strategies. Thus, the evolutionary approach suggests that psychiatry should sometimes think differently about distress and impairment. The complexity of the human brain, including normal functioning and potential for dysfunctions, has developed over evolutionary time and has been shaped by natural selection. Understanding the evolutionary origins of psychiatric conditions is therefore a crucial component to a complete understanding of etiology. © The Author(s) 2016.

  13. Evolutionary Game Theory: A Renaissance

    Directory of Open Access Journals (Sweden)

    Jonathan Newton

    2018-05-01

    Full Text Available Economic agents are not always rational or farsighted and can make decisions according to simple behavioral rules that vary according to situation and can be studied using the tools of evolutionary game theory. Furthermore, such behavioral rules are themselves subject to evolutionary forces. Paying particular attention to the work of young researchers, this essay surveys the progress made over the last decade towards understanding these phenomena, and discusses open research topics of importance to economics and the broader social sciences.

  14. Freud: the first evolutionary psychologist?

    Science.gov (United States)

    LeCroy, D

    2000-04-01

    An evolutionary perspective on attachment theory and psychoanalytic theory brings these two fields together in interesting ways. Application of the evolutionary principle of parent-offspring conflict to attachment theory suggests that attachment styles represent context-sensitive, evolved (adaptive) behaviors. In addition, an emphasis on offspring counter-strategies to adult reproductive strategies leads to consideration of attachment styles as overt manifestations of psychodynamic mediating processes, including the defense mechanisms of repression and reaction formation.

  15. IDEA: Interactive Display for Evolutionary Analyses.

    Science.gov (United States)

    Egan, Amy; Mahurkar, Anup; Crabtree, Jonathan; Badger, Jonathan H; Carlton, Jane M; Silva, Joana C

    2008-12-08

    The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

  16. IDEA: Interactive Display for Evolutionary Analyses

    Directory of Open Access Journals (Sweden)

    Carlton Jane M

    2008-12-01

    Full Text Available Abstract Background The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. Results We have developed IDEA (Interactive Display for Evolutionary Analyses, an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. Conclusion IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

  17. Declination Calculator

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Declination is calculated using the current International Geomagnetic Reference Field (IGRF) model. Declination is calculated using the current World Magnetic Model...

  18. Completely continuous and weakly completely continuous abstract ...

    Indian Academy of Sciences (India)

    An algebra A is called right completely continuous (right weakly completely continuous) ... Moreover, some applications of these results in group algebras are .... A linear subspace S(G) of L1(G) is said to be a Segal algebra, if it satisfies the.

  19. A conceptual evolutionary aseismic decision support framework for hospitals

    Science.gov (United States)

    Hu, Yufeng; Dargush, Gary F.; Shao, Xiaoyun

    2012-12-01

    In this paper, aconceptual evolutionary framework for aseismic decision support for hospitalsthat attempts to integrate a range of engineering and sociotechnical models is presented. Genetic algorithms are applied to find the optimal decision sets. A case study is completed to demonstrate how the frameworkmay applytoa specific hospital.The simulations show that the proposed evolutionary decision support framework is able to discover robust policy sets in either uncertain or fixed environments. The framework also qualitatively identifies some of the characteristicbehavior of the critical care organization. Thus, by utilizing the proposedframework, the decision makers are able to make more informed decisions, especially toenhance the seismic safety of the hospitals.

  20. Evolutionary foundations for cancer biology.

    Science.gov (United States)

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.

  1. Evolutionary engineering for industrial microbiology.

    Science.gov (United States)

    Vanee, Niti; Fisher, Adam B; Fong, Stephen S

    2012-01-01

    Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

  2. Analytical calculation of the transition to complete phase ...

    Indian Academy of Sciences (India)

    Ciências e Humanidades, Universidade de S˜ao Paulo, Av. Arlindo Bettio 1000,. 03828-000 S˜ao Paulo, Brazil. 4Department of Physics, Faculty of Science, Ain Shams University, 11566 Cairo, Egypt. 5Department of Physics, Faculty of Education, University of Riyadh for Women,. P.O. Box 21034, 11942 Alkharj, Kingdom of ...

  3. Evolutionary Aesthetics and Print Advertising

    Directory of Open Access Journals (Sweden)

    Kamil Luczaj

    2015-06-01

    Full Text Available The article analyzes the extent to which predictions based on the theory of evolutionary aesthetics are utilized by the advertising industry. The purpose of a comprehensive content analysis of print advertising is to determine whether the items indicated by evolutionists such as animals, flowers, certain types of landscapes, beautiful humans, and some colors are part of real advertising strategies. This article has shown that many evolutionary hypotheses (although not all of them are supported by empirical data. Along with these hypotheses, some inferences from Bourdieu’s cultural capital theory were tested. It turned out that advertising uses both biological schemata and cultural patterns to make an image more likable.

  4. The evolutionary psychology of hunger.

    Science.gov (United States)

    Al-Shawaf, Laith

    2016-10-01

    An evolutionary psychological perspective suggests that emotions can be understood as coordinating mechanisms whose job is to regulate various psychological and physiological programs in the service of solving an adaptive problem. This paper suggests that it may also be fruitful to approach hunger from this coordinating mechanism perspective. To this end, I put forward an evolutionary task analysis of hunger, generating novel a priori hypotheses about the coordinating effects of hunger on psychological processes such as perception, attention, categorization, and memory. This approach appears empirically fruitful in that it yields a bounty of testable new hypotheses. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...

  6. phyloXML: XML for evolutionary biology and comparative genomics.

    Science.gov (United States)

    Han, Mira V; Zmasek, Christian M

    2009-10-27

    Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.org.

  7. Optimizing a reconfigurable material via evolutionary computation

    Science.gov (United States)

    Wilken, Sam; Miskin, Marc Z.; Jaeger, Heinrich M.

    2015-08-01

    Rapid prototyping by combining evolutionary computation with simulations is becoming a powerful tool for solving complex design problems in materials science. This method of optimization operates in a virtual design space that simulates potential material behaviors and after completion needs to be validated by experiment. However, in principle an evolutionary optimizer can also operate on an actual physical structure or laboratory experiment directly, provided the relevant material parameters can be accessed by the optimizer and information about the material's performance can be updated by direct measurements. Here we provide a proof of concept of such direct, physical optimization by showing how a reconfigurable, highly nonlinear material can be tuned to respond to impact. We report on an entirely computer controlled laboratory experiment in which a 6 ×6 grid of electromagnets creates a magnetic field pattern that tunes the local rigidity of a concentrated suspension of ferrofluid and iron filings. A genetic algorithm is implemented and tasked to find field patterns that minimize the force transmitted through the suspension. Searching within a space of roughly 1010 possible configurations, after testing only 1500 independent trials the algorithm identifies an optimized configuration of layered rigid and compliant regions.

  8. Evolutionary Psychology and Intelligence Research

    Science.gov (United States)

    Kanazawa, Satoshi

    2010-01-01

    This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative…

  9. Darwinian foundations for evolutionary economics

    NARCIS (Netherlands)

    Stoelhorst, J.W.

    2008-01-01

    This paper engages with the methodological debate on the contribution of Darwinism to Veblen's (1898) evolutionary research program for economics. I argue that ontological continuity, generalized Darwinism, and multi-level selection are necessary building blocks for an explanatory framework that can

  10. Ernst Mayr and Evolutionary Biology

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 7. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology. Renee M Borges. General Article Volume 10 Issue 7 July 2005 pp 21-33. Fulltext. Click here to view fulltext PDF. Permanent link:

  11. Evolutionary Biology Research in India

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 10. Evolutionary Biology Research in India. Information and Announcements Volume 5 Issue 10 October 2000 pp 102-104. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/005/10/0102-0104 ...

  12. Realism, Relativism, and Evolutionary Psychology

    NARCIS (Netherlands)

    Derksen, M.

    Against recent attempts to forge a reconciliation between constructionism and realism, I contend that, in psychology at least, stirring up conflict is a more fruitful strategy. To illustrate this thesis, I confront a school of psychology with strong realist leanings, evolutionary psychology, with

  13. Ancient Biomolecules and Evolutionary Inference

    DEFF Research Database (Denmark)

    Cappellini, Enrico; Prohaska, Ana; Racimo, Fernando

    2018-01-01

    Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleo...

  14. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  15. Evolutionary trends in directional hearing

    DEFF Research Database (Denmark)

    Carr, Catherine E; Christensen-Dalsgaard, Jakob

    2016-01-01

    Tympanic hearing is a true evolutionary novelty that arose in parallel within early tetrapods. We propose that in these tetrapods, selection for sound localization in air acted upon pre-existing directionally sensitive brainstem circuits, similar to those in fishes. Auditory circuits in birds...

  16. Evolutionary dynamics of mammalian karyotypes

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2012-12-01

    Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

  17. Haldane and modern evolutionary genetics

    Indian Academy of Sciences (India)

    Brian Charlesworth

    2017-11-24

    Nov 24, 2017 ... q(t) of an allele at a locus among the gametes produced at time t, to its .... the importance of disease as an evolutionary factor, which is now a ..... VII. Selection intensity as a function of mortality rate. Proc. Camb. Philos. Soc.

  18. Evolutionary paths of streptococcal and staphylococcal superantigens

    Directory of Open Access Journals (Sweden)

    Okumura Kayo

    2012-08-01

    Full Text Available Abstract Background Streptococcus pyogenes (GAS harbors several superantigens (SAgs in the prophage region of its genome, although speG and smez are not located in this region. The diversity of SAgs is thought to arise during horizontal transfer, but their evolutionary pathways have not yet been determined. We recently completed sequencing the entire genome of S. dysgalactiae subsp. equisimilis (SDSE, the closest relative of GAS. Although speG is the only SAg gene of SDSE, speG was present in only 50% of clinical SDSE strains and smez in none. In this study, we analyzed the evolutionary paths of streptococcal and staphylococcal SAgs. Results We compared the sequences of the 12–60 kb speG regions of nine SDSE strains, five speG+ and four speG–. We found that the synteny of this region was highly conserved, whether or not the speG gene was present. Synteny analyses based on genome-wide comparisons of GAS and SDSE indicated that speG is the direct descendant of a common ancestor of streptococcal SAgs, whereas smez was deleted from SDSE after SDSE and GAS split from a common ancestor. Cumulative nucleotide skew analysis of SDSE genomes suggested that speG was located outside segments of steeper slopes than the stable region in the genome, whereas the region flanking smez was unstable, as expected from the results of GAS. We also detected a previously undescribed staphylococcal SAg gene, selW, and a staphylococcal SAg -like gene, ssl, in the core genomes of all Staphylococcus aureus strains sequenced. Amino acid substitution analyses, based on dN/dS window analysis of the products encoded by speG, selW and ssl suggested that all three genes have been subjected to strong positive selection. Evolutionary analysis based on the Bayesian Markov chain Monte Carlo method showed that each clade included at least one direct descendant. Conclusions Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and

  19. CONTAIN calculations

    International Nuclear Information System (INIS)

    Scholtyssek, W.

    1995-01-01

    In the first phase of a benchmark comparison, the CONTAIN code was used to calculate an assumed EPR accident 'medium-sized leak in the cold leg', especially for the first two days after initiation of the accident. The results for global characteristics compare well with those of FIPLOC, MELCOR and WAVCO calculations, if the same materials data are used as input. However, significant differences show up for local quantities such as flows through leakages. (orig.)

  20. Evolutionary tracks of extended radio sources

    International Nuclear Information System (INIS)

    Baldwin, J.E.

    1982-01-01

    We know almost nothing about the evolutionary tracks of extragalactic radio sources but those tracks are, however, strongly constrained by the distribution of sources in the radio luminosity, P, overall physical size, D, diagram. The P-D diagram for the 3CR 166 source sample of Jenkins et al. (1977) is presented with later additions. Most of the sources are identified and have known redshifts. Because of doubts about the completeness of the sample in this region, the author has made searches in the 6C 151MHz survey for sources with specific surface brightnesses. The numbers found to a limiting flux density of 1-2 Jy suggest that there is no serious underestimate of the numbers in 166 source sample. (Auth.)

  1. Towards a mechanistic foundation of evolutionary theory.

    Science.gov (United States)

    Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

    2017-02-15

    Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics. In evolutionary birth-death processes, fitness is at best a derived quantity, and owing to the potential complexity of such processes, there is no guarantee that there is a simple scalar, such as fitness, that would describe long-term evolutionary outcomes. We discuss how evolutionary birth-death processes can provide useful perspectives on a number of central issues in evolution.

  2. Applied evolutionary economics and economic geography

    NARCIS (Netherlands)

    Frenken, K.

    2007-01-01

    Applied Evolutionary Economics and Economic Geography" aims to further advance empirical methodologies in evolutionary economics, with a special emphasis on geography and firm location. It does so by bringing together a select group of leading scholars including economists, geographers and

  3. Evolutionary biology of bacterial and fungal pathogens

    National Research Council Canada - National Science Library

    Baquero, F

    2008-01-01

    ... and Evolutionary Dynamics of Pathogens * 21 Keith A. Crandall and Marcos Pérez-Losada II. Evolutionary Genetics of Microbial Pathogens 4. Environmental and Social Influences on Infectious Disea...

  4. The citation field of evolutionary economics

    NARCIS (Netherlands)

    Dolfsma, Wilfred; Leydesdorff, Loet

    2010-01-01

    Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal

  5. Essays on nonlinear evolutionary game dynamics

    NARCIS (Netherlands)

    Ochea, M.I.

    2010-01-01

    Evolutionary game theory has been viewed as an evolutionary repair of rational actor game theory in the hope that a population of boundedly rational players may attain convergence to classic rational solutions, such as the Nash Equilibrium, via some learning or evolutionary process. In this thesis

  6. Complete Normal Ordering 1: Foundations

    CERN Document Server

    Ellis, John; Skliros, Dimitri P.

    2016-01-01

    We introduce a new prescription for quantising scalar field theories perturbatively around a true minimum of the full quantum effective action, which is to `complete normal order' the bare action of interest. When the true vacuum of the theory is located at zero field value, the key property of this prescription is the automatic cancellation, to any finite order in perturbation theory, of all tadpole and, more generally, all `cephalopod' Feynman diagrams. The latter are connected diagrams that can be disconnected into two pieces by cutting one internal vertex, with either one or both pieces free from external lines. In addition, this procedure of `complete normal ordering' (which is an extension of the standard field theory definition of normal ordering) reduces by a substantial factor the number of Feynman diagrams to be calculated at any given loop order. We illustrate explicitly the complete normal ordering procedure and the cancellation of cephalopod diagrams in scalar field theories with non-derivative i...

  7. Normalization of Complete Genome Characteristics: Application to Evolution from Primitive Organisms to Homo sapiens.

    Science.gov (United States)

    Sorimachi, Kenji; Okayasu, Teiji; Ohhira, Shuji

    2015-04-01

    Normalized nucleotide and amino acid contents of complete genome sequences can be visualized as radar charts. The shapes of these charts depict the characteristics of an organism's genome. The normalized values calculated from the genome sequence theoretically exclude experimental errors. Further, because normalization is independent of both target size and kind, this procedure is applicable not only to single genes but also to whole genomes, which consist of a huge number of different genes. In this review, we discuss the applications of the normalization of the nucleotide and predicted amino acid contents of complete genomes to the investigation of genome structure and to evolutionary research from primitive organisms to Homo sapiens. Some of the results could never have been obtained from the analysis of individual nucleotide or amino acid sequences but were revealed only after the normalization of nucleotide and amino acid contents was applied to genome research. The discovery that genome structure was homogeneous was obtained only after normalization methods were applied to the nucleotide or predicted amino acid contents of genome sequences. Normalization procedures are also applicable to evolutionary research. Thus, normalization of the contents of whole genomes is a useful procedure that can help to characterize organisms.

  8. Schroedinger operators and evolutionary strategies

    International Nuclear Information System (INIS)

    Asselmeyer, T.

    1997-01-01

    First we introduce a simple model for the description of evolutionary algorithms, which is based on 2nd order partial differential equations for the distribution function of the individuals. Then we turn to the properties of Boltzmann's and Darwin's strategy. the next chapter is dedicated to the mathematical properties of Schroedinger operators. Both statements on the spectral density and their reproducibility during the simulation are summarized. The remaining of this chapter are dedicated to the analysis of the kernel as well as the dependence of the Schroedinger operator on the potential. As conclusion from the results of this chapter we obtain the classification of the strategies in dependence of the fitness. We obtain the classification of the evolutionary strategies, which are described by a 2nd order partial differential equation, in relation to their solution behaviour. Thereafter we are employed with the variation of the mutation distribution

  9. Exponential Expansion in Evolutionary Economics

    DEFF Research Database (Denmark)

    Frederiksen, Peter; Jagtfelt, Tue

    2013-01-01

    This article attempts to solve current problems of conceptual fragmentation within the field of evolutionary economics. One of the problems, as noted by a number of observers, is that the field suffers from an assemblage of fragmented and scattered concepts (Boschma and Martin 2010). A solution...... to this problem is proposed in the form of a model of exponential expansion. The model outlines the overall structure and function of the economy as exponential expansion. The pictographic model describes four axiomatic concepts and their exponential nature. The interactive, directional, emerging and expanding...... concepts are described in detail. Taken together it provides the rudimentary aspects of an economic system within an analytical perspective. It is argued that the main dynamic processes of the evolutionary perspective can be reduced to these four concepts. The model and concepts are evaluated in the light...

  10. Passivity and Evolutionary Game Dynamics

    KAUST Repository

    Park, Shinkyu; Shamma, Jeff S.; Martins, Nuno C.

    2018-01-01

    This paper investigates an energy conservation and dissipation -- passivity -- aspect of dynamic models in evolutionary game theory. We define a notion of passivity using the state-space representation of the models, and we devise systematic methods to examine passivity and to identify properties of passive dynamic models. Based on the methods, we describe how passivity is connected to stability in population games and illustrate stability of passive dynamic models using numerical simulations.

  11. Passivity and Evolutionary Game Dynamics

    KAUST Repository

    Park, Shinkyu

    2018-03-21

    This paper investigates an energy conservation and dissipation -- passivity -- aspect of dynamic models in evolutionary game theory. We define a notion of passivity using the state-space representation of the models, and we devise systematic methods to examine passivity and to identify properties of passive dynamic models. Based on the methods, we describe how passivity is connected to stability in population games and illustrate stability of passive dynamic models using numerical simulations.

  12. [Evolutionary perspective in precocious puberty].

    Science.gov (United States)

    Hochberg, Ze'ev

    2014-10-01

    Pubertal development is subject to substantial heritability, but much variation remains to be explained, including fast changes over the last 150 years, that cannot be explained by changes of gene frequency in the population. This article discusses the influence of environmental factors to adjust maturational tempo in the service of fitness goals. Utilizing evolutionary development thinking (evo-devo), the author examines adolescence as an evolutionary life-history stage in its developmental context. The transition from the preceding stage of juvenility entails adaptive plasticity in response to energy resources, social needs of adolescence and maturation toward youth and adulthood. Using Belsky's evolutionary theory of socialization, I show that familial psychosocial environment during the infancy-childhood and childhood-juvenility transitions foster a fast life-history and reproductive strategy rather than early maturation being just a risk factor for aggression and delinquency. The implications of the evo-devo framework for theory building, illuminates new directions in the understanding of precocious puberty other than a diagnosis of a disease.

  13. Incorporating Development Into Evolutionary Psychology

    Directory of Open Access Journals (Sweden)

    David F. Bjorklund

    2016-09-01

    Full Text Available Developmental thinking is gradually becoming integrated within mainstream evolutionary psychology. This is most apparent with respect to the role of parenting, with proponents of life history theory arguing that cognitive and behavioral plasticity early in life permits children to select different life history strategies, with such strategies being adaptive solutions to different fitness trade-offs. I argue that adaptations develop and are based on the highly plastic nature of infants’ and children’s behavior/cognition/brains. The concept of evolved probabilistic cognitive mechanisms is introduced, defined as information processing mechanisms evolved to solve recurrent problems faced by ancestral populations that are expressed in a probabilistic fashion in each individual in a generation and are based on the continuous and bidirectional interaction over time at all levels of organization, from the genetic through the cultural. Early perceptual/cognitive biases result in behavior that, when occurring in a species-typical environment, produce continuous adaptive changes in behavior (and cognition, yielding adaptive outcomes. Examples from social learning and tool use are provided, illustrating the development of adaptations via evolved probabilistic cognitive mechanisms. The integration of developmental concepts into mainstream evolutionary psychology (and evolutionary concepts into mainstream developmental psychology will provide a clearer picture of what it means to be human.

  14. Testing evolutionary convergence on Europa

    Energy Technology Data Exchange (ETDEWEB)

    Chela-Flores, Julian [Instituto de Estudios Avanzados, Caracas (Venezuela); [Abdus Salam International Centre for Theoretical Physics, Trieste (Italy)

    2002-11-01

    A major objective in solar system exploration is the insertion of appropriate biology-oriented experiments in future missions. We discuss various reasons for suggesting that this type of research be considered a high priority for feasibility studies and, subsequently, for technological development of appropriate melters and submersibles. Based on numerous examples, we argue in favour of the assumption that Darwin's theory is valid for the evolution of life anywhere in the universe. We have suggested how to obtain preliminary insights into the question of the distribution of life in the universe. Universal evolution of intelligent behaviour is at the end of an evolutionary pathway, in which evolution of ion channels in the membrane of microorganisms occurs in its early stages. Further, we have argued that a preliminary test of this conjecture is feasible with experiments on the Europan surface or ocean, involving evolutionary biosignatures (ion channels). This aspect of the exploration for life in the solar system should be viewed as a complement to the astronomical approach for the search of evidence of the later stages of the evolutionary pathways towards intelligent behaviour. (author)

  15. Evolutionary ecology of virus emergence.

    Science.gov (United States)

    Dennehy, John J

    2017-02-01

    The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment. © 2016 New York Academy of Sciences.

  16. A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes

    OpenAIRE

    Mukherjee, Krishanu; Brocchieri, Luciano; B?rglin, Thomas R.

    2009-01-01

    The full complement of homeobox transcription factor sequences, including genes and pseudogenes, was determined from the analysis of 10 complete genomes from flowering plants, moss, Selaginella, unicellular green algae, and red algae. Our exhaustive genome-wide searches resulted in the discovery in each class of a greater number of homeobox genes than previously reported. All homeobox genes can be unambiguously classified by sequence evolutionary analysis into 14 distinct classes also charact...

  17. Burnout calculation

    International Nuclear Information System (INIS)

    Li, D.

    1980-01-01

    Reviewed is the effect of heat flux of different system parameters on critical density in order to give an initial view on the value of several parameters. A thorough analysis of different equations is carried out to calculate burnout is steam-water flows in uniformly heated tubes, annular, and rectangular channels and rod bundles. Effect of heat flux density distribution and flux twisting on burnout and storage determination according to burnout are commended [ru

  18. Latino College Completion: Hawaii

    Science.gov (United States)

    Excelencia in Education (NJ1), 2012

    2012-01-01

    In 2009, Excelencia in Education launched the Ensuring America's Future initiative to inform, organize, and engage leaders in a tactical plan to increase Latino college completion. An executive summary of Latino College Completion in 50 states synthesizes information on 50 state factsheets and builds on the national benchmarking guide. Each…

  19. Latino College Completion: Pennsylvania

    Science.gov (United States)

    Excelencia in Education (NJ1), 2012

    2012-01-01

    In 2009, Excelencia in Education launched the Ensuring America's Future initiative to inform, organize, and engage leaders in a tactical plan to increase Latino college completion. An executive summary of Latino College Completion in 50 states synthesizes information on 50 state factsheets and builds on the national benchmarking guide. Each…

  20. Completeness, supervenience and ontology

    International Nuclear Information System (INIS)

    Maudlin, Tim W E

    2007-01-01

    In 1935, Einstein, Podolsky and Rosen raised the issue of the completeness of the quantum description of a physical system. What they had in mind is whether or not the quantum description is informationally complete, in that all physical features of a system can be recovered from it. In a collapse theory such as the theory of Ghirardi, Rimini and Weber, the quantum wavefunction is informationally complete, and this has often been taken to suggest that according to that theory the wavefunction is all there is. If we distinguish the ontological completeness of a description from its informational completeness, we can see that the best interpretations of the GRW theory must postulate more physical ontology than just the wavefunction

  1. Completeness, supervenience and ontology

    Energy Technology Data Exchange (ETDEWEB)

    Maudlin, Tim W E [Department of Philosophy, Rutgers University, 26 Nichol Avenue, New Brunswick, NJ 08901-1411 (United States)

    2007-03-23

    In 1935, Einstein, Podolsky and Rosen raised the issue of the completeness of the quantum description of a physical system. What they had in mind is whether or not the quantum description is informationally complete, in that all physical features of a system can be recovered from it. In a collapse theory such as the theory of Ghirardi, Rimini and Weber, the quantum wavefunction is informationally complete, and this has often been taken to suggest that according to that theory the wavefunction is all there is. If we distinguish the ontological completeness of a description from its informational completeness, we can see that the best interpretations of the GRW theory must postulate more physical ontology than just the wavefunction.

  2. Adaptive evolutionary walks require neutral intermediates in RNA fitness landscapes.

    Science.gov (United States)

    Rendel, Mark D

    2011-01-01

    In RNA fitness landscapes with interconnected networks of neutral mutations, neutral precursor mutations can play an important role in facilitating the accessibility of epistatic adaptive mutant combinations. I use an exhaustively surveyed fitness landscape model based on short sequence RNA genotypes (and their secondary structure phenotypes) to calculate the minimum rate at which mutants initially appearing as neutral are incorporated into an adaptive evolutionary walk. I show first, that incorporating neutral mutations significantly increases the number of point mutations in a given evolutionary walk when compared to estimates from previous adaptive walk models. Second, that incorporating neutral mutants into such a walk significantly increases the final fitness encountered on that walk - indeed evolutionary walks including neutral steps often reach the global optimum in this model. Third, and perhaps most importantly, evolutionary paths of this kind are often extremely winding in their nature and have the potential to undergo multiple mutations at a given sequence position within a single walk; the potential of these winding paths to mislead phylogenetic reconstruction is briefly considered. Copyright © 2010 Elsevier Inc. All rights reserved.

  3. [Evolutionary process unveiled by the maximum genetic diversity hypothesis].

    Science.gov (United States)

    Huang, Yi-Min; Xia, Meng-Ying; Huang, Shi

    2013-05-01

    As two major popular theories to explain evolutionary facts, the neutral theory and Neo-Darwinism, despite their proven virtues in certain areas, still fail to offer comprehensive explanations to such fundamental evolutionary phenomena as the genetic equidistance result, abundant overlap sites, increase in complexity over time, incomplete understanding of genetic diversity, and inconsistencies with fossil and archaeological records. Maximum genetic diversity hypothesis (MGD), however, constructs a more complete evolutionary genetics theory that incorporates all of the proven virtues of existing theories and adds to them the novel concept of a maximum or optimum limit on genetic distance or diversity. It has yet to meet a contradiction and explained for the first time the half-century old Genetic Equidistance phenomenon as well as most other major evolutionary facts. It provides practical and quantitative ways of studying complexity. Molecular interpretation using MGD-based methods reveal novel insights on the origins of humans and other primates that are consistent with fossil evidence and common sense, and reestablished the important role of China in the evolution of humans. MGD theory has also uncovered an important genetic mechanism in the construction of complex traits and the pathogenesis of complex diseases. We here made a series of sequence comparisons among yeasts, fishes and primates to illustrate the concept of limit on genetic distance. The idea of limit or optimum is in line with the yin-yang paradigm in the traditional Chinese view of the universal creative law in nature.

  4. Evaluating alternative gait strategies using evolutionary robotics.

    Science.gov (United States)

    Sellers, William I; Dennis, Louise A; W -J, Wang; Crompton, Robin H

    2004-05-01

    Evolutionary robotics is a branch of artificial intelligence concerned with the automatic generation of autonomous robots. Usually the form of the robot is predefined and various computational techniques are used to control the machine's behaviour. One aspect is the spontaneous generation of walking in legged robots and this can be used to investigate the mechanical requirements for efficient walking in bipeds. This paper demonstrates a bipedal simulator that spontaneously generates walking and running gaits. The model can be customized to represent a range of hominoid morphologies and used to predict performance parameters such as preferred speed and metabolic energy cost. Because it does not require any motion capture data it is particularly suitable for investigating locomotion in fossil animals. The predictions for modern humans are highly accurate in terms of energy cost for a given speed and thus the values predicted for other bipeds are likely to be good estimates. To illustrate this the cost of transport is calculated for Australopithecus afarensis. The model allows the degree of maximum extension at the knee to be varied causing the model to adopt walking gaits varying from chimpanzee-like to human-like. The energy costs associated with these gait choices can thus be calculated and this information used to evaluate possible locomotor strategies in early hominids.

  5. Nash evolutionary algorithms : Testing problem size in reconstruction problems in frame structures

    OpenAIRE

    Greiner, D.; Periaux, Jacques; Emperador, J.M.; Galván, B.; Winter, G.

    2016-01-01

    The use of evolutionary algorithms has been enhanced in recent years for solving real engineering problems, where the requirements of intense computational calculations are needed, especially when computational engineering simulations are involved (use of finite element method, boundary element method, etc). The coupling of game-theory concepts in evolutionary algorithms has been a recent line of research which could enhance the efficiency of the optimum design procedure and th...

  6. Effects of Clonal Reproduction on Evolutionary Lag and Evolutionary Rescue.

    Science.gov (United States)

    Orive, Maria E; Barfield, Michael; Fernandez, Carlos; Holt, Robert D

    2017-10-01

    Evolutionary lag-the difference between mean and optimal phenotype in the current environment-is of keen interest in light of rapid environmental change. Many ecologically important organisms have life histories that include stage structure and both sexual and clonal reproduction, yet how stage structure and clonality interplay to govern a population's rate of evolution and evolutionary lag is unknown. Effects of clonal reproduction on mean phenotype partition into two portions: one that is phenotype dependent, and another that is genotype dependent. This partitioning is governed by the association between the nonadditive genetic plus random environmental component of phenotype of clonal offspring and their parents. While clonality slows phenotypic evolution toward an optimum, it can dramatically increase population survival after a sudden step change in optimal phenotype. Increased adult survival slows phenotypic evolution but facilitates population survival after a step change; this positive effect can, however, be lost given survival-fecundity trade-offs. Simulations indicate that the benefits of increased clonality under environmental change greatly depend on the nature of that change: increasing population persistence under a step change while decreasing population persistence under a continuous linear change requiring de novo variation. The impact of clonality on the probability of persistence for species in a changing world is thus inexorably linked to the temporal texture of the change they experience.

  7. Introduced species as evolutionary traps

    Science.gov (United States)

    Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.

    2005-01-01

    Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

  8. Multidimensional extended spatial evolutionary games.

    Science.gov (United States)

    Krześlak, Michał; Świerniak, Andrzej

    2016-02-01

    The goal of this paper is to study the classical hawk-dove model using mixed spatial evolutionary games (MSEG). In these games, played on a lattice, an additional spatial layer is introduced for dependence on more complex parameters and simulation of changes in the environment. Furthermore, diverse polymorphic equilibrium points dependent on cell reproduction, model parameters, and their simulation are discussed. Our analysis demonstrates the sensitivity properties of MSEGs and possibilities for further development. We discuss applications of MSEGs, particularly algorithms for modelling cell interactions during the development of tumours. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Feminist Encounters with Evolutionary Psychology

    OpenAIRE

    O'Neill, Rachel

    2016-01-01

    This Section of Australian Feminist Studies is the product of an event that took place at King’s College London in January 2015, hosted as part of the UK-based ‘Critical Sexology’ seminar series. Participants at this event – feminist scholars working across the fields of lin- guistics, cultural studies, sociology, and psychology – were invited to reflect on their encounters with evolutionary psychology (EP). As the event organiser, I was interested to prompt a discussion about how EP shapes t...

  10. Improving processes through evolutionary optimization.

    Science.gov (United States)

    Clancy, Thomas R

    2011-09-01

    As systems evolve over time, their natural tendency is to become increasingly more complex. Studies on complex systems have generated new perspectives on management in social organizations such as hospitals. Much of this research appears as a natural extension of the cross-disciplinary field of systems theory. This is the 18th in a series of articles applying complex systems science to the traditional management concepts of planning, organizing, directing, coordinating, and controlling. In this article, I discuss methods to optimize complex healthcare processes through learning, adaptation, and evolutionary planning.

  11. Historical change and evolutionary theory.

    Science.gov (United States)

    Masters, Roger D

    2007-09-01

    Despite advances in fields like genetics, evolutionary psychology, and human behavior and evolution--which generally focus on individual or small group behavior from a biological perspective--evolutionary biology has made little impact on studies of political change and social history. Theories of natural selection often seem inapplicable to human history because our social behavior is embedded in language (which makes possible the concepts of time and social identity on which what we call "history" depends). Peter Corning's Holistic Darwinism reconceptualizes evolutionary biology, making it possible to go beyond the barriers separating the social and natural sciences. Corning focuses on two primary processes: "synergy" (complex multivariate interactions at multiple levels between a species and its environment) and "cybernetics" (the information systems permitting communication between individuals and groups over time). Combining this frame of reference with inclusive fitness theory, it is possible to answer the most important (and puzzling) question in human history: How did a species that lived for millennia in hunter-gatherer bands form centralized states governing large populations of non-kin (including multi-ethnic empires as well as modern nation-states)? The fragility and contemporary ethnic violence in Kenya and the Congo should suffice as evidence that these issues need to be taken seriously. To explain the rise and fall of states as well as changes in human laws and customs--the core of historical research--it is essential to show how the provision of collective goods can overcome the challenge of self-interest and free-riding in some instances, yet fail to do so in others. To this end, it is now possible to consider how a state providing public goods can--under circumstances that often include effective leadership--contribute to enhanced inclusive fitness of virtually all its members. Because social behavior needs to adapt to ecology, but ecological

  12. Reliability calculations

    International Nuclear Information System (INIS)

    Petersen, K.E.

    1986-03-01

    Risk and reliability analysis is increasingly being used in evaluations of plant safety and plant reliability. The analysis can be performed either during the design process or during the operation time, with the purpose to improve the safety or the reliability. Due to plant complexity and safety and availability requirements, sophisticated tools, which are flexible and efficient, are needed. Such tools have been developed in the last 20 years and they have to be continuously refined to meet the growing requirements. Two different areas of application were analysed. In structural reliability probabilistic approaches have been introduced in some cases for the calculation of the reliability of structures or components. A new computer program has been developed based upon numerical integration in several variables. In systems reliability Monte Carlo simulation programs are used especially in analysis of very complex systems. In order to increase the applicability of the programs variance reduction techniques can be applied to speed up the calculation process. Variance reduction techniques have been studied and procedures for implementation of importance sampling are suggested. (author)

  13. Calculator calculus

    CERN Document Server

    McCarty, George

    1982-01-01

    How THIS BOOK DIFFERS This book is about the calculus. What distinguishes it, however, from other books is that it uses the pocket calculator to illustrate the theory. A computation that requires hours of labor when done by hand with tables is quite inappropriate as an example or exercise in a beginning calculus course. But that same computation can become a delicate illustration of the theory when the student does it in seconds on his calculator. t Furthermore, the student's own personal involvement and easy accomplishment give hi~ reassurance and en­ couragement. The machine is like a microscope, and its magnification is a hundred millionfold. We shall be interested in limits, and no stage of numerical approximation proves anything about the limit. However, the derivative of fex) = 67.SgX, for instance, acquires real meaning when a student first appreciates its values as numbers, as limits of 10 100 1000 t A quick example is 1.1 , 1.01 , 1.001 , •••• Another example is t = 0.1, 0.01, in the functio...

  14. Complete Ureteral Avulsion

    Directory of Open Access Journals (Sweden)

    V. Gupta

    2005-01-01

    Full Text Available Complete avulsion of the ureter is one of the most serious complications of ureteroscopy. It requires open or laparoscopic intervention for repair. This case report emphasizes its management and presents recommendations for prevention in current urological practice.

  15. Conceptual Barriers to Progress Within Evolutionary Biology.

    Science.gov (United States)

    Laland, Kevin N; Odling-Smee, John; Feldman, Marcus W; Kendal, Jeremy

    2009-08-01

    In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo-Darwinism fails to recognize a fundamental cause of evolutionary change, "niche construction". This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, including ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory.

  16. Reliability Calculations

    DEFF Research Database (Denmark)

    Petersen, Kurt Erling

    1986-01-01

    Risk and reliability analysis is increasingly being used in evaluations of plant safety and plant reliability. The analysis can be performed either during the design process or during the operation time, with the purpose to improve the safety or the reliability. Due to plant complexity and safety...... and availability requirements, sophisticated tools, which are flexible and efficient, are needed. Such tools have been developed in the last 20 years and they have to be continuously refined to meet the growing requirements. Two different areas of application were analysed. In structural reliability probabilistic...... approaches have been introduced in some cases for the calculation of the reliability of structures or components. A new computer program has been developed based upon numerical integration in several variables. In systems reliability Monte Carlo simulation programs are used especially in analysis of very...

  17. Evolutionary epistemology a multiparadigm program

    CERN Document Server

    Pinxten, Rik

    1987-01-01

    This volume has its already distant origin in an inter­national conference on Evolutionary Epistemology the editors organized at the University of Ghent in November 1984. This conference aimed to follow up the endeavor started at the ERISS (Epistemologically Relevant Internalist Sociology of Science) conference organized by Don Campbell and Alex Rosen­ berg at Cazenovia Lake, New York, in June 1981, whilst in­ jecting the gist of certain current continental intellectual developments into a debate whose focus, we thought, was in danger of being narrowed too much, considering the still underdeveloped state of affairs in the field. Broadly speaking, evolutionary epistemology today con­ sists of two interrelated, yet qualitatively distinct inves­ tigative efforts. Both are drawing on Darwinian concepts, which may explain why many people have failed to discriminate them. One is the study of the evolution of the cognitive apparatus of living organisms, which is first and foremost the province of biologists and...

  18. Evolutionary potential games on lattices

    International Nuclear Information System (INIS)

    Szabó, György; Borsos, István

    2016-01-01

    Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the “equilibrium state” by adding non-potential components representing games of cyclic dominance.

  19. Evolutionary potential games on lattices

    Energy Technology Data Exchange (ETDEWEB)

    Szabó, György, E-mail: szabo@mfa.kfki.hu; Borsos, István, E-mail: borsos@mfa.kfki.hu

    2016-04-05

    Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the “equilibrium state” by adding non-potential components representing games of cyclic dominance.

  20. Evolutionary potential games on lattices

    Science.gov (United States)

    Szabó, György; Borsos, István

    2016-04-01

    Game theory provides a general mathematical background to study the effect of pair interactions and evolutionary rules on the macroscopic behavior of multi-player games where players with a finite number of strategies may represent a wide scale of biological objects, human individuals, or even their associations. In these systems the interactions are characterized by matrices that can be decomposed into elementary matrices (games) and classified into four types. The concept of decomposition helps the identification of potential games and also the evaluation of the potential that plays a crucial role in the determination of the preferred Nash equilibrium, and defines the Boltzmann distribution towards which these systems evolve for suitable types of dynamical rules. This survey draws parallel between the potential games and the kinetic Ising type models which are investigated for a wide scale of connectivity structures. We discuss briefly the applicability of the tools and concepts of statistical physics and thermodynamics. Additionally the general features of ordering phenomena, phase transitions and slow relaxations are outlined and applied to evolutionary games. The discussion extends to games with three or more strategies. Finally we discuss what happens when the system is weakly driven out of the "equilibrium state" by adding non-potential components representing games of cyclic dominance.

  1. Ancient Biomolecules and Evolutionary Inference.

    Science.gov (United States)

    Cappellini, Enrico; Prohaska, Ana; Racimo, Fernando; Welker, Frido; Pedersen, Mikkel Winther; Allentoft, Morten E; de Barros Damgaard, Peter; Gutenbrunner, Petra; Dunne, Julie; Hammann, Simon; Roffet-Salque, Mélanie; Ilardo, Melissa; Moreno-Mayar, J Víctor; Wang, Yucheng; Sikora, Martin; Vinner, Lasse; Cox, Jürgen; Evershed, Richard P; Willerslev, Eske

    2018-04-25

    Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field. Expected final online publication date for the Annual Review of Biochemistry Volume 87 is June 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  2. Evolutionary Models for Simple Biosystems

    Science.gov (United States)

    Bagnoli, Franco

    The concept of evolutionary development of structures constituted a real revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of such systems has shown that indeed, systems under a flux of energy or matter can self-organize into complex patterns, think for instance to Rayleigh-Bernard convection, Liesegang rings, patterns formed by granular systems under shear. Following this line, one could characterize life as a state of matter, characterized by the slow, continuous process that we call evolution. In this paper we try to identify the organizational level of life, that spans several orders of magnitude from the elementary constituents to whole ecosystems. Although similar structures can be found in other contexts like ideas (memes) in neural systems and self-replicating elements (computer viruses, worms, etc.) in computer systems, we shall concentrate on biological evolutionary structure, and try to put into evidence the role and the emergence of network structure in such systems.

  3. Regional systems of innovation: an evolutionary perspective

    OpenAIRE

    P Cooke; M G Uranga; G Etxebarria

    1998-01-01

    The authors develop the concept of regional systems of innovation and relate it to preexisting research on national systems of innovation. They argue that work conducted in the 'new regional science' field is complementary to systems of innovation approaches. They seek to link new regional work to evolutionary economics, and argue for the development of evolutionary regional science. Common elements of interest to evolutionary innovation research and new regional science are important in unde...

  4. Towards resolving the complete fern tree of life.

    Science.gov (United States)

    Lehtonen, Samuli

    2011-01-01

    In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a 'supermatrix' approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.

  5. Evolutionary Acquisition and Spiral Development Tutorial

    National Research Council Canada - National Science Library

    Hantos, P

    2005-01-01

    .... NSS Acquisition Policy 03-01 provided some space-oriented customization and, similarly to the original DOD directives, also positioned Evolutionary Acquisition and Spiral Development as preferred...

  6. Completeness of Lyapunov Abstraction

    DEFF Research Database (Denmark)

    Wisniewski, Rafal; Sloth, Christoffer

    2013-01-01

    the vector field, which allows the generation of a complete abstraction. To compute the functions that define the subdivision of the state space in an algorithm, we formulate a sum of squares optimization problem. This optimization problem finds the best subdivisioning functions, with respect to the ability......This paper addresses the generation of complete abstractions of polynomial dynamical systems by timed automata. For the proposed abstraction, the state space is divided into cells by sublevel sets of functions. We identify a relation between these functions and their directional derivatives along...

  7. Asteroseismology of pulsating DA white dwarfs with fully evolutionary models

    Directory of Open Access Journals (Sweden)

    Althaus L.G.

    2013-03-01

    Full Text Available We present a new approach for asteroseismology of DA white dwarfs that consists in the employment of a large set of non-static, physically sound, fully evolutionary models representative of these stars. We already have applied this approach with success to pulsating PG1159 stars (GW Vir variables. Our white dwarf models, which cover a wide range of stellar masses, effective temperatures, and envelope thicknesses, are the result of fully evolutionary computations that take into account the complete history of the progenitor stars from the ZAMS. In particular, the models are characterized by self-consistent chemical structures from the centre to the surface, a crucial aspect of white dwarf asteroseismology. We apply this approach to an ensemble of 44 bright DAV (ZZ Ceti stars.

  8. General upper bounds on the runtime of parallel evolutionary algorithms.

    Science.gov (United States)

    Lässig, Jörg; Sudholt, Dirk

    2014-01-01

    We present a general method for analyzing the runtime of parallel evolutionary algorithms with spatially structured populations. Based on the fitness-level method, it yields upper bounds on the expected parallel runtime. This allows for a rigorous estimate of the speedup gained by parallelization. Tailored results are given for common migration topologies: ring graphs, torus graphs, hypercubes, and the complete graph. Example applications for pseudo-Boolean optimization show that our method is easy to apply and that it gives powerful results. In our examples the performance guarantees improve with the density of the topology. Surprisingly, even sparse topologies such as ring graphs lead to a significant speedup for many functions while not increasing the total number of function evaluations by more than a constant factor. We also identify which number of processors lead to the best guaranteed speedups, thus giving hints on how to parameterize parallel evolutionary algorithms.

  9. Fixation Probabilities of Evolutionary Graphs Based on the Positions of New Appearing Mutants

    Directory of Open Access Journals (Sweden)

    Pei-ai Zhang

    2014-01-01

    Full Text Available Evolutionary graph theory is a nice measure to implement evolutionary dynamics on spatial structures of populations. To calculate the fixation probability is usually regarded as a Markov chain process, which is affected by the number of the individuals, the fitness of the mutant, the game strategy, and the structure of the population. However the position of the new mutant is important to its fixation probability. Here the position of the new mutant is laid emphasis on. The method is put forward to calculate the fixation probability of an evolutionary graph (EG of single level. Then for a class of bilevel EGs, their fixation probabilities are calculated and some propositions are discussed. The conclusion is obtained showing that the bilevel EG is more stable than the corresponding one-rooted EG.

  10. Construction completion report

    International Nuclear Information System (INIS)

    1990-01-01

    This Construction Completion Report documents the major construction projects at the Waste Isolation Pilot Plant (WIPP) site and related information on contracts, schedules, and other areas which affected construction. This report is not intended to be an exhaustive detailed analysis of construction, but is a general overview and summary of the WIPP construction. 10 refs., 29 figs

  11. Complete Rerouting Protection

    DEFF Research Database (Denmark)

    Stidsen, Thomas K.; Kjærulff, Peter

    2005-01-01

    In this paper we present a new protection method: Complete Rerouting. This is the most capacity e cient protection method for circuit switched networks and it is, to the best of our knowledge, the first time it has been described. We implement a column generation algorithm and test the performance...

  12. Complete French Teach Yourself

    CERN Document Server

    Graham, Gaelle

    2010-01-01

    The best-selling complete course for a fun and effective way to learn French. This ISBN is for the paperback book. The corresponding audio support (ISBN: 9781444100068) is also available. The book and audio support can also be purchased as a pack (ISBN: 9781444100051).

  13. Completeness of Lyapunov Abstraction

    Directory of Open Access Journals (Sweden)

    Rafael Wisniewski

    2013-08-01

    Full Text Available In this work, we continue our study on discrete abstractions of dynamical systems. To this end, we use a family of partitioning functions to generate an abstraction. The intersection of sub-level sets of the partitioning functions defines cells, which are regarded as discrete objects. The union of cells makes up the state space of the dynamical systems. Our construction gives rise to a combinatorial object - a timed automaton. We examine sound and complete abstractions. An abstraction is said to be sound when the flow of the time automata covers the flow lines of the dynamical systems. If the dynamics of the dynamical system and the time automaton are equivalent, the abstraction is complete. The commonly accepted paradigm for partitioning functions is that they ought to be transversal to the studied vector field. We show that there is no complete partitioning with transversal functions, even for particular dynamical systems whose critical sets are isolated critical points. Therefore, we allow the directional derivative along the vector field to be non-positive in this work. This considerably complicates the abstraction technique. For understanding dynamical systems, it is vital to study stable and unstable manifolds and their intersections. These objects appear naturally in this work. Indeed, we show that for an abstraction to be complete, the set of critical points of an abstraction function shall contain either the stable or unstable manifold of the dynamical system.

  14. Dual completion method

    Energy Technology Data Exchange (ETDEWEB)

    Mamedov, N Ya; Kadymova, K S; Dzhafarov, Sh T

    1963-10-28

    One type of dual completion method utilizes a single tubing string. Through the use of the proper tubing equipment, the fluid from the low-productive upper formation is lifted by utilizing the surplus energy of a submerged pump, which handles the production from the lower stratum.

  15. A complete woman

    Indian Academy of Sciences (India)

    Lawrence

    treated me like a son in the way he encouraged my education, while my mother ... cine gives me a lot of satisfaction when I see my patients getting cured. Teaching ... thing in life as a complete woman in different roles – daughter, wife, mother ...

  16. Complete normal ordering 1: Foundations

    Directory of Open Access Journals (Sweden)

    John Ellis

    2016-08-01

    Full Text Available We introduce a new prescription for quantising scalar field theories (in generic spacetime dimension and background perturbatively around a true minimum of the full quantum effective action, which is to ‘complete normal order’ the bare action of interest. When the true vacuum of the theory is located at zero field value, the key property of this prescription is the automatic cancellation, to any finite order in perturbation theory, of all tadpole and, more generally, all ‘cephalopod’ Feynman diagrams. The latter are connected diagrams that can be disconnected into two pieces by cutting one internal vertex, with either one or both pieces free from external lines. In addition, this procedure of ‘complete normal ordering’ (which is an extension of the standard field theory definition of normal ordering reduces by a substantial factor the number of Feynman diagrams to be calculated at any given loop order. We illustrate explicitly the complete normal ordering procedure and the cancellation of cephalopod diagrams in scalar field theories with non-derivative interactions, and by using a point splitting ‘trick’ we extend this result to theories with derivative interactions, such as those appearing as non-linear σ-models in the world-sheet formulation of string theory. We focus here on theories with trivial vacua, generalising the discussion to non-trivial vacua in a follow-up paper.

  17. Quantum Mechanics predicts evolutionary biology.

    Science.gov (United States)

    Torday, J S

    2018-07-01

    Nowhere are the shortcomings of conventional descriptive biology more evident than in the literature on Quantum Biology. In the on-going effort to apply Quantum Mechanics to evolutionary biology, merging Quantum Mechanics with the fundamentals of evolution as the First Principles of Physiology-namely negentropy, chemiosmosis and homeostasis-offers an authentic opportunity to understand how and why physics constitutes the basic principles of biology. Negentropy and chemiosmosis confer determinism on the unicell, whereas homeostasis constitutes Free Will because it offers a probabilistic range of physiologic set points. Similarly, on this basis several principles of Quantum Mechanics also apply directly to biology. The Pauli Exclusion Principle is both deterministic and probabilistic, whereas non-localization and the Heisenberg Uncertainty Principle are both probabilistic, providing the long-sought after ontologic and causal continuum from physics to biology and evolution as the holistic integration recognized as consciousness for the first time. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Evolutionary dynamics of incubation periods.

    Science.gov (United States)

    Ottino-Loffler, Bertrand; Scott, Jacob G; Strogatz, Steven H

    2017-12-21

    The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease.

  19. Evolutionary Games and Social Conventions

    DEFF Research Database (Denmark)

    Hansen, Pelle Guldborg

    2007-01-01

    -defined metaphors of individual learning and social imitation processes, from which a revised theory of convention may be erected (see Sugden 2004, Binmore 1993 and Young 1998). This paper makes a general argument in support of the evolutionary turn in the theory of convention by a progressive exposition of its...... in Aumann (1976) and which, together with the assumptions of perfect rationality, came to be defining of classical game theory. However, classical game theory is currently undergoing severe crisis as a tool for exploring social phenomena; a crisis emerging from the problem of equilibrium selection around......Some thirty years ago Lewis published his Convention: A Philosophical Study (Lewis, 2002). This laid the foundation for a game-theoretic approach to social conventions, but became more famously known for its seminal analysis of common knowledge; the concept receiving its canonical analysis...

  20. Bacterial Actins? An Evolutionary Perspective

    Science.gov (United States)

    Doolittle, Russell F.; York, Amanda L.

    2003-01-01

    According to the conventional wisdom, the existence of a cytoskeleton in eukaryotes and its absence in prokaryotes constitute a fundamental divide between the two domains of life. An integral part of the dogma is that a cytoskeleton enabled an early eukaryote to feed upon prokaryotes, a consequence of which was the occasional endosymbiosis and the eventual evolution of organelles. Two recent papers present compelling evidence that actin, one of the principal components of a cytoskeleton, has a homolog in Bacteria that behaves in many ways like eukaryotic actin. Sequence comparisons reveml that eukaryotic actin and the bacterial homolog (mreB protein), unlike many other proteins common to eukaryotes and Bacteria, have very different and more highly extended evolutionary histories.

  1. EDEN: evolutionary dynamics within environments

    Science.gov (United States)

    Münch, Philipp C.; Stecher, Bärbel; McHardy, Alice C.

    2017-01-01

    Abstract Summary Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses. Availability and implementation EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden. Contact alice.mchardy@helmholtz-hzi.de Supplementary information Supplementary data are available at Bioinformatics online. PMID:28637301

  2. Evolutionary adaptations to dietary changes.

    Science.gov (United States)

    Luca, F; Perry, G H; Di Rienzo, A

    2010-08-21

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area.

  3. Steps towards an evolutionary physics

    CERN Document Server

    Tiezzi, E

    2006-01-01

    If thermodynamics is to physics as logic is to philosophy, recent theoretical advancements lend new coherence to the marvel and dynamism of life on Earth. Enzo Tiezzi's "Steps Towards an Evolutionary Physics" is a primer and guide, to those who would to stand on the shoulders of giants to attain this view: Heisenberg, Planck, Bateson, Varela, and Prigogine as well as notable contemporary scientists. The adventure of such a free and enquiring spirit thrives not so much on answers as on new questions. The book offers a new gestalt on the uncertainty principle and concept of probability. A wide range of examples, enigmas, and paradoxes lead one's imagination on an exquisite dance. Among the applications are: songs and shapes of nature, oscillatory reactions, orientors, goal functions and configurations of processes, and "dissipative structures and the city". Ecodynamics is a new science, which proposes a cross-fertilization between Charles Darwin and Ilya Prigogine. As an enigma in thermodynamics, Entropy forms ...

  4. Numerical and Evolutionary Optimization Workshop

    CERN Document Server

    Trujillo, Leonardo; Legrand, Pierrick; Maldonado, Yazmin

    2017-01-01

    This volume comprises a selection of works presented at the Numerical and Evolutionary Optimization (NEO) workshop held in September 2015 in Tijuana, Mexico. The development of powerful search and optimization techniques is of great importance in today’s world that requires researchers and practitioners to tackle a growing number of challenging real-world problems. In particular, there are two well-established and widely known fields that are commonly applied in this area: (i) traditional numerical optimization techniques and (ii) comparatively recent bio-inspired heuristics. Both paradigms have their unique strengths and weaknesses, allowing them to solve some challenging problems while still failing in others. The goal of the NEO workshop series is to bring together people from these and related fields to discuss, compare and merge their complimentary perspectives in order to develop fast and reliable hybrid methods that maximize the strengths and minimize the weaknesses of the underlying paradigms. Throu...

  5. Markov Networks in Evolutionary Computation

    CERN Document Server

    Shakya, Siddhartha

    2012-01-01

    Markov networks and other probabilistic graphical modes have recently received an upsurge in attention from Evolutionary computation community, particularly in the area of Estimation of distribution algorithms (EDAs).  EDAs have arisen as one of the most successful experiences in the application of machine learning methods in optimization, mainly due to their efficiency to solve complex real-world optimization problems and their suitability for theoretical analysis. This book focuses on the different steps involved in the conception, implementation and application of EDAs that use Markov networks, and undirected models in general. It can serve as a general introduction to EDAs but covers also an important current void in the study of these algorithms by explaining the specificities and benefits of modeling optimization problems by means of undirected probabilistic models. All major developments to date in the progressive introduction of Markov networks based EDAs are reviewed in the book. Hot current researc...

  6. Evolutionary primacy of sodium bioenergetics

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2008-04-01

    Full Text Available Abstract Background The F- and V-type ATPases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of ATP. Both the F-type (found in most bacteria and eukaryotic mitochondria and chloroplasts and V-type (found in archaea, some bacteria, and eukaryotic vacuoles ATPases can translocate either protons or sodium ions. The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments. Results We combine structural and phylogenetic analyses to clarify the evolutionary relation between the proton- and sodium-translocating ATPases. A comparison of the structures of the membrane-embedded oligomeric proteolipid rings of sodium-dependent F- and V-ATPases reveals nearly identical sets of amino acids involved in sodium binding. We show that the sodium-dependent ATPases are scattered among proton-dependent ATPases in both the F- and the V-branches of the phylogenetic tree. Conclusion Barring convergent emergence of the same set of ligands in several lineages, these findings indicate that the use of sodium gradient for ATP synthesis is the ancestral modality of membrane bioenergetics. Thus, a primitive, sodium-impermeable but proton-permeable cell membrane that harboured a set of sodium-transporting enzymes appears to have been the evolutionary predecessor of the more structurally demanding proton-tight membranes. The use of proton as the coupling ion appears to be a later innovation that emerged on several independent occasions. Reviewers This article was reviewed by J. Peter Gogarten, Martijn A. Huynen, and Igor B. Zhulin. For the full reviews, please go to the Reviewers' comments section.

  7. Evolutionary design assistants for architecture

    Directory of Open Access Journals (Sweden)

    N. Onur Sönmez

    2015-04-01

    Full Text Available In its parallel pursuit of an increased competitivity for design offices and more pleasurable and easier workflows for designers, artificial design intelligence is a technical, intellectual, and political challenge. While human-machine cooperation has become commonplace through Computer Aided Design (CAD tools, a more improved collaboration and better support appear possible only through an endeavor into a kind of artificial design intelligence, which is more sensitive to the human perception of affairs. Considered as part of the broader Computational Design studies, the research program of this quest can be called Artificial / Autonomous / Automated Design (AD. The current available level of Artificial Intelligence (AI for design is limited and a viable aim for current AD would be to develop design assistants that are capable of producing drafts for various design tasks. Thus, the overall aim of this thesis is the development of approaches, techniques, and tools towards artificial design assistants that offer a capability for generating drafts for sub-tasks within design processes. The main technology explored for this aim is Evolutionary Computation (EC, and the target design domain is architecture. The two connected research questions of the study concern, first, the investigation of the ways to develop an architectural design assistant, and secondly, the utilization of EC for the development of such assistants. While developing approaches, techniques, and computational tools for such an assistant, the study also carries out a broad theoretical investigation into the main problems, challenges, and requirements towards such assistants on a rather overall level. Therefore, the research is shaped as a parallel investigation of three main threads interwoven along several levels, moving from a more general level to specific applications. The three research threads comprise, first, theoretical discussions and speculations with regard to both

  8. Evolutionary sequence of models of planetary nebulae

    International Nuclear Information System (INIS)

    Vil'koviskij, Eh.Ya.; Kondrat'eva, L.N.; Tambovtseva, L.V.

    1983-01-01

    The evolutionary sequences of model planetary nebulae of different masses have been calculated. The computed emission line intensities are compared with the observed ones by means of the parameter ''reduced size of the nebula'', Rsub(n). It is shown that the evolution tracks of Schonberner for the central stars are consistent with the observed data. Part of ionized mass Mi in any nebulae does not not exceed 0.3 b and in the average Msu(i) 3 years at actual values of radius Rsub(i) <0.025 ps. Then the luminosity growth slows down to the maximum temperature which central star reaches and decreases with sharp decrease of the star luminosity. At that, the radius of ionized zone of greater mass nebulae can even decrease, inspite of the constant expansion of the nebula. As a result nebulae of great masses having undergone the evolution can be included in the number of observed compact objects (Rsub(n) < 0.1 ps)

  9. Protein structure database search and evolutionary classification.

    Science.gov (United States)

    Yang, Jinn-Moon; Tung, Chi-Hua

    2006-01-01

    As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

  10. Handbook of differential equations evolutionary equations

    CERN Document Server

    Dafermos, CM

    2008-01-01

    The material collected in this volume discusses the present as well as expected future directions of development of the field with particular emphasis on applications. The seven survey articles present different topics in Evolutionary PDE's, written by leading experts.- Review of new results in the area- Continuation of previous volumes in the handbook series covering Evolutionary PDEs- Written by leading experts

  11. On economic applications of evolutionary game theory

    OpenAIRE

    Daniel Friedman

    1998-01-01

    Evolutionary games have considerable unrealized potential for modeling substantive economic issues. They promise richer predictions than orthodox game models but often require more extensive specifications. This paper exposits the specification of evolutionary game models and classifies the possible asymptotic behavior for one and two dimensional models.

  12. Evolutionary principles and their practical application.

    Science.gov (United States)

    Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

    2011-03-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.

  13. Research traditions and evolutionary explanations in medicine.

    Science.gov (United States)

    Méthot, Pierre-Olivier

    2011-02-01

    In this article, I argue that distinguishing 'evolutionary' from 'Darwinian' medicine will help us assess the variety of roles that evolutionary explanations can play in a number of medical contexts. Because the boundaries of evolutionary and Darwinian medicine overlap to some extent, however, they are best described as distinct 'research traditions' rather than as competing paradigms. But while evolutionary medicine does not stand out as a new scientific field of its own, Darwinian medicine is united by a number of distinctive theoretical and methodological claims. For example, evolutionary medicine and Darwinian medicine can be distinguished with respect to the styles of evolutionary explanations they employ. While the former primarily involves 'forward looking' explanations, the latter depends mostly on 'backward looking' explanations. A forward looking explanation tries to predict the effects of ongoing evolutionary processes on human health and disease in contemporary environments (e.g., hospitals). In contrast, a backward looking explanation typically applies evolutionary principles from the vantage point of humans' distant biological past in order to assess present states of health and disease. Both approaches, however, are concerned with the prevention and control of human diseases. In conclusion, I raise some concerns about the claim that 'nothing in medicine makes sense except in the light of evolution'.

  14. Algorithmic Mechanism Design of Evolutionary Computation.

    Science.gov (United States)

    Pei, Yan

    2015-01-01

    We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm.

  15. Democratizing evolutionary biology, lessons from insects

    DEFF Research Database (Denmark)

    Dunn, Robert Roberdeau; Beasley, DeAnna E.

    2016-01-01

    The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales. This ...

  16. A Hybrid Chaotic Quantum Evolutionary Algorithm

    DEFF Research Database (Denmark)

    Cai, Y.; Zhang, M.; Cai, H.

    2010-01-01

    A hybrid chaotic quantum evolutionary algorithm is proposed to reduce amount of computation, speed up convergence and restrain premature phenomena of quantum evolutionary algorithm. The proposed algorithm adopts the chaotic initialization method to generate initial population which will form a pe...... tests. The presented algorithm is applied to urban traffic signal timing optimization and the effect is satisfied....

  17. On the Evolutionary Stability of Bargaining Inefficiency

    DEFF Research Database (Denmark)

    Poulsen, Anders

    This paper investigates whether 'tough' bargaining behavior, which gives rise to inefficiency, can be evolutionary stable. We show that in a two-stage Nash Demand Game tough behavior survives. Indeed, almost all the surplus may be wasted. We also study the Ultimatum Game. Here evolutionary select...

  18. The complete cosmicomics

    CERN Document Server

    Calvino, Italo

    2014-01-01

    The definitive edition of Calvino’s cosmicomics, bringing together all of these enchanting stories—including some never before translated—in one volume for the first time. In Italo Calvino’s cosmicomics, primordial beings cavort on the nearby surface of the moon, play marbles with atoms, and bear ecstatic witness to Earth’s first dawn. Exploring natural phenomena and the origins of the universe, these beloved tales relate complex scientific concepts to our common sensory, emotional, human world. Now, The Complete Cosmicomics brings together all of the cosmicomic stories for the first time. Containing works previously published in Cosmicomics, t zero, and Numbers in the Dark, this single volume also includes seven previously uncollected stories, four of which have never been published in translation in the United States. This “complete and definitive collection” (Evening Standard) reconfirms the cosmicomics as a crowning literary achievement and makes them available to new generations of reader...

  19. CMS Is Finally Completed

    CERN Multimedia

    2008-01-01

    Yet another step in the completion of the Large Hadron Collider was taken yesterday morning, as the final element of the Compact Muon Solenoid was lowered nearly 100 meters bellow ground. After more than eight years of work at the world's most powerful particle accelerator, scientists hope that they will be able to start initial experiments with the LHC until the end of this year.

  20. LEAR construction completed

    CERN Multimedia

    CERN PhotoLab

    1982-01-01

    In July 1982, LEAR construction was completed, the individual systems had been dry-tested. On 16 July, the first 50 MeV (309 MeV/c) protons from Linac 1 were injected and circulated. On 11 October, the first antiprotons from the AA, decelerated in the PS to 609 MeV/c, were injected. Also in 1982, acceleration, deceleration and stochastic cooling were successfully tested. See 9007366 for a more detailed description. See also 8201061, 8204131, 8309026.

  1. SHIVA laser: nearing completion

    International Nuclear Information System (INIS)

    Glaze, J.A.; Godwin, R.O.

    1977-01-01

    Construction of the Shiva laser system is nearing completion. This laser will be operating in fall 1977 and will produce over 20 terawatts of focusable power in a subnanosecond pulse. Fusion experiments will begin early in 1978. It is anticipated that thermonuclear energy release equal to one percent that of the incident light energy will be achieved with sub-millimeter deuterium-tritium targets. From other experiments densities in excess of a thousand times that of liquid are also expected

  2. SCT Barrel Assembly Complete

    CERN Multimedia

    L. Batchelor

    As reported in the April 2005 issue of the ATLAS eNews, the first of the four Semiconductor Tracker (SCT) barrels, complete with modules and services, arrived safely at CERN in January of 2005. In the months since January, the other three completed barrels arrived as well, and integration of the four barrels into the entire barrel assembly commenced at CERN, in the SR1 building on the ATLAS experimental site, in July. Assembly was completed on schedule in September, with the addition of the innermost layer to the 4-barrel assembly. Work is now underway to seal the barrel thermal enclosure. This is necessary in order to enclose the silicon tracker in a nitrogen atmosphere and provide it with faraday-cage protection, and is a delicate and complicated task: 352 silicon module powertapes, 352 readout-fibre bundles, and over 400 Detector Control System sensors must be carefully sealed into the thermal enclosure bulkhead. The team is currently verifying the integrity of the low mass cooling system, which must be d...

  3. IR Observations of a Complete Unbiased Sample of Bright Seyfert Galaxies

    Science.gov (United States)

    Malkan, Matthew; Bendo, George; Charmandaris, Vassilis; Smith, Howard; Spinoglio, Luigi; Tommasin, Silvia

    2008-03-01

    IR spectra will measure the 2 main energy-generating processes by which galactic nuclei shine: black hole accretion and star formation. Both of these play roles in galaxy evolution, and they appear connected. To obtain a complete sample of AGN, covering the range of luminosities and column-densities, we will combine 2 complete all-sky samples with complementary selections, minimally biased by dust obscuration: the 116 IRAS 12um AGN and the 41 Swift/BAT hard Xray AGN. These galaxies have been extensively studied across the entire EM spectrum. Herschel observations have been requested and will be synergistic with the Spitzer database. IRAC and MIPS imaging will allow us to separate the nuclear and galactic continua. We are completing full IR observations of the local AGN population, most of which have already been done. The only remaining observations we request are 10 IRS/HIRES, 57 MIPS-24 and 30 IRAC pointings. These high-quality observations of bright AGN in the bolometric-flux-limited samples should be completed, for the high legacy value of complete uniform datasets. We will measure quantitatively the emission at each wavelength arising from stars and from accretion in each galactic center. Since our complete samples come from flux-limited all-sky surveys in the IR and HX, we will calculate the bi-variate AGN and star formation Luminosity Functions for the local population of active galaxies, for comparison with higher redshifts.Our second aim is to understand the physical differences between AGN classes. This requires statistical comparisons of full multiwavelength observations of complete representative samples. If the difference between Sy1s and Sy2s is caused by orientation, their isotropic properties, including those of the surrounding galactic centers, should be similar. In contrast, if they are different evolutionary stages following a galaxy encounter, then we may find observational evidence that the circumnuclear ISM of Sy2s is relatively younger.

  4. Comparison of evolutionary computation algorithms for solving bi ...

    Indian Academy of Sciences (India)

    failure probability. Multiobjective Evolutionary Computation algorithms (MOEAs) are well-suited for Multiobjective task scheduling on heterogeneous environment. The two Multi-Objective Evolutionary Algorithms such as Multiobjective Genetic. Algorithm (MOGA) and Multiobjective Evolutionary Programming (MOEP) with.

  5. Complete pancreas traumatic transsection

    Directory of Open Access Journals (Sweden)

    H. Hodžić

    2005-02-01

    Full Text Available This report presents a case of a twenty-year old male with complete pancreas breakdown in the middle of its corpus, which was caused by a strong abdomen compression, with injuries of the spleen, the firstjejunumcurve,mesocolon transversum, left kidney, and appereance of retroperitoneal haemathoma. Surgical treatment started 70 minutes after the injury. The treatment consisted of left pancreatectomy with previous spleenectomy, haemostasis of ruptured mesocolon transversum blood vessels, left kidney exploration, suturing of the firstjejunumcurvelession and double abdomen drainage. Posttraumatic pancreatitis which appeared on the second postoperative day and prolonged drain secretion were successfully solved by conservative treatment.

  6. Complete rerouting protection

    DEFF Research Database (Denmark)

    Stidsen, Thomas K.; Kjærulff, Peter

    2006-01-01

    Protection of communication against network failures is becoming increasingly important and in this paper we present the most capacity efficient protection method possible, the complete rerouting protection method, when requiring that all communication should be restored in case of a single link...... network failure. We present a linear programming model of the protection method and a column generation algorithm. For 6 real world networks, the minimal restoration overbuild network capacity is between 13% and 78%. We further study the importance of the density of the network, derive analytical bounds...

  7. Completion of treatment planning

    International Nuclear Information System (INIS)

    Lief, Eugene

    2008-01-01

    The outline of the lecture included the following topics: entering prescription; plan printout; print and transfer DDR; segment BEV; export to R and V; physician approval; and second check. Considerable attention, analysis and discussion. The summary is as follows: Treatment planning completion is a very responsible process which requires maximum attention; Should be independently checked by the planner, physicist, radiation oncologist and a therapist; Should not be done in a last minute rush; Proper communication between team members; Properly set procedure should prevent propagation of an error by one individual to the treatment: the error should be caught by somebody else. (P.A.)

  8. TestComplete cookbook

    CERN Document Server

    Alpaev, Gennadiy

    2013-01-01

    A practical cookbook, with a perfect package of simple, medium, and advanced recipes targeted at basic programmers as well as expert software testers, who will learn to create, manage, and run automated tests. It is packed with problem-solving recipes that are supported by simple examples.If you are a software tester or a programmer who is involved with testing automation using TestComplete, this book is ideal for you! You will be introduced to the very basics of using the tool, as well as polish any previously gained knowledge in using the tool. If you are already aware of programming basics,

  9. Motivational and evolutionary aspects of a physical exercise training program: a longitudinal study.

    Directory of Open Access Journals (Sweden)

    João Paulo Pereira Rosa

    2015-05-01

    Full Text Available Several studies have indicated that motivational level and prior expectations are relevant aspects to increase commitment to physical activity. Moreover, these aspects are not properly described in terms of proximal (Self Determination Theory and distal (evolutionary explanations in the literature. This paper aims to verify if level of motivation (BREQ-2 and expectations regarding regular physical exercise (IMPRAF-54 before starting a one-year exercise program could determine likelihood of completion. Ninety-four volunteers (53 women included a completed protocol group (CPG n=21 and drop-out group (DG n=73. The IMPRAF-54 scale was used to assess six different expectations associated with physical activity, and the BREQ-2 inventory was used to assess the level of motivation in five steps (from amotivation to intrinsic motivation. Both questionnaires were assessed before the regular exercise program. The CPG group presented higher sociability and lower pleasure scores according to IMPRAF-54 domains. A logistic regression showed that a one-point increment on sociability score increased the chance of completing the program by 10%, and the same one-point increment on pleasure score reduced the chance of completing the protocol by 16%. ROC curves were also calculated to establish IMPRAF-54 cutoffs for adherence (Sociability - 18.5 points – 81% sensibility/50% specificity and dropout (Pleasure – 25.5 points – 86% sensibility/20% specificity of the exercise protocol. Our results indicate that an expectation of social interaction was a positive factor in predicting adherence to exercise. Grounded in SDT and its innate needs (competence, autonomy, relatedness, physical exercise is not an end; it is a means to achieve autonomy and self-cohesion. The association of physical activity with social practices, like in hunter-gathering groups, can engage people to be physically active and can provide better results in adherence exercise programs for the

  10. Motivational and evolutionary aspects of a physical exercise training program: a longitudinal study

    Science.gov (United States)

    Rosa, João P. P.; de Souza, Altay A. L.; de Lima, Giscard H. O.; Rodrigues, Dayane F.; de Aquino Lemos, Valdir; da Silva Alves, Eduardo; Tufik, Sergio; de Mello, Marco T.

    2015-01-01

    Several studies have indicated that motivational level and prior expectations influence one’s commitment to physical activity. Moreover, these aspects are not properly described in terms of proximal (SDT, Self Determination Theory) and distal (evolutionary) explanations in the literature. This paper aims to verify if level of motivation (BREQ-2, Behavioral Regulation in Exercise Questionnaire-2) and expectations regarding regular physical exercise (IMPRAF-54) before starting a 1-year exercise program could determine likelihood of completion. Ninety-four volunteers (53 women) included a completed protocol group (CPG; n = 21) and drop-out group (n = 73). The IMPRAF-54 scale was used to assess six different expectations associated with physical activity, and the BREQ-2 inventory was used to assess the level of motivation in five steps (from amotivation to intrinsic motivation). Both questionnaires were assessed before starting a regular exercise program. The CPG group presented higher sociability and lower pleasure scores according to IMPRAF-54 domains. A logistic regression analysis showed that a one-point increment on sociability score increased the chance of completing the program by 10%, and the same one-point increment on pleasure score reduced the chance of completing the protocol by 16%. ROC curves were also calculated to establish IMPRAF-54 cutoffs for adherence (Sociability – 18.5 points – 81% sensibility/50% specificity) and dropout (Pleasure – 25.5 points – 86% sensibility/20% specificity) of the exercise protocol. Our results indicate that an expectation of social interaction was a positive factor in predicting adherence to exercise. Grounded in SDT and its innate needs (competence, autonomy, relatedness), physical exercise is not an end; it is a means to achieve autonomy and self-cohesion. The association of physical activity with social practices, as occurs in hunter-gathering groups, can engage people to be physically active and can provide

  11. Complete atrioventricular canal.

    Science.gov (United States)

    Calabrò, Raffaele; Limongelli, Giuseppe

    2006-04-05

    Complete atrioventricular canal (CAVC), also referred to as complete atrioventricular septal defect, is characterised by an ostium primum atrial septal defect, a common atrioventricular valve and a variable deficiency of the ventricular septum inflow. CAVC is an uncommon congenital heart disease, accounting for about 3% of cardiac malformations. Atrioventricular canal occurs in two out of every 10,000 live births. Both sexes are equally affected and a striking association with Down syndrome was found. Depending on the morphology of the superior leaflet of the common atrioventricular valve, 3 types of CAVC have been delineated (type A, B and C, according to Rastelli's classification). CAVC results in a significant interatrial and interventricular systemic-to-pulmonary shunt, thus inducing right ventricular pressure and volume overload and pulmonary hypertension. It becomes symptomatic in infancy due to congestive heart failure and failure to thrive. Diagnosis of CAVC might be suspected from electrocardiographic and chest X-ray findings. Echocardiography confirms it and gives anatomical details. Over time, pulmonary hypertension becomes irreversible, thus precluding the surgical therapy. This is the reason why cardiac catheterisation is not mandatory in infants (less than 6 months) but is indicated in older patients if irreversible pulmonary hypertension is suspected. Medical treatment (digitalis, diuretics, vasodilators) plays a role only as a bridge toward surgery, usually performed between the 3rd and 6th month of life.

  12. Complete atrioventricular canal

    Directory of Open Access Journals (Sweden)

    Limongelli Giuseppe

    2006-04-01

    Full Text Available Abstract Complete atrioventricular canal (CAVC, also referred to as complete atrioventricular septal defect, is characterised by an ostium primum atrial septal defect, a common atrioventricular valve and a variable deficiency of the ventricular septum inflow. CAVC is an uncommon congenital heart disease, accounting for about 3% of cardiac malformations. Atrioventricular canal occurs in two out of every 10,000 live births. Both sexes are equally affected and a striking association with Down syndrome was found. Depending on the morphology of the superior leaflet of the common atrioventricular valve, 3 types of CAVC have been delineated (type A, B and C, according to Rastelli's classification. CAVC results in a significant interatrial and interventricular systemic-to-pulmonary shunt, thus inducing right ventricular pressure and volume overload and pulmonary hypertension. It becomes symptomatic in infancy due to congestive heart failure and failure to thrive. Diagnosis of CAVC might be suspected from electrocardiographic and chest X-ray findings. Echocardiography confirms it and gives anatomical details. Over time, pulmonary hypertension becomes irreversible, thus precluding the surgical therapy. This is the reason why cardiac catheterisation is not mandatory in infants (less than 6 months but is indicated in older patients if irreversible pulmonary hypertension is suspected. Medical treatment (digitalis, diuretics, vasodilators plays a role only as a bridge toward surgery, usually performed between the 3rd and 6th month of life.

  13. Barnett shale completions

    Energy Technology Data Exchange (ETDEWEB)

    Schein, G. [BJ Services, Dallas, TX (United States)

    2006-07-01

    Fractured shales yield oil and gas in various basins across the United States. A map indicating these fractured shale source-reservoir systems in the United States was presented along with the numerous similarities and differences that exist among these systems. Hydrocarbons in the organic rich black shale come from the bacterial decomposition of organic matter, primary thermogenic decomposition of organic matter or secondary thermogenic cracking of oil. The shale may be the reservoir or other horizons may be the primary or secondary reservoir. The reservoir has induced micro fractures or tectonic fractures. This paper described the well completions in the Barnett Shale in north Texas with reference to major players, reservoir properties, mineralogy, fluid sensitivity, previous treatments, design criteria and production examples. The Barnett Shale is an organic, black shale with thickness ranging from 100 to 1000 feet. The total organic carbon (TOC) averages 4.5 per cent. The unit has undergone high rate frac treatments. A review of the vertical wells in the Barnett Shale was presented along with the fracture treatment schedule and technology changes. A discussion of refracturing opportunities and proppant settling and transport revealed that additional proppant increases fluid recovery and enhances production. Compatible scale inhibitors and biocides can be beneficial. Horizontal completions in the Barnett Shale have shown better results than vertical wells, as demonstrated in a production comparison of 3 major horizontal wells in the basin. tabs., figs.

  14. The complete sequence of human chromosome 5

    Energy Technology Data Exchange (ETDEWEB)

    Schmutz, Jeremy; Martin, Joel; Terry, Astrid; Couronne, Olivier; Grimwood, Jane; Lowry, State; Gordon, Laurie A.; Scott, Duncan; Xie, Gary; Huang, Wayne; Hellsten, Uffe; Tran-Gyamfi, Mary; She, Xinwei; Prabhakar, Shyam; Aerts, Andrea; Altherr, Michael; Bajorek, Eva; Black, Stacey; Branscomb, Elbert; Caoile, Chenier; Challacombe, Jean F.; Chan, Yee Man; Denys, Mirian; Detter, Chris; Escobar, Julio; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstenin, David; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Israni, Sanjay; Jett, Jamie; Kadner, Kristen; Kimbal, Heather; Kobayashi, Arthur; Lopez, Frederick; Lou, Yunian; Martinez, Diego; Medina, Catherine; Morgan, Jenna; Nandkeshwar, Richard; Noonan, James P.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Priest, James; Ramirez, Lucia; Rash, Sam; Retterer, James; Rodriguez, Alex; Rogers, Stephanie; Salamov, Asaf; Salazar, Angelica; Thayer, Nina; Tice, Hope; Tsai, Ming; Ustaszewska, Anna; Vo, Nu; Wheeler, Jeremy; Wu, Kevin; Yang, Joan; Dickson, Mark; Cheng, Jan-Fang; Eichler, Evan E.; Olsen, Anne; Pennacchio, Len A.; Rokhsar, Daniel S.; Richardson, Paul; Lucas, Susan M.; Myers, Richard M.; Rubin, Edward M.

    2004-04-15

    Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-encoding genes including the protocadherin and interleukin gene families and the first complete versions of each of the large chromosome 5 specific internal duplications. These duplications are very recent evolutionary events and play a likely mechanistic role, since deletions of these regions are the cause of debilitating disorders including spinal muscular atrophy (SMA).

  15. Joy and happiness: a simultaneous and evolutionary concept analysis.

    Science.gov (United States)

    Cottrell, Laura

    2016-07-01

    To report a simultaneous and evolutionary analysis of the concepts of joy and long-term happiness. Joy and happiness are underrepresented in the nursing literature, though negative concepts are well represented. When mentioned in the literature, neither joy nor happiness is adequately defined, explained, or clearly understood. To promote further investigation of these concepts in nursing and to explore their relationship with health and healing, conceptual clarity is an essential first step. Concept analysis. The following databases were searched, without time restrictions, for articles in English: Academic Search Complete, Anthropology Plus; ATLA Religious Database with ATLASerials; Cumulative Index of Nursing and Allied Health Literature (CINAHL); Education Research Complete; Humanities International Complete; Psych EXTRA; and SocINDEX with Full Text. The final sample size consists of 61 articles and one book, published between 1978-2014. An adapted combination of Rodgers' Evolutionary Model and Haase et al.'s Simultaneous Concept Analysis (SCA) method. Though both are positive concepts, joy and happiness have significant differences. Attributes of joy describe a spontaneous, sudden and transient concept associated with connection, awareness, and freedom. Attributes of happiness describe a pursued, long-lasting, stable mental state associated with virtue and self-control. Further exploration of joy and happiness is necessary to ascertain their relationship with health and their value to nursing practice and theory development. Nurses are encouraged to consider the value of positive concepts to all areas of nursing. © 2016 John Wiley & Sons Ltd.

  16. Phylogenetic inference with weighted codon evolutionary distances.

    Science.gov (United States)

    Criscuolo, Alexis; Michel, Christian J

    2009-04-01

    We develop a new approach to estimate a matrix of pairwise evolutionary distances from a codon-based alignment based on a codon evolutionary model. The method first computes a standard distance matrix for each of the three codon positions. Then these three distance matrices are weighted according to an estimate of the global evolutionary rate of each codon position and averaged into a unique distance matrix. Using a large set of both real and simulated codon-based alignments of nucleotide sequences, we show that this approach leads to distance matrices that have a significantly better treelikeness compared to those obtained by standard nucleotide evolutionary distances. We also propose an alternative weighting to eliminate the part of the noise often associated with some codon positions, particularly the third position, which is known to induce a fast evolutionary rate. Simulation results show that fast distance-based tree reconstruction algorithms on distance matrices based on this codon position weighting can lead to phylogenetic trees that are at least as accurate as, if not better, than those inferred by maximum likelihood. Finally, a well-known multigene dataset composed of eight yeast species and 106 codon-based alignments is reanalyzed and shows that our codon evolutionary distances allow building a phylogenetic tree which is similar to those obtained by non-distance-based methods (e.g., maximum parsimony and maximum likelihood) and also significantly improved compared to standard nucleotide evolutionary distance estimates.

  17. Natural pedagogy as evolutionary adaptation.

    Science.gov (United States)

    Csibra, Gergely; Gergely, György

    2011-04-12

    We propose that the cognitive mechanisms that enable the transmission of cultural knowledge by communication between individuals constitute a system of 'natural pedagogy' in humans, and represent an evolutionary adaptation along the hominin lineage. We discuss three kinds of arguments that support this hypothesis. First, natural pedagogy is likely to be human-specific: while social learning and communication are both widespread in non-human animals, we know of no example of social learning by communication in any other species apart from humans. Second, natural pedagogy is universal: despite the huge variability in child-rearing practices, all human cultures rely on communication to transmit to novices a variety of different types of cultural knowledge, including information about artefact kinds, conventional behaviours, arbitrary referential symbols, cognitively opaque skills and know-how embedded in means-end actions. Third, the data available on early hominin technological culture are more compatible with the assumption that natural pedagogy was an independently selected adaptive cognitive system than considering it as a by-product of some other human-specific adaptation, such as language. By providing a qualitatively new type of social learning mechanism, natural pedagogy is not only the product but also one of the sources of the rich cultural heritage of our species.

  18. The Evolutionary Origins of Hierarchy.

    Science.gov (United States)

    Mengistu, Henok; Huizinga, Joost; Mouret, Jean-Baptiste; Clune, Jeff

    2016-06-01

    Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.

  19. Evolutionary dynamics under interactive diversity

    Science.gov (United States)

    Su, Qi; Li, Aming; Wang, Long

    2017-10-01

    As evidenced by many cases in human societies, individuals often make different behavior decisions in different interactions, and adaptively adjust their behavior in changeable interactive scenarios. However, up to now, how such diverse interactive behavior affects cooperation dynamics has still remained unknown. Here we develop a general framework of interactive diversity, which models individuals’ separated behavior against distinct opponents and their adaptive adjustment in response to opponents’ strategies, to explore the evolution of cooperation. We find that interactive diversity enables individuals to reciprocate every single opponent, and thus sustains large-scale reciprocal interactions. Our work witnesses an impressive boost of cooperation for a notably extensive range of parameters and for all pairwise games. These results are robust against well-mixed and various networked populations, and against degree-normalized and cumulative payoff patterns. From the perspective of network dynamics, distinguished from individuals competing for nodes in most previous work, in this paper, the system evolves in the form of behavior disseminating along edges. We propose a theoretical method based on evolution of edges, which predicts well both the frequency of cooperation and the compact cooperation clusters. Our thorough investigation clarifies the positive role of interactive diversity in resolving social dilemmas and highlights the significance of understanding evolutionary dynamics from the viewpoint of edge dynamics.

  20. The Evolutionary Origins of Hierarchy

    Science.gov (United States)

    Huizinga, Joost; Clune, Jeff

    2016-01-01

    Hierarchical organization—the recursive composition of sub-modules—is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force–the cost of connections–promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics. PMID:27280881

  1. The Evolutionary Origins of Hierarchy.

    Directory of Open Access Journals (Sweden)

    Henok Mengistu

    2016-06-01

    Full Text Available Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments. Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.

  2. Evolutionary games in the multiverse.

    Science.gov (United States)

    Gokhale, Chaitanya S; Traulsen, Arne

    2010-03-23

    Evolutionary game dynamics of two players with two strategies has been studied in great detail. These games have been used to model many biologically relevant scenarios, ranging from social dilemmas in mammals to microbial diversity. Some of these games may, in fact, take place between a number of individuals and not just between two. Here we address one-shot games with multiple players. As long as we have only two strategies, many results from two-player games can be generalized to multiple players. For games with multiple players and more than two strategies, we show that statements derived for pairwise interactions no longer hold. For two-player games with any number of strategies there can be at most one isolated internal equilibrium. For any number of players with any number of strategies , there can be at most isolated internal equilibria. Multiplayer games show a great dynamical complexity that cannot be captured based on pairwise interactions. Our results hold for any game and can easily be applied to specific cases, such as public goods games or multiplayer stag hunts.

  3. Evolutionary advantages of adaptive rewarding

    International Nuclear Information System (INIS)

    Szolnoki, Attila; Perc, Matjaž

    2012-01-01

    Our well-being depends on both our personal success and the success of our society. The realization of this fact makes cooperation an essential trait. Experiments have shown that rewards can elevate our readiness to cooperate, but since giving a reward inevitably entails paying a cost for it, the emergence and stability of such behavior remains elusive. Here we show that allowing for the act of rewarding to self-organize in dependence on the success of cooperation creates several evolutionary advantages that instill new ways through which collaborative efforts are promoted. Ranging from indirect territorial battle to the spontaneous emergence and destruction of coexistence, phase diagrams and the underlying spatial patterns reveal fascinatingly rich social dynamics that explain why this costly behavior has evolved and persevered. Comparisons with adaptive punishment, however, uncover an Achilles heel of adaptive rewarding, coming from over-aggression, which in turn hinders optimal utilization of network reciprocity. This may explain why, despite its success, rewarding is not as firmly embedded into our societal organization as punishment. (paper)

  4. Natural pedagogy as evolutionary adaptation

    Science.gov (United States)

    Csibra, Gergely; Gergely, György

    2011-01-01

    We propose that the cognitive mechanisms that enable the transmission of cultural knowledge by communication between individuals constitute a system of ‘natural pedagogy’ in humans, and represent an evolutionary adaptation along the hominin lineage. We discuss three kinds of arguments that support this hypothesis. First, natural pedagogy is likely to be human-specific: while social learning and communication are both widespread in non-human animals, we know of no example of social learning by communication in any other species apart from humans. Second, natural pedagogy is universal: despite the huge variability in child-rearing practices, all human cultures rely on communication to transmit to novices a variety of different types of cultural knowledge, including information about artefact kinds, conventional behaviours, arbitrary referential symbols, cognitively opaque skills and know-how embedded in means-end actions. Third, the data available on early hominin technological culture are more compatible with the assumption that natural pedagogy was an independently selected adaptive cognitive system than considering it as a by-product of some other human-specific adaptation, such as language. By providing a qualitatively new type of social learning mechanism, natural pedagogy is not only the product but also one of the sources of the rich cultural heritage of our species. PMID:21357237

  5. Flourishing: An Evolutionary Concept Analysis.

    Science.gov (United States)

    Agenor, Christine; Conner, Norma; Aroian, Karen

    2017-11-01

    Mental health is an important measure of public health (WHO, 2004); however, nursing practice and research continues to prioritize mental illness, rather than well-being (Wand, 2011). Flourishing is a recent concept in the field of well-being. The term has been used sparingly in nursing practice and research, and conceptual clarification is needed to promote comprehensive understanding of the phenomenon. The purpose of this study is to critically analyze flourishing, assess the maturity of the concept, and provide recommendations for future research, education, and practice. The concept of flourishing was analyzed using the evolutionary approach to concept analysis (Rodgers, 2000). A search for articles on flourishing within the context of well-being was conducted through CINAHL, MEDLINE, and PsycINFO. A sample of 32 articles and 1 book was reviewed. Data were reviewed for concept attributes, antecedents, consequences, surrogate terms and related concepts. Four models of flourishing were identified with six overlapping attributes: meaning, positive relationships, engagement, competence, positive emotion, and self-esteem. Limited longitudinal and predictive studies have been conducted, but there is evidence for several antecedents and outcomes of flourishing. Research is ongoing primarily in psychology and sociology and is lacking in other disciplines. The concept of flourishing is immature; however, evidence is building for related concepts. A lack of consistent terminology regarding flourishing prevents knowledge development of flourishing as a distinct concept. Further multidisciplinary research is needed to establish standard operational and conceptual definitions and develop effective interventions.

  6. An Evolutionary Formulation of the Crossing Number Problem

    Directory of Open Access Journals (Sweden)

    Che Sheng Gan

    2009-01-01

    Full Text Available A graph drawing algorithm is presented which results in complete graphs having minimum crossings equal to that of Guy's conjecture. It is then generalized and formulated in an evolutionary algorithm (EA to perform constrained search for the crossing numbers. The main objective of this work is to present a suitable two-dimensional scheme which can greatly reduce the complexity of finding crossing numbers by using computer. Program performance criteria are presented and discussed. It is shown that the EA implementation provides good confirmation of the predicted crossing numbers.

  7. Evolutionary theory and the naturalist fallacy

    DEFF Research Database (Denmark)

    Grodal, Torben Kragh

    2008-01-01

    that great work of art are also automatically fitness-enhancing in the present day environment, at that there are simple correllations between whether a work of art has a high aesthetic value and whether it is fitness-enhancing or not.  Keywords :  Evolutionary aesthetics, film theory, literary theory......The article is an invited response to a target article by Joseph Carroll entitled "An evolutionary paradigm for literary study". It argues that the target article  misuse the fact that works of art are based on adaptations that were fitness-enhancing in the era of evolutionary adaptations to claim...

  8. GOGOL: ACADEMIC AND COMPLETE

    Directory of Open Access Journals (Sweden)

    Yuri V. Mann

    2016-12-01

    Full Text Available The ever-increasing international interest to Gogol explains the necessity of publishing a new edition of his works. The present Complete Collection of Gogol’s Works and Letters is an academic edition prepared and published by the A. M. Gorky Institute of World Literature of the Russian Academy of Sciences. It draws on rich experience of studying and publishing Gogol’s heritage in Russia but at the same time questions and underscores Gogol’s relevance for the modern reader and his place in the world culture of our time. It intends to fill in the gaps left by the previous scholarly tradition that failed to recognize some of Gogol’s texts as part of his heritage. Such are, for example, dedicatory descriptions in books and business notes. The present edition accounts not only for the completeness of texts but also for their place within the body of Gogol’s work, as part of his life-long creative process. By counterpoising different editions, it attempts to trace down the dynamics of Gogol’s creative thought while at the same time underscores the autonomy and relevance of each period in his career. For example, this collection publishes two different versions (editions of the same work: while the most recent version has become canonical at the expense of the preceding one, the latter still preserves its meaning and historical relevance. The present edition has the advantage over its predecessors since it has an actual, physical opportunity to erase the gaps, e.g. to publish the hitherto unpublished texts. However, the editors realize that new, hitherto unknown gaps may appear and the present edition will become, in its turn, outdated. At this point, there will be a necessity in the new edition.

  9. Evolutionary programming for goal-driven dynamic planning

    Science.gov (United States)

    Vaccaro, James M.; Guest, Clark C.; Ross, David O.

    2002-03-01

    Many complex artificial intelligence (IA) problems are goal- driven in nature and the opportunity exists to realize the benefits of a goal-oriented solution. In many cases, such as in command and control, a goal-oriented approach may be the only option. One of many appropriate applications for such an approach is War Gaming. War Gaming is an important tool for command and control because it provides a set of alternative courses of actions so that military leaders can contemplate their next move in the battlefield. For instance, when making decisions that save lives, it is necessary to completely understand the consequences of a given order. A goal-oriented approach provides a slowly evolving tractably reasoned solution that inherently follows one of the principles of war: namely concentration on the objective. Future decision-making will depend not only on the battlefield, but also on a virtual world where military leaders can wage wars and determine their options by playing computer war games much like the real world. The problem with these games is that the built-in AI does not learn nor adapt and many times cheats, because the intelligent player has access to all the information, while the user has access to limited information provided on a display. These games are written for the purpose of entertainment and actions are calculated a priori and off-line, and are made prior or during their development. With these games getting more sophisticated in structure and less domain specific in scope, there needs to be a more general intelligent player that can adapt and learn in case the battlefield situations or the rules of engagement change. One such war game that might be considered is Risk. Risk incorporates the principles of war, is a top-down scalable model, and provides a good application for testing a variety of goal- oriented AI approaches. By integrating a goal-oriented hybrid approach, one can develop a program that plays the Risk game effectively and move

  10. Evolutionary biology and life histories

    Directory of Open Access Journals (Sweden)

    Brown, C. R.

    2004-06-01

    Full Text Available The demographic processes that drive the spread of populations through environments and in turn determine the abundance of organisms are the same demographic processes that drive the spread of genes through populations and in turn determine gene frequencies and fitness. Conceptually, marked similarities exist in the dynamic processes underlying population ecology and those underlying evolutionary biology. Central to an understanding of both disciplines is life history and its component demographic rates, such as survival, fecundity, and age of first breeding, and biologists from both fields have a vested interest in good analytical machinery for the estimation and analysis of these demographic rates. In the EURING conferences, we have been striving since the mid 1980s to promote a quantitative understanding of demographic rates through interdisciplinary collaboration between ecologists and statisticians. From the ecological side, the principal impetus has come from population biology, and in particular from wildlife biology, but the importance of good quantitative insights into demographic processes has long been recognized by a number of evolutionary biologists (e.g., Nichols & Kendall, 1995; Clobert, 1995; Cooch et al., 2002. In organizing this session, we have aimed to create a forum for those committed to gaining the best possible understanding of evolutionary processes through the application of modern quantitative methods for the collection and interpretation of data on marked animal populations. Here we present a short overview of the material presented in the session on evolutionary biology and life histories. In a plenary talk, Brown & Brown (2004 explored how mark–recapture methods have allowed a better understanding of the evolution of group–living and alternative reproductive tactics in colonial cliff swallows (Petrochelidon pyrrhonota. By estimating the number of transient birds passing through colonies of different sizes, they

  11. [Evolutionary Concept Analysis of Spirituality].

    Science.gov (United States)

    Ko, Il Sun; Choi, So Young; Kim, Jin Sook

    2017-04-01

    This study was done to clarify attributes, antecedents, and consequences of spirituality. Rodgers's evolutionary concept analysis was used to analyze fifty seven studies from the literature related to spirituality as it appears in systematic literature reviews of theology, medicine, counseling & psychology, social welfare, and nursing. Spirituality was found to consist of two dimensions and eight attributes: 1) vertical dimension: 'intimacy and connectedness with God' and 'holy life and belief', 2) horizontal dimension: 'self-transcendence', 'meaning and purpose in life', 'self-integration', and 'self-creativity' in relationship with self, 'connectedness' and 'trust' in relationship with others·neighbors·nature. Antecedents of spirituality were socio-demographic, religious, psychological, and health related characteristics. Consequences of spirituality were positive and negative. Being positive included 'life centered on God' in vertical dimension, and among horizontal dimension 'joy', 'hope', 'wellness', 'inner peace', and 'self-actualization' in relationship with self, 'doing in love' and 'extended life toward neighbors and the world' in relationship with others·neighbors·nature. Being negative was defined as having 'guilt', 'inner conflict', 'loneliness', and 'spiritual distress'. Facilitators of spirituality were stressful life events and experiences. Spirituality is a multidimensional concept. Unchangeable attributes of spirituality are 'connectedness with God', 'self-transcendence', 'meaning of life' and 'connectedness with others·nature'. Unchangeable consequences of spirituality are 'joy' and 'hope'. The findings suggest that the dimensional framework of spirituality can be used to assess the current spiritual state of patients. Based on these results, the development of a Korean version of the scale measuring spirituality is recommended. © 2017 Korean Society of Nursing Science

  12. Evolutionary Transgenomics: prospects and challenges

    Directory of Open Access Journals (Sweden)

    Raul eCorrea

    2015-10-01

    Full Text Available AbstractMany advances in our understanding of the genetic basis of species differences have arisen from transformation experiments, which allow us to study the effect of genes from one species (the donor when placed in the genetic background of another species (the recipient. Such interspecies transformation experiments are usually focused on candidate genes – genes that, based on work in model systems, are suspected to be responsible for certain phenotypic differences between the donor and recipient species. We suggest that the high efficiency of transformation in a few plant species, most notably Arabidopsis thaliana, combined with the small size of typical plant genes and their cis-regulatory regions allow implementation of a screening strategy that does not depend upon a priori candidate gene identification. This approach, transgenomics, entails moving many large genomic inserts of a donor species into the wild type background of a recipient species and then screening for dominant phenotypic effects. As a proof of concept, we recently conducted a transgenomic screen that analyzed more than 1100 random, large genomic inserts of the Alabama gladecress Leavenworthia alabamica for dominant phenotypic effects in the A. thaliana background. This screen identified one insert that shortens fruit and decreases A. thaliana fertility. In this paper we discuss the principles of transgenomic screens and suggest methods to help minimize the frequencies of false positive and false negative results. We argue that, because transgenomics avoids committing in advance to candidate genes it has the potential to help us identify truly novel genes or cryptic functions of known genes. Given the valuable knowledge that is likely to be gained, we believe the time is ripe for the plant evolutionary community to invest in transgenomic screens, at least in the mustard family Brassicaceae Burnett where many species are amenable to efficient transformation.

  13. Evolutionary algorithms for mobile ad hoc networks

    CERN Document Server

    Dorronsoro, Bernabé; Danoy, Grégoire; Pigné, Yoann; Bouvry, Pascal

    2014-01-01

    Describes how evolutionary algorithms (EAs) can be used to identify, model, and minimize day-to-day problems that arise for researchers in optimization and mobile networking. Mobile ad hoc networks (MANETs), vehicular networks (VANETs), sensor networks (SNs), and hybrid networks—each of these require a designer’s keen sense and knowledge of evolutionary algorithms in order to help with the common issues that plague professionals involved in optimization and mobile networking. This book introduces readers to both mobile ad hoc networks and evolutionary algorithms, presenting basic concepts as well as detailed descriptions of each. It demonstrates how metaheuristics and evolutionary algorithms (EAs) can be used to help provide low-cost operations in the optimization process—allowing designers to put some “intelligence” or sophistication into the design. It also offers efficient and accurate information on dissemination algorithms topology management, and mobility models to address challenges in the ...

  14. Evolutionary medicine: its scope, interest and potential.

    Science.gov (United States)

    Stearns, Stephen C

    2012-11-07

    This review is aimed at readers seeking an introductory overview, teaching courses and interested in visionary ideas. It first describes the range of topics covered by evolutionary medicine, which include human genetic variation, mismatches to modernity, reproductive medicine, degenerative disease, host-pathogen interactions and insights from comparisons with other species. It then discusses priorities for translational research, basic research and health management. Its conclusions are that evolutionary thinking should not displace other approaches to medical science, such as molecular medicine and cell and developmental biology, but that evolutionary insights can combine with and complement established approaches to reduce suffering and save lives. Because we are on the cusp of so much new research and innovative insights, it is hard to estimate how much impact evolutionary thinking will have on medicine, but it is already clear that its potential is enormous.

  15. Exploitation of linkage learning in evolutionary algorithms

    CERN Document Server

    Chen, Ying-ping

    2010-01-01

    The exploitation of linkage learning is enhancing the performance of evolutionary algorithms. This monograph examines recent progress in linkage learning, with a series of focused technical chapters that cover developments and trends in the field.

  16. Evolutionary Robotics: What, Why, and Where to

    Directory of Open Access Journals (Sweden)

    Stephane eDoncieux

    2015-03-01

    Full Text Available Evolutionary robotics applies the selection, variation, and heredity principles of natural evolution to the design of robots with embodied intelligence. It can be considered as a subfield of robotics that aims to create more robust and adaptive robots. A pivotal feature of the evolutionary approach is that it considers the whole robot at once, and enables the exploitation of robot features in a holistic manner. Evolutionary robotics can also be seen as an innovative approach to the study of evolution based on a new kind of experimentalism. The use of robots as a substrate can help address questions that are difficult, if not impossible, to investigate through computer simulations or biological studies. In this paper we consider the main achievements of evolutionary robotics, focusing particularly on its contributions to both engineering and biology. We briefly elaborate on methodological issues, review some of the most interesting findings, and discuss important open issues and promising avenues for future work.

  17. Mean-Potential Law in Evolutionary Games

    Science.gov (United States)

    Nałecz-Jawecki, Paweł; Miekisz, Jacek

    2018-01-01

    The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1 /3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.

  18. Hybridizing Evolutionary Algorithms with Opportunistic Local Search

    DEFF Research Database (Denmark)

    Gießen, Christian

    2013-01-01

    There is empirical evidence that memetic algorithms (MAs) can outperform plain evolutionary algorithms (EAs). Recently the first runtime analyses have been presented proving the aforementioned conjecture rigorously by investigating Variable-Depth Search, VDS for short (Sudholt, 2008). Sudholt...

  19. Genetic variations and evolutionary relationships among radishes ...

    African Journals Online (AJOL)

    vera 1

    To determine the genetic diversity and evolutionary relationships among red radishes, 37 accessions ... determined that plant height, fresh leaf weight, and root ... Flower-shaped. Red .... according to Levan's karyotype classification standards.

  20. Evolutionary genetics: 150 years of natural selection

    Indian Academy of Sciences (India)

    This year marks a hundred and fifty years since the formal enunciation of the ... publication of R. A. Fisher's landmark paper reconciling the statistical results of the ... applications of evolutionary thinking that has emerged over the past fifteen.

  1. Evolutionary principles and their practical application

    DEFF Research Database (Denmark)

    Hendry, A. P.; Kinnison, M. T.; Heino, M.

    2011-01-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles...... are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design...... of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently...

  2. A view on reactions of complete fusion

    International Nuclear Information System (INIS)

    Delchev, I.I.; Petkov, I.J.

    1978-11-01

    Complete fusion reactions are analysed within the framework of a theoretical model. Energy density interaction potentials are made use of and are renormalized for the purpose. A large number of heavy ion reactions are studied and the calculated critical angular moments are compared with experimental data

  3. Defining fitness in evolutionary models

    Indian Academy of Sciences (India)

    2008-12-23

    Dec 23, 2008 ... guish it from rates of increase calculated with other factors included). .... offspring produced by a female at the end of the season that survive to ...... VII. The demography and evolution of iteroparity. Am. Nat. 133, 901–923.

  4. Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals.

    Science.gov (United States)

    Huang, Bing-Hong; Liao, Pei-Chun

    2015-07-01

    Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  5. Evolutionary Game Theory Analysis of Tumor Progression

    Science.gov (United States)

    Wu, Amy; Liao, David; Sturm, James; Austin, Robert

    2014-03-01

    Evolutionary game theory applied to two interacting cell populations can yield quantitative prediction of the future densities of the two cell populations based on the initial interaction terms. We will discuss how in a complex ecology that evolutionary game theory successfully predicts the future densities of strains of stromal and cancer cells (multiple myeloma), and discuss the possible clinical use of such analysis for predicting cancer progression. Supported by the National Science Foundation and the National Cancer Institute.

  6. Endogenous money: the evolutionary versus revolutionary views

    OpenAIRE

    Louis-Philippe Rochon; Sergio Rossi

    2013-01-01

    The purpose of this paper is to shed light on the endogenous nature of money. Contrary to the established post-Keynesian, or evolutionary, view, this paper argues that money has always been endogenous, irrespective of the historical period. Instead of the evolutionary theory of money and banking that can be traced back to Chick (1986), this paper puts forward a revolutionary definition of endogenous money consistent with many aspects of post-Keynesian economics as well as with the monetary ci...

  7. Avoiding Local Optima with Interactive Evolutionary Robotics

    Science.gov (United States)

    2012-07-09

    the top of a flight of stairs selects for climbing ; suspending the robot and the target object above the ground and creating rungs between the two will...REPORT Avoiding Local Optimawith Interactive Evolutionary Robotics 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The main bottleneck in evolutionary... robotics has traditionally been the time required to evolve robot controllers. However with the continued acceleration in computational resources, the

  8. Applied evolutionary economics and economic geography

    OpenAIRE

    Peter Sunley

    2008-01-01

    Applied Evolutionary Economics and Economic Geography aims to further advance empirical methodologies in evolutionary economics, with a special emphasis on geography and firm location. It does so by bringing together a select group of leading scholars including economists, geographers and sociologists, all of whom share an interest in explaining the uneven distribution of economic activities in space and the historical processes that have produced these patterns.

  9. Dynamic and photometric evolutionary models of tidal tails and ripples

    International Nuclear Information System (INIS)

    Wallin, J.F.

    1989-01-01

    An investigation into the causes of star formation in tidal tails has been conducted using a restricted three-body dynamical model in conjunction with a broad-band photometric evolutionary code. In these models, regions of compression form inside the disk and along the tidal tail and tidal bridge. The effects these density changes have on the colors of the tidal features are examined with a broad-band photometric evolutionary code. A spiral galaxy population is synthesized and the effects of modest changes in the star formation rate are explored. Limits on the density changes needed to make detectable changes in the colors are calculated using a Schmidt (1959) law. These models suggest that the blue colors and knotty features observed in the tidal features of some galaxies result from increased rates of star formation induced by tidally produced density increases. Limitations of this model are discussed along with photometric evolutionary models based on the density evolution in the tails. The Lynds and Toomre (1976) interpretation of ring galaxies as the natural result of a nearly head-on collision between a disk galaxy and a companion galaxy has become widely accepted. Similarly, Quinn's (1984) interpretation of the shells in elliptical galaxies as the aftermath of the cannibalization of a low-mass companion has been quite successful in accounting for the observations. Restricted three-body calculations of high inclination, low impact parameter encounters demonstrate that the shell-like ripples observed in a number of disk galaxies can also be produced as collisional artifacts from internal oscillations much as in ring galaxies

  10. Evolutionary cell biology: two origins, one objective.

    Science.gov (United States)

    Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

    2014-12-02

    All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

  11. Evolutionary computation in zoology and ecology.

    Science.gov (United States)

    Boone, Randall B

    2017-12-01

    Evolutionary computational methods have adopted attributes of natural selection and evolution to solve problems in computer science, engineering, and other fields. The method is growing in use in zoology and ecology. Evolutionary principles may be merged with an agent-based modeling perspective to have individual animals or other agents compete. Four main categories are discussed: genetic algorithms, evolutionary programming, genetic programming, and evolutionary strategies. In evolutionary computation, a population is represented in a way that allows for an objective function to be assessed that is relevant to the problem of interest. The poorest performing members are removed from the population, and remaining members reproduce and may be mutated. The fitness of the members is again assessed, and the cycle continues until a stopping condition is met. Case studies include optimizing: egg shape given different clutch sizes, mate selection, migration of wildebeest, birds, and elk, vulture foraging behavior, algal bloom prediction, and species richness given energy constraints. Other case studies simulate the evolution of species and a means to project shifts in species ranges in response to a changing climate that includes competition and phenotypic plasticity. This introduction concludes by citing other uses of evolutionary computation and a review of the flexibility of the methods. For example, representing species' niche spaces subject to selective pressure allows studies on cladistics, the taxon cycle, neutral versus niche paradigms, fundamental versus realized niches, community structure and order of colonization, invasiveness, and responses to a changing climate.

  12. Calculation Methods for Wallenius’ Noncentral Hypergeometric Distribution

    DEFF Research Database (Denmark)

    Fog, Agner

    2008-01-01

    Two different probability distributions are both known in the literature as "the" noncentral hypergeometric distribution. Wallenius' noncentral hypergeometric distribution can be described by an urn model without replacement with bias. Fisher's noncentral hypergeometric distribution...... is the conditional distribution of independent binomial variates given their sum. No reliable calculation method for Wallenius' noncentral hypergeometric distribution has hitherto been described in the literature. Several new methods for calculating probabilities from Wallenius' noncentral hypergeometric...... distribution are derived. Range of applicability, numerical problems, and efficiency are discussed for each method. Approximations to the mean and variance are also discussed. This distribution has important applications in models of biased sampling and in models of evolutionary systems....

  13. Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae).

    Science.gov (United States)

    Poliseno, Angelo; Feregrino, Christian; Sartoretto, Stéphane; Aurelle, Didier; Wörheide, Gert; McFadden, Catherine S; Vargas, Sergio

    2017-10-01

    Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Theologies, ideologies and evolutionary biology.

    Science.gov (United States)

    Scudo, Francesco M

    2010-01-01

    Since a century evolution has mostly been interpreted by two simple, "opposite" kinds of "theories" — i.e. as due either to fitness differences among genotypes or to some other simple mechanism — while bona fide, more complex theories were less popular throughout. In particular by far the most complete theories ever produced were suddenly, almost universally abandoned just after World War II, though not as a consequence of major breakthroughs. The causes of this situation are examined by analogy with much earlier developments and their demise by Cartesianism. The down to earth solutions these "complete" theories provide to the problems of "speciation" and the origins of cells are contrasted with the "miraculous" approaches by systemic neo-Darwinists.

  15. Configuration space Faddeev calculations

    International Nuclear Information System (INIS)

    Payne, G.L.; Klink, W.H.; Ployzou, W.N.

    1991-01-01

    The detailed study of few-body systems provides one of the most precise tools for studying the dynamics of nuclei. Our research program consists of a careful theoretical study of the nuclear few-body systems. During the past year we have completed several aspects of this program. We have continued our program of using the trinucleon system to investigate the validity of various realistic nucleon-nucleon potentials. Also, the effects of meson-exchange currents in nuclear systems have been studied. Initial calculations using the configuration-space Faddeev equations for nucleon-deuteron scattering have been completed. With modifications to treat relativistic systems, few-body methods can be applied to phenomena that are sensitive to the structure of the individual hadrons. We have completed a review of Relativistic Hamiltonian Dynamics in Nuclear and Particle Physics for Advances in Nuclear Physics. Although it is called a review, it is a large document that contains a significant amount of new research

  16. BOOK REVIEW: Complete Physics

    Science.gov (United States)

    Carson, Simon

    2000-03-01

    ', begins with an emphasis on the correct use of units in calculations that is very good (although again only really appropriate for more able students) and considers scientific notation and SI units. The use of triangles for rearranging three variable equations is introduced without any discussion of how to do the algebra properly. I found this rather out of place in a book of this level; I should personally hope to see those intending to pursue the subject beyond GCSE capable of rearranging equations without recourse to methods which convey no understanding of the physical relationship. The section on the `History of Key Ideas' has a double page spread on `Forces, Motion and Energy', `Rays, Waves and Particles' and `The Earth and Beyond', followed by a chronology of physics from 400 BC to 1990. These sections are necessarily very brief. The final section, `Experimental Physics', has some useful reminders for students about investigative work and a photocopiable checklist. The book has some very attractive features. Most pages include a boxed list of `essentials' that are useful either in skimming the text to find useful information or in revision. Each double page spread into which the material is arranged includes some fairly straightforward questions to test the basic ideas. Each section ends with a set of examination questions and with a checklist of ideas that can be photocopied for students to tick off what has been covered. The contents pages of the book may also be photocopied for students to check their progress. Given that this is a brand new book, I found the inclusion of a spread on ticker-tape rather old-fashioned: video is a much better way of analysing motion. The language of the text, too, can be rather dry and academic, and the organization reflects a traditional approach to the physics curriculum. The book would be most useful, I think, to able students studying single-subject physics courses at GCSE or to those beginning A-level. At £14.00 a copy, it

  17. The Nothoaspis amazoniensis Complete Mitogenome: A Comparative and Phylogenetic Analysis

    Directory of Open Access Journals (Sweden)

    Paulo H. C. Lima

    2018-03-01

    Full Text Available The molecular biology era, together with morphology, molecular phylogenetics, bioinformatics, and high-throughput sequencing technologies, improved the taxonomic identification of Argasidae family members, especially when considering specimens at different development stages, which remains a great difficulty for acarologists. These tools could provide important data and insights on the history and evolutionary relationships of argasids. To better understand these relationships, we sequenced and assembled the first complete mitochondrial genome of Nothoaspis amazoniensis. We used phylogenomics to identify the evolutionary history of this species of tick, comparing the data obtained with 26 complete mitochondrial sequences available in biological databases. The results demonstrated the absence of genetic rearrangements, high similarity and identity, and a close organizational link between the mitogenomes of N. amazoniensis and other argasids analyzed. In addition, the mitogenome had a monophyletic cladistic taxonomic arrangement, encompassed by representatives of the Afrotropical and Neotropical regions, with specific parasitism in bats, which may be indicative of an evolutionary process of cospeciation between vectors and the host.

  18. Understanding the mind from an evolutionary perspective: an overview of evolutionary psychology.

    Science.gov (United States)

    Shackelford, Todd K; Liddle, James R

    2014-05-01

    The theory of evolution by natural selection provides the only scientific explanation for the existence of complex adaptations. The design features of the brain, like any organ, are the result of selection pressures operating over deep time. Evolutionary psychology posits that the human brain comprises a multitude of evolved psychological mechanisms, adaptations to specific and recurrent problems of survival and reproduction faced over human evolutionary history. Although some mistakenly view evolutionary psychology as promoting genetic determinism, evolutionary psychologists appreciate and emphasize the interactions between genes and environments. This approach to psychology has led to a richer understanding of a variety of psychological phenomena, and has provided a powerful foundation for generating novel hypotheses. Critics argue that evolutionary psychologists resort to storytelling, but as with any branch of science, empirical testing is a vital component of the field, with hypotheses standing or falling with the weight of the evidence. Evolutionary psychology is uniquely suited to provide a unifying theoretical framework for the disparate subdisciplines of psychology. An evolutionary perspective has provided insights into several subdisciplines of psychology, while simultaneously demonstrating the arbitrary nature of dividing psychological science into such subdisciplines. Evolutionary psychologists have amassed a substantial empirical and theoretical literature, but as a relatively new approach to psychology, many questions remain, with several promising directions for future research. For further resources related to this article, please visit the WIREs website. The authors have declared no conflicts of interest for this article. © 2014 John Wiley & Sons, Ltd.

  19. A finite-buffer queue with a single vacation policy: An analytical study with evolutionary positioning

    Directory of Open Access Journals (Sweden)

    Woźniak Marcin

    2014-12-01

    Full Text Available In this paper, application of an evolutionary strategy to positioning a GI/M/1/N-type finite-buffer queueing system with exhaustive service and a single vacation policy is presented. The examined object is modeled by a conditional joint transform of the first busy period, the first idle time and the number of packets completely served during the first busy period. A mathematical model is defined recursively by means of input distributions. In the paper, an analytical study and numerical experiments are presented. A cost optimization problem is solved using an evolutionary strategy for a class of queueing systems described by exponential and Erlang distributions.

  20. Evolutionary public health: introducing the concept.

    Science.gov (United States)

    Wells, Jonathan C K; Nesse, Randolph M; Sear, Rebecca; Johnstone, Rufus A; Stearns, Stephen C

    2017-07-29

    The emerging discipline of evolutionary medicine is breaking new ground in understanding why people become ill. However, the value of evolutionary analyses of human physiology and behaviour is only beginning to be recognised in the field of public health. Core principles come from life history theory, which analyses the allocation of finite amounts of energy between four competing functions-maintenance, growth, reproduction, and defence. A central tenet of evolutionary theory is that organisms are selected to allocate energy and time to maximise reproductive success, rather than health or longevity. Ecological interactions that influence mortality risk, nutrient availability, and pathogen burden shape energy allocation strategies throughout the life course, thereby affecting diverse health outcomes. Public health interventions could improve their own effectiveness by incorporating an evolutionary perspective. In particular, evolutionary approaches offer new opportunities to address the complex challenges of global health, in which populations are differentially exposed to the metabolic consequences of poverty, high fertility, infectious diseases, and rapid changes in nutrition and lifestyle. The effect of specific interventions is predicted to depend on broader factors shaping life expectancy. Among the important tools in this approach are mathematical models, which can explore probable benefits and limitations of interventions in silico, before their implementation in human populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. A teleofunctional account of evolutionary mismatch.

    Science.gov (United States)

    Cofnas, Nathan

    When the environment in which an organism lives deviates in some essential way from that to which it is adapted, this is described as "evolutionary mismatch," or "evolutionary novelty." The notion of mismatch plays an important role, explicitly or implicitly, in evolution-informed cognitive psychology, clinical psychology, and medicine. The evolutionary novelty of our contemporary environment is thought to have significant implications for our health and well-being. However, scientists have generally been working without a clear definition of mismatch. This paper defines mismatch as deviations in the environment that render biological traits unable, or impaired in their ability, to produce their selected effects (i.e., to perform their proper functions in Neander's sense). The machinery developed by Millikan in connection with her account of proper function, and with her related teleosemantic account of representation, is used to identify four major types, and several subtypes, of evolutionary mismatch. While the taxonomy offered here does not in itself resolve any scientific debates, the hope is that it can be used to better formulate empirical hypotheses concerning the effects of mismatch. To illustrate, it is used to show that the controversial hypothesis that general intelligence evolved as an adaptation to handle evolutionary novelty can, contra some critics, be formulated in a conceptually coherent way.

  2. Multiobjective Multifactorial Optimization in Evolutionary Multitasking.

    Science.gov (United States)

    Gupta, Abhishek; Ong, Yew-Soon; Feng, Liang; Tan, Kay Chen

    2016-05-03

    In recent decades, the field of multiobjective optimization has attracted considerable interest among evolutionary computation researchers. One of the main features that makes evolutionary methods particularly appealing for multiobjective problems is the implicit parallelism offered by a population, which enables simultaneous convergence toward the entire Pareto front. While a plethora of related algorithms have been proposed till date, a common attribute among them is that they focus on efficiently solving only a single optimization problem at a time. Despite the known power of implicit parallelism, seldom has an attempt been made to multitask, i.e., to solve multiple optimization problems simultaneously. It is contended that the notion of evolutionary multitasking leads to the possibility of automated transfer of information across different optimization exercises that may share underlying similarities, thereby facilitating improved convergence characteristics. In particular, the potential for automated transfer is deemed invaluable from the standpoint of engineering design exercises where manual knowledge adaptation and reuse are routine. Accordingly, in this paper, we present a realization of the evolutionary multitasking paradigm within the domain of multiobjective optimization. The efficacy of the associated evolutionary algorithm is demonstrated on some benchmark test functions as well as on a real-world manufacturing process design problem from the composites industry.

  3. The evolutionary ecology of molecular replicators.

    Science.gov (United States)

    Nee, Sean

    2016-08-01

    By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology.

  4. An Evolutionary Psychology Approach to Consumer Choice

    Directory of Open Access Journals (Sweden)

    ZURINA BT MOHAIDIN

    2013-07-01

    Full Text Available Human behaviour can be explained not only through experience and environments but also by incorporating evolutionary explanation. Consumer behaviour could not be understood accurately without infusing Darwinian evolutionary theory which has contributed in the knowledge of human nature. Evolutionary psychology revolves around the human’s evolved mental and the impact on human’s traits and behaviour where the influence of the environment to our genes would determine our individual behaviour and traits, resulting in variation among us. Foraging which is a part of behavioural ecology involves many sequences or repetitions of animals’ activities and decision making which is useful to relate these patterns of activities to the decisions made in human consumption. The aim of this research is to investigate the similarities of human consumption and ecological behaviour by employing interpretative and comparative approach. It is hoped that by applying the evolutionary theory in explaining consumer choice, this study is able to contribute to the development of behavioural ecology in human consumption. The analysis of the data is done aggregately for 200 consumers and individually for 20 consumers, who have purchased four product categories over a year. This study concludes that the theories of evolutionary psychology can fit to the consumers’ buying behaviour implicating its usefulness in explaining the consumers’ choice.

  5. Evolutionary heritage influences Amazon tree ecology

    Science.gov (United States)

    Coelho de Souza, Fernanda; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J. W.; Chave, Jerome; Galbraith, David R.; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R. Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E. O. C.; Araujo-Murakami, Alejandro; Arets, Eric J. M. M.; Aymard C, Gerardo A.; Baraloto, Christopher; Barroso, Jorcely G.; Bonal, Damien; Boot, Rene G. A.; Camargo, José L. C.; Comiskey, James A.; Valverde, Fernando Cornejo; de Camargo, Plínio B.; Di Fiore, Anthony; Erwin, Terry L.; Feldpausch, Ted R.; Ferreira, Leandro; Fyllas, Nikolaos M.; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N.; Killeen, Timothy J.; Laurance, William F.; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E.; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S.; Marimon-Junior, Ben H.; Mendoza, Casimiro; Morandi, Paulo; Neill, David A.; Vargas, Percy Núñez; Oliveira, Edmar A.; Lenza, Eddie; Palacios, Walter A.; Peñuela-Mora, Maria C.; Pipoly, John J.; Pitman, Nigel C. A.; Prieto, Adriana; Quesada, Carlos A.; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P.; Silveira, Marcos; ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M. F.; van der Meer, Peter J.; Vasquez, Rodolfo V.; Vieira, Simone A.; Vilanova, Emilio; Vos, Vincent A.; Wang, Ophelia; Young, Kenneth R.; Zagt, Roderick J.; Baker, Timothy R.

    2016-01-01

    Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. PMID:27974517

  6. Evolutionary heritage influences Amazon tree ecology.

    Science.gov (United States)

    Coelho de Souza, Fernanda; Dexter, Kyle G; Phillips, Oliver L; Brienen, Roel J W; Chave, Jerome; Galbraith, David R; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E O C; Araujo-Murakami, Alejandro; Arets, Eric J M M; Aymard C, Gerardo A; Baraloto, Christopher; Barroso, Jorcely G; Bonal, Damien; Boot, Rene G A; Camargo, José L C; Comiskey, James A; Valverde, Fernando Cornejo; de Camargo, Plínio B; Di Fiore, Anthony; Elias, Fernando; Erwin, Terry L; Feldpausch, Ted R; Ferreira, Leandro; Fyllas, Nikolaos M; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N; Killeen, Timothy J; Laurance, William F; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S; Marimon-Junior, Ben H; Mendoza, Casimiro; Morandi, Paulo; Neill, David A; Vargas, Percy Núñez; Oliveira, Edmar A; Lenza, Eddie; Palacios, Walter A; Peñuela-Mora, Maria C; Pipoly, John J; Pitman, Nigel C A; Prieto, Adriana; Quesada, Carlos A; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P; Silveira, Marcos; Stropp, Juliana; Ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M F; van der Meer, Peter J; Vasquez, Rodolfo V; Vieira, Simone A; Vilanova, Emilio; Vos, Vincent A; Wang, Ophelia; Young, Kenneth R; Zagt, Roderick J; Baker, Timothy R

    2016-12-14

    Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. © 2016 The Authors.

  7. Evolutionary accounts of human behavioural diversity

    Science.gov (United States)

    Brown, Gillian R.; Dickins, Thomas E.; Sear, Rebecca; Laland, Kevin N.

    2011-01-01

    Human beings persist in an extraordinary range of ecological settings, in the process exhibiting enormous behavioural diversity, both within and between populations. People vary in their social, mating and parental behaviour and have diverse and elaborate beliefs, traditions, norms and institutions. The aim of this theme issue is to ask whether, and how, evolutionary theory can help us to understand this diversity. In this introductory article, we provide a background to the debate surrounding how best to understand behavioural diversity using evolutionary models of human behaviour. In particular, we examine how diversity has been viewed by the main subdisciplines within the human evolutionary behavioural sciences, focusing in particular on the human behavioural ecology, evolutionary psychology and cultural evolution approaches. In addition to differences in focus and methodology, these subdisciplines have traditionally varied in the emphasis placed on human universals, ecological factors and socially learned behaviour, and on how they have addressed the issue of genetic variation. We reaffirm that evolutionary theory provides an essential framework for understanding behavioural diversity within and between human populations, but argue that greater integration between the subfields is critical to developing a satisfactory understanding of diversity. PMID:21199836

  8. Evolutionary stability concepts in a stochastic environment

    Science.gov (United States)

    Zheng, Xiu-Deng; Li, Cong; Lessard, Sabin; Tao, Yi

    2017-09-01

    Over the past 30 years, evolutionary game theory and the concept of an evolutionarily stable strategy have been not only extensively developed and successfully applied to explain the evolution of animal behaviors, but also widely used in economics and social sciences. Nonetheless, the stochastic dynamical properties of evolutionary games in randomly fluctuating environments are still unclear. In this study, we investigate conditions for stochastic local stability of fixation states and constant interior equilibria in a two-phenotype model with random payoffs following pairwise interactions. Based on this model, we develop the concepts of stochastic evolutionary stability (SES) and stochastic convergence stability (SCS). We show that the condition for a pure strategy to be SES and SCS is more stringent than in a constant environment, while the condition for a constant mixed strategy to be SES is less stringent than the condition to be SCS, which is less stringent than the condition in a constant environment.

  9. The evolutionary implications of epigenetic inheritance.

    Science.gov (United States)

    Jablonka, Eva

    2017-10-06

    The Modern Evolutionary Synthesis (MS) forged in the mid-twentieth century was built on a notion of heredity that excluded soft inheritance, the inheritance of the effects of developmental modifications. However, the discovery of molecular mechanisms that generate random and developmentally induced epigenetic variations is leading to a broadening of the notion of biological heredity that has consequences for ideas about evolution. After presenting some old challenges to the MS that were raised, among others, by Karl Popper, I discuss recent research on epigenetic inheritance, which provides experimental and theoretical support for these challenges. There is now good evidence that epigenetic inheritance is ubiquitous and is involved in adaptive evolution and macroevolution. I argue that the many evolutionary consequences of epigenetic inheritance open up new research areas and require the extension of the evolutionary synthesis beyond the current neo-Darwinian model.

  10. Human compulsivity: A perspective from evolutionary medicine.

    Science.gov (United States)

    Stein, Dan J; Hermesh, Haggai; Eilam, David; Segalas, Cosi; Zohar, Joseph; Menchon, Jose; Nesse, Randolph M

    2016-05-01

    Biological explanations address not only proximal mechanisms (for example, the underlying neurobiology of obsessive-compulsive disorder), but also distal mechanisms (that is, a consideration of how particular neurobiological mechanisms evolved). Evolutionary medicine has emphasized a series of explanations for vulnerability to disease, including constraints, mismatch, and tradeoffs. The current paper will consider compulsive symptoms in obsessive-compulsive and related disorders and behavioral addictions from this evolutionary perspective. It will argue that while obsessive-compulsive disorder (OCD) is typically best conceptualized as a dysfunction, it is theoretically and clinically valuable to understand some symptoms of obsessive-compulsive and related disorders in terms of useful defenses. The symptoms of behavioral addictions can also be conceptualized in evolutionary terms (for example, mismatch), which in turn provides a sound foundation for approaching assessment and intervention. Copyright © 2016. Published by Elsevier B.V.

  11. Evolutionary Sound Synthesis Controlled by Gestural Data

    Directory of Open Access Journals (Sweden)

    Jose Fornari

    2011-05-01

    Full Text Available This article focuses on the interdisciplinary research involving Computer Music and Generative Visual Art. We describe the implementation of two interactive artistic systems based on principles of Gestural Data (WILSON, 2002 retrieval and self-organization (MORONI, 2003, to control an Evolutionary Sound Synthesis method (ESSynth. The first implementation uses, as gestural data, image mapping of handmade drawings. The second one uses gestural data from dynamic body movements of dance. The resulting computer output is generated by an interactive system implemented in Pure Data (PD. This system uses principles of Evolutionary Computation (EC, which yields the generation of a synthetic adaptive population of sound objects. Considering that music could be seen as “organized sound” the contribution of our study is to develop a system that aims to generate "self-organized sound" – a method that uses evolutionary computation to bridge between gesture, sound and music.

  12. Evolutionary genomics and HIV restriction factors.

    Science.gov (United States)

    Pyndiah, Nitisha; Telenti, Amalio; Rausell, Antonio

    2015-03-01

    To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.

  13. Do we need an extended evolutionary synthesis?

    Science.gov (United States)

    Pigliucci, Massimo

    2007-12-01

    The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin's days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes.

  14. Infrastructure system restoration planning using evolutionary algorithms

    Science.gov (United States)

    Corns, Steven; Long, Suzanna K.; Shoberg, Thomas G.

    2016-01-01

    This paper presents an evolutionary algorithm to address restoration issues for supply chain interdependent critical infrastructure. Rapid restoration of infrastructure after a large-scale disaster is necessary to sustaining a nation's economy and security, but such long-term restoration has not been investigated as thoroughly as initial rescue and recovery efforts. A model of the Greater Saint Louis Missouri area was created and a disaster scenario simulated. An evolutionary algorithm is used to determine the order in which the bridges should be repaired based on indirect costs. Solutions were evaluated based on the reduction of indirect costs and the restoration of transportation capacity. When compared to a greedy algorithm, the evolutionary algorithm solution reduced indirect costs by approximately 12.4% by restoring automotive travel routes for workers and re-establishing the flow of commodities across the three rivers in the Saint Louis area.

  15. Concatenated image completion via tensor augmentation and completion

    OpenAIRE

    Bengua, Johann A.; Tuan, Hoang D.; Phien, Ho N.; Do, Minh N.

    2016-01-01

    This paper proposes a novel framework called concatenated image completion via tensor augmentation and completion (ICTAC), which recovers missing entries of color images with high accuracy. Typical images are second- or third-order tensors (2D/3D) depending if they are grayscale or color, hence tensor completion algorithms are ideal for their recovery. The proposed framework performs image completion by concatenating copies of a single image that has missing entries into a third-order tensor,...

  16. The evolutionary position of nematodes

    Directory of Open Access Journals (Sweden)

    Gojobori Takashi

    2002-04-01

    Full Text Available Abstract Background The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans, an insect (Drosophila melanogaster, and a vertebrate (Homo sapiens. Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes. Results We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes. Conclusion We conclude that insects (arthropods are genetically and evolutionarily closer to humans than to nematode worms.

  17. On Reciprocal Causation in the Evolutionary Process.

    Science.gov (United States)

    Svensson, Erik I

    2018-01-01

    Recent calls for a revision of standard evolutionary theory (SET) are based partly on arguments about the reciprocal causation. Reciprocal causation means that cause-effect relationships are bi-directional, as a cause could later become an effect and vice versa. Such dynamic cause-effect relationships raise questions about the distinction between proximate and ultimate causes, as originally formulated by Ernst Mayr. They have also motivated some biologists and philosophers to argue for an Extended Evolutionary Synthesis (EES). The EES will supposedly expand the scope of the Modern Synthesis (MS) and SET, which has been characterized as gene-centred, relying primarily on natural selection and largely neglecting reciprocal causation. Here, I critically examine these claims, with a special focus on the last conjecture. I conclude that reciprocal causation has long been recognized as important by naturalists, ecologists and evolutionary biologists working in the in the MS tradition, although it it could be explored even further. Numerous empirical examples of reciprocal causation in the form of positive and negative feedback are now well known from both natural and laboratory systems. Reciprocal causation have also been explicitly incorporated in mathematical models of coevolutionary arms races, frequency-dependent selection, eco-evolutionary dynamics and sexual selection. Such dynamic feedback were already recognized by Richard Levins and Richard Lewontin in their bok The Dialectical Biologist . Reciprocal causation and dynamic feedback might also be one of the few contributions of dialectical thinking and Marxist philosophy in evolutionary theory. I discuss some promising empirical and analytical tools to study reciprocal causation and the implications for the EES. Finally, I briefly discuss how quantitative genetics can be adapated to studies of reciprocal causation, constructive inheritance and phenotypic plasticity and suggest that the flexibility of this approach

  18. Evolutionary dynamics of protein domain architecture in plants

    Directory of Open Access Journals (Sweden)

    Zhang Xue-Cheng

    2012-01-01

    Full Text Available Abstract Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing

  19. Evolutionary Genomics of Life in (and from) the Sea

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Dehal, Paramvir; Fuerstenberg, Susan I.

    2006-01-09

    High throughput genome sequencing centers that were originally built for the Human Genome Project (Lander et al., 2001; Venter et al., 2001) have now become an engine for comparative genomics. The six largest centers alone are now producing over 150 billion nucleotides per year, more than 50 times the amount of DNA in the human genome, and nearly all of this is directed at projects that promise great insights into the pattern and processes of evolution. Unfortunately, this data is being produced at a pace far exceeding the capacity of the scientific community to provide insightful analysis, and few scientists with training and experience in evolutionary biology have played prominent roles to date. One of the consequences is that poor quality analyses are typical; for example, orthology among genes is generally determined by simple measures of sequence similarity, when this has been discredited by molecular evolutionary biologists decades ago. Here we discuss the how genomes are chosen for sequencing and how the scientific community can have input. We describe the PhIGs database and web tools (Dehal and Boore 2005a; http://PhIGs.org), which provide phylogenetic analysis of all gene families for all completely sequenced genomes and the associated 'Synteny Viewer', which allows comparisons of the relative positions of orthologous genes. This is the best tool available for inferring gene function across multiple genomes. We also describe how we have used the PhIGs methods with the whole genome sequences of a tunicate, fish, mouse, and human to conclusively demonstrate that two rounds of whole genome duplication occurred at the base of vertebrates (Dehal and Boore 2005b). This evidence is found in the large scale structure of the positions of paralogous genes that arose from duplications inferred by evolutionary analysis to have occurred at the base of vertebrates.

  20. Evolutionary cost management in the nuclear industry

    International Nuclear Information System (INIS)

    Lombardi, C.G.; Mazzini, R.A.

    1986-01-01

    The reader is urged to consider the material in ''The Evolutionary Theory of Cost Management'' carefully before proceeding with the material in this paper. The recommendations in this paper flow from the revised line of thinking generated by the evolutionary approach. The suggestions will be difficult to accept in the absence of an understanding of the underlying theory. Although the authors briefly discuss some of the theory, it is nevertheless recommended that the reader develop a fuller understanding of the concepts by studying the prior paper

  1. Evolutionary dynamics of complex communications networks

    CERN Document Server

    Karyotis, Vasileios; Papavassiliou, Symeon

    2013-01-01

    Until recently, most network design techniques employed a bottom-up approach with lower protocol layer mechanisms affecting the development of higher ones. This approach, however, has not yielded fascinating results in the case of wireless distributed networks. Addressing the emerging aspects of modern network analysis and design, Evolutionary Dynamics of Complex Communications Networks introduces and develops a top-bottom approach where elements of the higher layer can be exploited in modifying the lowest physical topology-closing the network design loop in an evolutionary fashion similar to

  2. Evolutionary optimization of production materials workflow processes

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee; Jacobsen, Peter

    2014-01-01

    We present an evolutionary optimisation technique for stochastic production processes, which is able to find improved production materials workflow processes with respect to arbitrary combinations of numerical quantities associated with the production process. Working from a core fragment...... of the BPMN language, we employ an evolutionary algorithm where stochastic model checking is used as a fitness function to determine the degree of improvement of candidate processes derived from the original process through mutation and cross-over operations. We illustrate this technique using a case study...

  3. Evolutionary Algorithms Application Analysis in Biometric Systems

    Directory of Open Access Journals (Sweden)

    N. Goranin

    2010-01-01

    Full Text Available Wide usage of biometric information for person identity verification purposes, terrorist acts prevention measures and authenticationprocess simplification in computer systems has raised significant attention to reliability and efficiency of biometricsystems. Modern biometric systems still face many reliability and efficiency related issues such as reference databasesearch speed, errors while recognizing of biometric information or automating biometric feature extraction. Current scientificinvestigations show that application of evolutionary algorithms may significantly improve biometric systems. In thisarticle we provide a comprehensive review of main scientific research done in sphere of evolutionary algorithm applicationfor biometric system parameter improvement.

  4. Langley's CSI evolutionary model: Phase O

    Science.gov (United States)

    Belvin, W. Keith; Elliott, Kenny B.; Horta, Lucas G.; Bailey, Jim P.; Bruner, Anne M.; Sulla, Jeffrey L.; Won, John; Ugoletti, Roberto M.

    1991-01-01

    A testbed for the development of Controls Structures Interaction (CSI) technology to improve space science platform pointing is described. The evolutionary nature of the testbed will permit the study of global line-of-sight pointing in phases 0 and 1, whereas, multipayload pointing systems will be studied beginning with phase 2. The design, capabilities, and typical dynamic behavior of the phase 0 version of the CSI evolutionary model (CEM) is documented for investigator both internal and external to NASA. The model description includes line-of-sight pointing measurement, testbed structure, actuators, sensors, and real time computers, as well as finite element and state space models of major components.

  5. Evolutionary Graphs with Frequency Dependent Fitness

    Science.gov (United States)

    Nie, Pu-Yan; Zhang, Pei-Ai

    Evolutionary graph theory was recently proposed by Lieberman et al. in 2005. In the previous papers about evolutionary graphs (EGs), the fitness of the residents in the EGs is in general assumed to be unity, and the fitness of a mutant is assumed to be a constant r. We aim to extend EG to general cases in this paper, namely, the fitness of a mutant is heavily dependent upon frequency. The corresponding properties for these new EGs are analyzed, and the fixation probability is obtained for large population.

  6. Configuration space Faddeev calculations

    International Nuclear Information System (INIS)

    Payne, G.L.; Klink, W.H.; Polyzou, W.N.

    1989-01-01

    The detailed study of few-body systems provides one of the most effective means for studying nuclear physics at subnucleon distance scales. For few-body systems the model equations can be solved numerically with errors less than the experimental uncertainties. We have used such systems to investigate the size of relativistic effects, the role of meson-exchange currents, and the importance of quark degrees of freedom in the nucleus. Complete calculations for momentum-dependent potentials have been performed, and the properties of the three-body bound state for these potentials have been studied. Few-body calculations of the electromagnetic form factors of the deuteron and pion have been carried out using a front-form formulation of relativistic quantum mechanics. The decomposition of the operators transforming convariantly under the Poincare group into kinematical and dynamical parts has been studies. New ways for constructing interactions between particles, as well as interactions which lead to the production of particles, have been constructed in the context of a relativistic quantum mechanics. To compute scattering amplitudes in a nonperturbative way, classes of operators have been generated out of which the phase operator may be constructed. Finally, we have worked out procedures for computing Clebsch-Gordan and Racah coefficients on a computer, as well as giving procedures for dealing with the multiplicity problem

  7. p-topological Cauchy completions

    Directory of Open Access Journals (Sweden)

    J. Wig

    1999-01-01

    Full Text Available The duality between “regular” and “topological” as convergence space properties extends in a natural way to the more general properties “p-regular” and “p-topological.” Since earlier papers have investigated regular, p-regular, and topological Cauchy completions, we hereby initiate a study of p-topological Cauchy completions. A p-topological Cauchy space has a p-topological completion if and only if it is “cushioned,” meaning that each equivalence class of nonconvergent Cauchy filters contains a smallest filter. For a Cauchy space allowing a p-topological completion, it is shown that a certain class of Reed completions preserve the p-topological property, including the Wyler and Kowalsky completions, which are, respectively, the finest and the coarsest p-topological completions. However, not all p-topological completions are Reed completions. Several extension theorems for p-topological completions are obtained. The most interesting of these states that any Cauchy-continuous map between Cauchy spaces allowing p-topological and p′-topological completions, respectively, can always be extended to a θ-continuous map between any p-topological completion of the first space and any p′-topological completion of the second.

  8. Accurate quantum chemical calculations

    Science.gov (United States)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  9. Structure completion for facade layouts

    KAUST Repository

    Fan, Lubin; Musialski, Przemyslaw; Liu, Ligang; Wonka, Peter

    2014-01-01

    completion with large missing parts is an ill-posed problem. Therefore, we combine two sources of information to derive our solution: the observed shapes and a database of complete layouts. The problem is also very difficult, because shape positions

  10. Evolutionary thinking: "A conversation with Carter Phipps about the role of evolutionary thinking in modern culture".

    Science.gov (United States)

    Hunt, Tam

    2014-12-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution-both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place-has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps' book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging "integral" or "evolutionary" cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps.

  11. Safeguards as an evolutionary system

    International Nuclear Information System (INIS)

    Carlson, J.

    1998-01-01

    NPT safeguards pursuant to INFCIRC/153 retain a strong emphasis on materials accountancy, and are primarily concerned with verifying nuclear activities as declared by the State - the correctness of States' declarations. This decade, failure to adequately address the possibility of undeclared nuclear activities - the issue of the completeness of States' declarations - has been recognized as a major shortcoming in the safeguards system. Since the 'classical' safeguards system is unable to provide credible assurance of the absence of clandestine nuclear activities, substantial efforts are being made to strengthen the IAEA's capabilities in this regard. Agreement has been reached on a Model Protocol substantially extending the Agency's authority, and good progress has been made in developing the new approaches, technologies and techniques required to ensure this authority is used effectively. Increasingly, safeguards will involve more qualitative judgements. Transparency will be very important - without a clear understanding by Member States of how the Agency goes about its new tasks and reaches its conclusions about the absence of undeclared activities, the safeguards system will not fulfil its vital confidence-building role. A major theme in current safeguards thinking is integration, the rationalization of classical safeguards with the new safeguards strengthening measures. As part of the rationalization process, it is timely to re-assess traditional safeguards implementation practices. One of these is uniformity in the way safeguards activities are implemented in different States. Another is whether the traditional concept of safeguards confidentiality is consistent with the increasing importance of transparency. (author)

  12. Iris double recognition based on modified evolutionary neural network

    Science.gov (United States)

    Liu, Shuai; Liu, Yuan-Ning; Zhu, Xiao-Dong; Huo, Guang; Liu, Wen-Tao; Feng, Jia-Kai

    2017-11-01

    Aiming at multicategory iris recognition under illumination and noise interference, this paper proposes a method of iris double recognition based on a modified evolutionary neural network. An equalization histogram and Laplace of Gaussian operator are used to process the iris to suppress illumination and noise interference and Haar wavelet to convert the iris feature to binary feature encoding. Calculate the Hamming distance for the test iris and template iris , and compare with classification threshold, determine the type of iris. If the iris cannot be identified as a different type, there needs to be a secondary recognition. The connection weights in back-propagation (BP) neural network use modified evolutionary neural network to adaptively train. The modified neural network is composed of particle swarm optimization with mutation operator and BP neural network. According to different iris libraries in different circumstances of experimental results, under illumination and noise interference, the correct recognition rate of this algorithm is higher, the ROC curve is closer to the coordinate axis, the training and recognition time is shorter, and the stability and the robustness are better.

  13. Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors

    Directory of Open Access Journals (Sweden)

    Tatiana Tatarinova

    2015-01-01

    Full Text Available Proteins of the same functional family (for example, kinases may have significantly different lengths. It is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. The main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. We believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome rank and genome property, is a reasonable approach in revealing such evolutionary driving factors. As we demonstrated earlier, our chosen approach, Bubble-sort, combines stability, accuracy, and computational efficiency as compared to other ranking methods. Application of Bubble Sort to the set of 1390 prokaryotic genomes confirmed that genes of Archaeal species are generally shorter than Bacterial ones. We observed that gene lengths are affected by various factors: within each domain, different phyla have preferences for short or long genes; thermophiles tend to have shorter genes than the soil-dwellers; halophiles tend to have longer genes. We also found that species with overrepresentation of cytosines and guanines in the third position of the codon (GC3 content tend to have longer genes than species with low GC3 content.

  14. Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors.

    Science.gov (United States)

    Tatarinova, Tatiana; Salih, Bilal; Dien Bard, Jennifer; Cohen, Irit; Bolshoy, Alexander

    2015-01-01

    Proteins of the same functional family (for example, kinases) may have significantly different lengths. It is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. The main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. We believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome rank and genome property, is a reasonable approach in revealing such evolutionary driving factors. As we demonstrated earlier, our chosen approach, Bubble-sort, combines stability, accuracy, and computational efficiency as compared to other ranking methods. Application of Bubble Sort to the set of 1390 prokaryotic genomes confirmed that genes of Archaeal species are generally shorter than Bacterial ones. We observed that gene lengths are affected by various factors: within each domain, different phyla have preferences for short or long genes; thermophiles tend to have shorter genes than the soil-dwellers; halophiles tend to have longer genes. We also found that species with overrepresentation of cytosines and guanines in the third position of the codon (GC3 content) tend to have longer genes than species with low GC3 content.

  15. Evolutionary dynamics of fluctuating populations with strong mutualism

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David

    2013-03-01

    Evolutionary game theory with finite interacting populations is receiving increased attention, including subtle phenomena associated with number fluctuations, i.e., ``genetic drift.'' Models of cooperation and competition often utilize a simplified Moran model, with a strictly fixed total population size. We explore a more general evolutionary model with independent fluctuations in the numbers of two distinct species, in a regime characterized by ``strong mutualism.'' The model has two absorbing states, each corresponding to fixation of one of the two species, and allows exploration of the interplay between growth, competition, and mutualism. When mutualism is favored, number fluctuations eventually drive the system away from a stable fixed point, characterized by cooperation, to one of the absorbing states. Well-mixed populations will thus be taken over by a single species in a finite time, despite the bias towards cooperation. We calculate both the fixation probability and the mean fixation time as a function of the initial conditions and carrying capacities in the strong mutualism regime, using the method of matched asymptotic expansions. Our results are compared to computer simulations.

  16. New pillars of evolutionary theory in the light of genomics

    International Nuclear Information System (INIS)

    Lopez Carrascal, Camilo Ernesto

    2011-01-01

    The evolutionist theory proposed by Darwin is one of the fundamental pillars in biology. Darwin's theory was solidified with the modern synthesis of evolutionary biology thanks to the rediscovery of Mendel's work, which laid the genetic basis of heredity. In recent years, great progress has been acquired in the sequencing and analyses of complete genomes, which have provided several elements to discuss some Darwinists tenets of evolution. The evidence of gene duplication and whole-genome duplication, the horizontal gene transfer and the endosymbiosis process question the idea that evolution proceeds through the gradual accumulation of infinitesimally small random changes. The new evidence of neutral selection on the genomics context reveals other mechanisms of evolution not necessarily related with the idea of progress or with an adaptationist program as was originally stated by the Darwin's theory. in this paper, I present these and other concepts such as gene regulation, molecular mechanisms of development and some environmental aspects (epigenesis and phenotypic plasticity) as starting points to think in the necessity to update the evolutionary theory which in my opinion should be more inclusive, pluralistic and consistent with our current knowledge.

  17. Lessons in modularity: the evolutionary ecology of colonial invertebrates

    Directory of Open Access Journals (Sweden)

    Roger N. Hughes

    2005-06-01

    Full Text Available Benthic colonial invertebrates share with higher plants a modular construction and a sessile adult life. Both types of organism show parallel evolutionary responses to common selective forces, but in contrast to the long-established focus on plants, comparable study of colonial invertebrates has developed relatively recently, largely owing to the application of new techniques in image processing and molecular biology. Species whose life cycles are readily completed under laboratory conditions and whose colonies are easily propagated from cuttings provide powerful models for experimentally investigating fundamental evolutionary problems, including metabolic allometry, the manifestation of ageing and the origin of allorecognition systems. Free of the confounding influences of behavioural manipulation and costs of copulation, colonial invertebrates whose water-borne sperm fertilize retained eggs lend themselves well to the experimental study of cryptic female choice, sperm competition and sexual conflict. In these respects, it will be productive to adopt and extend theoretical frameworks developed for flowering plants to guide experimental investigation of modular animals. Since mate choice occurs at the cellular level in modular animals, reproductive isolation is uncorrelated with morphology and cryptic speciation is likely to be widespread.

  18. Late replication domains are evolutionary conserved in the Drosophila genome.

    Science.gov (United States)

    Andreyenkova, Natalya G; Kolesnikova, Tatyana D; Makunin, Igor V; Pokholkova, Galina V; Boldyreva, Lidiya V; Zykova, Tatyana Yu; Zhimulev, Igor F; Belyaeva, Elena S

    2013-01-01

    Drosophila chromosomes are organized into distinct domains differing in their predominant chromatin composition, replication timing and evolutionary conservation. We show on a genome-wide level that genes whose order has remained unaltered across 9 Drosophila species display late replication timing and frequently map to the regions of repressive chromatin. This observation is consistent with the existence of extensive domains of repressive chromatin that replicate extremely late and have conserved gene order in the Drosophila genome. We suggest that such repressive chromatin domains correspond to a handful of regions that complete replication at the very end of S phase. We further demonstrate that the order of genes in these regions is rarely altered in evolution. Substantial proportion of such regions significantly coincide with large synteny blocks. This indicates that there are evolutionary mechanisms maintaining the integrity of these late-replicating chromatin domains. The synteny blocks corresponding to the extremely late-replicating regions in the D. melanogaster genome consistently display two-fold lower gene density across different Drosophila species.

  19. Development links psychological causes to evolutionary explanations.

    Science.gov (United States)

    Fedyk, Mark; Kushnir, Tamar

    2014-04-01

    Our conscious abilities are learned in environments that have evolved to support them. This insight provides an alternative way of framing Huang & Bargh's (H&B's) provocative hypothesis. To understand the conflict between unconscious goals and consciousness, we can study the emergence of conscious thought and control in childhood. These developmental processes are also central to the best available current evolutionary theories.

  20. Evolutionary Algorithms for Boolean Queries Optimization

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Snášel, Václav; Neruda, Roman; Owais, S.S.J.; Krömer, P.

    2006-01-01

    Roč. 3, č. 1 (2006), s. 15-20 ISSN 1790-0832 R&D Projects: GA AV ČR 1ET100300414 Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary algorithms * genetic algorithms * information retrieval * Boolean query Subject RIV: BA - General Mathematics

  1. Function Follows Performance in Evolutionary Computational Processing

    DEFF Research Database (Denmark)

    Pasold, Anke; Foged, Isak Worre

    2011-01-01

    As the title ‘Function Follows Performance in Evolutionary Computational Processing’ suggests, this paper explores the potentials of employing multiple design and evaluation criteria within one processing model in order to account for a number of performative parameters desired within varied...

  2. Evolutionary convergence and biologically embodied cognition

    NARCIS (Netherlands)

    Keijzer, Franciscus

    2017-01-01

    The study of evolutionary patterns of cognitive convergence would be greatly helped by a clear demarcation of cognition. Cognition is often used as an equivalent of mind, making it difficult to pin down empirically or to apply it confidently beyond the human condition. Recent developments in

  3. Indoor Thermal Comfort, an Evolutionary Biology Perspective

    Energy Technology Data Exchange (ETDEWEB)

    Stoops, John L.

    2006-04-15

    As is becoming increasingly clear, the human species evolvedin the East African savannah. Details of the precise evolutionary chainremain unresolved however it appears that the process lasted severalmillion years, culminating with the emergence of modern Homo sapiensroughly 200,000 years ago. Following that final evolutionary developmentmodern Homo sapiens relatively quickly populated the entire world.Clearly modern Homo sapiens is a successful, resourceful and adaptablespecies. In the developed societies, modern humans live an existence farremoved from our evolutionary ancestors. As we have learned over the lastcentury, this "new" lifestyle can often result in unintendedconsequences. Clearly, our modern access to food, shelter, transportationand healthcare has resulted in greatly expanded expected lifespan butthis new lifestyle can also result in the emergence of different kinds ofdiseases and health problems. The environment in modern buildings haslittle resemblance to the environment of the savannah. We strive tocreate environments with little temperature, air movement and lightvariation. Building occupants often express great dissatisfaction withthese modern created environments and a significant fraction even developsomething akin to allergies to specific buildings (sick buildingsyndrome). Are the indoor environments we are creating fundamentallyunhealthy -- when examined from an evolutionary perspective?

  4. On evolutionary ray-projection dynamics

    NARCIS (Netherlands)

    Joosten, Reinoud A.M.G.; Roorda, Berend

    2011-01-01

    We introduce the ray-projection dynamics in evolutionary game theory by employing a ray projection of the relative fitness (vector) function, i.e., a projection unto the unit simplex along a ray through the origin. Ray-projection dynamics are weakly compatible in the terminology of Friedman

  5. Evolutionary Biology: Its Value to Society

    Science.gov (United States)

    Carson, Hampton L.

    1972-01-01

    Cites examples of the contribution of basic research in evolutionary biology to the solution of problems facing society (1) by dispelling myths about human origins, the nature of the individual, and the nature of race (2) by providing basic data concerning the effects of overpopulation, the production of improved sources of food, resistance of…

  6. 2004 Structural, Function and Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  7. Static and evolutionary quantum public goods games

    Energy Technology Data Exchange (ETDEWEB)

    Liao Zeyang; Qin Gan; Hu Lingzhi; Li Songjian; Xu Nanyang [Hefei National Laboratory for Physical Science at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026 (China); Du Jiangfeng [Hefei National Laboratory for Physical Science at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026 (China); Fachbereich Physik, Universitaet Dortmund, 44221 Dortmund (Germany)], E-mail: djf@ustc.edu.cn

    2008-05-12

    We apply the continuous-variable quantization scheme to quantize public goods game and find that new pure strategy Nash equilibria emerge in the static case. Furthermore, in the evolutionary public goods game, entanglement can also contribute to the persistence of cooperation under various population structures without altruism, voluntary participation, and punishment.

  8. Special issue on evolutionary theories of religion

    DEFF Research Database (Denmark)

    McKay, Ryan

    Redaktionen af et temanummer i Journal for the Cognitive Science of Religion 4 (1) 2016: 1-90 med en række bidrag som respons til en targetartikel skrevet af Jonathan H. Turner med titlen "Using Neurosociology and Evolutionary Sociology to Explain the Origin and Evolution of Religions". Der er ko...

  9. On the Evolutionary Bases of Consumer Reinforcement

    Science.gov (United States)

    Nicholson, Michael; Xiao, Sarah Hong

    2010-01-01

    This article locates consumer behavior analysis within the modern neo-Darwinian synthesis, seeking to establish an interface between the ultimate-level theorizing of human evolutionary psychology and the proximate level of inquiry typically favored by operant learning theorists. Following an initial overview of the central tenets of neo-Darwinism,…

  10. The essence of Schumpeter's evolutionary economics

    DEFF Research Database (Denmark)

    Andersen, Esben Sloth

    Schumpeter’s unique type of evolutionary analysis can hardly be understood unless we recognise that he developed it in relation to a study of the strength and weaknesses of the Walrasian form of neoclassical economics. The paper demonstrates that Schumpeter’s major steps were already performed in...

  11. Food processing optimization using evolutionary algorithms | Enitan ...

    African Journals Online (AJOL)

    Evolutionary algorithms are widely used in single and multi-objective optimization. They are easy to use and provide solution(s) in one simulation run. They are used in food processing industries for decision making. Food processing presents constrained and unconstrained optimization problems. This paper reviews the ...

  12. BEAST: Bayesian evolutionary analysis by sampling trees

    Directory of Open Access Journals (Sweden)

    Drummond Alexei J

    2007-11-01

    Full Text Available Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

  13. The Microfoundations of Macroeconomics: An Evolutionary Perspective

    NARCIS (Netherlands)

    Bergh, van den Jeroen C.J.M.; Gowdy, John M.

    2000-01-01

    We consider the microfoundations controversy from the perspective ofeconomic evolution and show that the debate can benefit from lessons learned in evolutionary biology. Although the analogy between biology and economics has been noted before, it has rarely focused on clarifying the micro-macro

  14. Structured synthesis of MEMS using evolutionary approaches

    DEFF Research Database (Denmark)

    Fan, Zhun; Wang, Jiachuan; Achiche, Sofiane

    2008-01-01

    In this paper, we discuss the hierarchy that is involved in a typical MEMS design and how evolutionary approaches can be used to automate the hierarchical synthesis process for MEMS. The paper first introduces the flow of a structured MEMS design process and emphasizes that system-level lumped...

  15. Face Alignment Using Boosting and Evolutionary Search

    NARCIS (Netherlands)

    Zhang, Hua; Liu, Duanduan; Poel, Mannes; Nijholt, Antinus; Zha, H.; Taniguchi, R.-I.; Maybank, S.

    2010-01-01

    In this paper, we present a face alignment approach using granular features, boosting, and an evolutionary search algorithm. Active Appearance Models (AAM) integrate a shape-texture-combined morphable face model into an efficient fitting strategy, then Boosting Appearance Models (BAM) consider the

  16. Genetic variations and evolutionary relationships among radishes ...

    African Journals Online (AJOL)

    To determine the genetic diversity and evolutionary relationships among red radishes, 37 accessions with different flesh colors were analyzed in terms of the red pigment content, karyotypes, and simple sequence repeat markers. Red pigment content of red radish was 3.4 to 28.8% with an average of 15.62%. The karyotype ...

  17. The emerging empirics of evolutionary economic geography

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.

    2011-01-01

    Following last decade’s programmatic papers on Evolutionary Economic Geography, we report on recent empirical advances and how this empirical work can be positioned vis-a`-vis other strands of research in economic geography. First, we review studies on the path dependent nature of clustering, and

  18. The emerging empirics of evolutionary economic geography

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.

    2010-01-01

    Following last decade’s programmatic papers on Evolutionary Economic Geography, we report on recent empirical advances and how this empirical work can be positioned vis-à-vis other strands of research in economic geography. First, we review studies on the path dependent nature of clustering, and how

  19. The emerging empirics of evolutionary economic geography.

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.

    2011-01-01

    Following last decade’s programmatic papers on Evolutionary Economic Geography, we report on recent empirical advances and how this empirical work can be positioned vis-a`-vis other strands of research in economic geography. First, we review studies on the path dependent nature of clustering, and

  20. An Evolutionary Perspective on War Heroism

    NARCIS (Netherlands)

    Rusch, Hannes; Störmer, C.

    2015-01-01

    Humans are one of the most cooperative and altruistic species on the planet. At the same time, humans have a long history of violent and deadly intergroup conflicts or wars. Recently, contemporary evolutionary theorists have revived Charles Darwin’s idea that human in-group altruism and out-group

  1. Evolutionary heritage influences amazon tree ecology

    NARCIS (Netherlands)

    Souza, De Fernanda Coelho; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J.W.; Chave, Jerome; Galbraith, David R.; Gonzalez, Gabriela Lopez; Mendoza, Abel Monteagudo; Toby Pennington, R.; Poorter, Lourens; Arets, E.J.M.M.; Boot, Rene G.A.; Meer, van der Peter J.

    2016-01-01

    Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of

  2. A Clustal Alignment Improver Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene; Fogel, Gary B.; Krink, Thimo

    2002-01-01

    Multiple sequence alignment (MSA) is a crucial task in bioinformatics. In this paper we extended previous work with evolutionary algorithms (EA) by using MSA solutions obtained from the wellknown Clustal V algorithm as a candidate solution seed of the initial EA population. Our results clearly show...

  3. An evolutionary basis for pollination ecology

    NARCIS (Netherlands)

    Willemstein, S.C.

    1987-01-01

    In the introduction and chapter 2 the incentives and way of reasoning are given for the description of an evolutionary basis of pollination ecology. Starting from the until recently rather anecdotical character of the study of pollination ecology as a whole, and in the absence of large-scale

  4. EvolQG - An R package for evolutionary quantitative genetics [version 2; referees: 1 approved, 2 approved with reservations

    Directory of Open Access Journals (Sweden)

    Diogo Melo

    2016-06-01

    Full Text Available We present an open source package for performing evolutionary quantitative genetics analyses in the R environment for statistical computing. Evolutionary theory shows that evolution depends critically on the available variation in a given population. When dealing with many quantitative traits this variation is expressed in the form of a covariance matrix, particularly the additive genetic covariance matrix or sometimes the phenotypic matrix, when the genetic matrix is unavailable and there is evidence the phenotypic matrix is sufficiently similar to the genetic matrix. Given this mathematical representation of available variation, the EvolQG package provides functions for calculation of relevant evolutionary statistics; estimation of sampling error; corrections for this error; matrix comparison via correlations, distances and matrix decomposition; analysis of modularity patterns; and functions for testing evolutionary hypotheses on taxa diversification.

  5. Zero Temperature Hope Calculations

    International Nuclear Information System (INIS)

    Rozsnyai, B. F.

    2002-01-01

    The primary purpose of the HOPE code is to calculate opacities over a wide temperature and density range. It can also produce equation of state (EOS) data. Since the experimental data at the high temperature region are scarce, comparisons of predictions with the ample zero temperature data provide a valuable physics check of the code. In this report we show a selected few examples across the periodic table. Below we give a brief general information about the physics of the HOPE code. The HOPE code is an ''average atom'' (AA) Dirac-Slater self-consistent code. The AA label in the case of finite temperature means that the one-electron levels are populated according to the Fermi statistics, at zero temperature it means that the ''aufbau'' principle works, i.e. no a priory electronic configuration is set, although it can be done. As such, it is a one-particle model (any Hartree-Fock model is a one particle model). The code is an ''ion-sphere'' model, meaning that the atom under investigation is neutral within the ion-sphere radius. Furthermore, the boundary conditions for the bound states are also set at the ion-sphere radius, which distinguishes the code from the INFERNO, OPAL and STA codes. Once the self-consistent AA state is obtained, the code proceeds to generate many-electron configurations and proceeds to calculate photoabsorption in the ''detailed configuration accounting'' (DCA) scheme. However, this last feature is meaningless at zero temperature. There is one important feature in the HOPE code which should be noted; any self-consistent model is self-consistent in the space of the occupied orbitals. The unoccupied orbitals, where electrons are lifted via photoexcitation, are unphysical. The rigorous way to deal with that problem is to carry out complete self-consistent calculations both in the initial and final states connecting photoexcitations, an enormous computational task. The Amaldi correction is an attempt to address this problem by distorting the

  6. The four cornerstones of Evolutionary Toxicology.

    Science.gov (United States)

    Bickham, John W

    2011-05-01

    Evolutionary Toxicology is the study of the effects of chemical pollutants on the genetics of natural populations. Research in Evolutionary Toxicology uses experimental designs familiar to the ecotoxicologist with matched reference and contaminated sites and the selection of sentinel species. It uses the methods of molecular genetics and population genetics, and is based on the theories and concepts of evolutionary biology and conservation genetics. Although it is a relatively young field, interest is rapidly growing among ecotoxicologists and more and more field studies and even controlled laboratory experiments are appearing in the literature. A number of population genetic impacts have been observed in organisms exposed to pollutants which I refer to here as the four cornerstones of Evolutionary Toxicology. These include (1) genome-wide changes in genetic diversity, (2) changes in allelic or genotypic frequencies caused by contaminant-induced selection acting at survivorship loci, (3) changes in dispersal patterns or gene flow which alter the genetic relationships among populations, and (4) changes in allelic or genotypic frequencies caused by increased mutation rates. It is concluded that population genetic impacts of pollution exposure are emergent effects that are not necessarily predictable from the mode of toxicity of the pollutant. Thus, to attribute an effect to a particular contaminant requires a careful experimental design which includes selection of appropriate reference sites, detailed chemistry analyses of environmental samples and tissues, and the use of appropriate biomarkers to establish exposure and effect. This paper describes the field of Evolutionary Toxicology and discusses relevant field studies and their findings. © Springer Science+Business Media, LLC 2011

  7. Shaping communicative colour signals over evolutionary time

    Science.gov (United States)

    Oyola Morales, José R.; Vital-García, Cuauhcihuatl; Hews, Diana K.; Martins, Emília P.

    2016-01-01

    Many evolutionary forces can shape the evolution of communicative signals, and the long-term impact of each force may depend on relative timing and magnitude. We use a phylogenetic analysis to infer the history of blue belly patches of Sceloporus lizards, and a detailed spectrophotometric analysis of four species to explore the specific forces shaping evolutionary change. We find that the ancestor of Sceloporus had blue patches. We then focus on four species; the first evolutionary shift (captured by comparison of S. merriami and S. siniferus) represents an ancient loss of the belly patch by S. siniferus, and the second evolutionary shift, bounded by S. undulatus and S. virgatus, represents a more recent loss of blue belly patch by S. virgatus. Conspicuousness measurements suggest that the species with the recent loss (S. virgatus) is the least conspicuous. Results for two other species (S. siniferus and S. merriami) suggest that over longer periods of evolutionary time, new signal colours have arisen which minimize absolute contrast with the habitat while maximizing conspicuousness to a lizard receiver. Specifically, males of the species representing an ancient loss of blue patch (S. siniferus) are more conspicuous than are females in the UV, whereas S. merriami males have evolved a green element that makes their belly patches highly sexually dimorphic but no more conspicuous than the white bellies of S. merriami females. Thus, our results suggest that natural selection may act more immediately to reduce conspicuousness, whereas sexual selection may have a more complex impact on communicative signals through the introduction of new colours. PMID:28018661

  8. Why is economic geography not an evolutionary science? ; towards an evolutionary economic geography

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.

    2006-01-01

    The paper explains the commonalities and differences between neoclassical, institutional and evolutionary approaches that have been influential in economic geography during the last couple of decades. By separating the three approaches in terms of theoretical content and research methodology, wecan

  9. Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes.

    Science.gov (United States)

    Li, H; Liu, J; Xiong, L; Zhang, H; Zhou, H; Yin, H; Jing, W; Li, J; Shi, Q; Wang, Y; Liu, J; Nie, L

    2017-05-01

    The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea + Pelodiscus + Dogania + Nilssonia + Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108 million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous-Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India-Asia collision and opening of the Bering Strait, which

  10. Hierarchical classification with a competitive evolutionary neural tree.

    Science.gov (United States)

    Adams, R G.; Butchart, K; Davey, N

    1999-04-01

    A new, dynamic, tree structured network, the Competitive Evolutionary Neural Tree (CENT) is introduced. The network is able to provide a hierarchical classification of unlabelled data sets. The main advantage that the CENT offers over other hierarchical competitive networks is its ability to self determine the number, and structure, of the competitive nodes in the network, without the need for externally set parameters. The network produces stable classificatory structures by halting its growth using locally calculated heuristics. The results of network simulations are presented over a range of data sets, including Anderson's IRIS data set. The CENT network demonstrates its ability to produce a representative hierarchical structure to classify a broad range of data sets.

  11. Android malware detection based on evolutionary super-network

    Science.gov (United States)

    Yan, Haisheng; Peng, Lingling

    2018-04-01

    In the paper, an android malware detection method based on evolutionary super-network is proposed in order to improve the precision of android malware detection. Chi square statistics method is used for selecting characteristics on the basis of analyzing android authority. Boolean weighting is utilized for calculating characteristic weight. Processed characteristic vector is regarded as the system training set and test set; hyper edge alternative strategy is used for training super-network classification model, thereby classifying test set characteristic vectors, and it is compared with traditional classification algorithm. The results show that the detection method proposed in the paper is close to or better than traditional classification algorithm. The proposed method belongs to an effective Android malware detection means.

  12. Towards resolving the complete fern tree of life.

    Directory of Open Access Journals (Sweden)

    Samuli Lehtonen

    Full Text Available In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a 'supermatrix' approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.

  13. Evolutionary and Ecological Consequences of Interspecific Hybridization in Cladocerans

    NARCIS (Netherlands)

    Schwenk, K.; Spaak, P.

    1995-01-01

    The evolutionary process of interspecific hybridization in cladocerans is reviewed based on ecological and population genetic data. The evolutionary consequences of hybridization, biogeographic patterns and fitness comparisons are analyzed within the conceptual framework of theories on

  14. Evolutionary epistemology, rationality, and the sociology of knowledge

    CERN Document Server

    Bartley, W W

    1993-01-01

    This collection of essays in support of the theory of evolutionary epistemology includes articles by Karl Popper, Peter Munz and Gerhard Vollmer. This volume attempts to show how an evolutionary and non-justificational approach affects the sociology of knowledge.

  15. Evolutionary allometry of the thoracolumbar centra in felids and bovids.

    Science.gov (United States)

    Jones, Katrina E

    2015-07-01

    Mammals have evolved a remarkable range of body sizes, yet their overall body plan remains unaltered. One challenge of evolutionary biology is to understand the mechanisms by which this size diversity is achieved, and how the mechanical challenges associated with changing body size are overcome. Despite the importance of the axial skeleton in body support and locomotion, and much interest in the allometry of the appendicular skeleton, little is known about vertebral allometry outside primates. This study compares evolutionary allometry of the thoracolumbar centra in two families of quadrupedal running mammals: Felidae and Bovidae. I test the hypothesis that, as size increases, the thoracolumbar region will resist increasing loads by becoming a) craniocaudally shorter, and b) larger in cross-sectional area, particularly in the sagittal plane. Length, width, and height of the thoracolumbar centra of 23 felid and 34 bovid species were taken. Thoracic, prediaphragmatic, lumbar, and postdiaphragmatic lengths were calculated, and diameters were compared at three equivalent positions: the midthoracic, the diaphragmatic and the midlumbar vertebra. Allometric slopes were calculated using a reduced major axis regression, on both raw and independent contrasts data. Slopes and elevations were compared using an ANCOVA. As size increases the thoracolumbar centra become more robust, showing preferential reinforcement in the sagittal plane. There was less allometric shortening of the thoracic than the lumbar region, perhaps reflecting constraints due to its connection with the respiratory apparatus. The thoracic region was more robust in bovids than felids, whereas the lumbar region was longer and more robust in felids than bovids. Elongation of lumbar centra increases the outlever of sagittal bending at intervertebral joints, increasing the total pelvic displacement during dorsomobile running. Both locomotor specializations and functional regionalization of the axial skeleton

  16. Autonomous Evolution of Complete Piano Pieces and Performances

    DEFF Research Database (Denmark)

    Dahlstedt, Palle

    2007-01-01

    Evolutionary algorithms are used to evolve musical score material and corresponding performance data, in an autonomous process. In this way complete piano compositions are created and subsequently performed on a computer-controlled grand piano. The efficiency of the creative evolution depends...... gestures. This is combined with a set of automated formalized selection criteria based on experiences from human selection processes in a previous, interactive version of the same system, leading to surprisingly musical output and convincing performances. The system is also capable of rudimentary learning...

  17. What Is Sexual Orientation All About? Explaining an Evolutionary Paradox

    OpenAIRE

    Brad Bowins

    2015-01-01

    Numerous psychological, biological, and evolutionary theories have been proposed to explain sexual orientation. For a theory to be valid it must account for the evolutionary or Darwinian paradox of how homosexual behavior seemingly blocking evolutionary fitness could have evolved. Typically it is only evolutionary based theories that attempt to address this issue. All theories proposed to date have limitations, a major one being that they tend to be specific for male or female sexual orientat...

  18. Magnetic Field Calculator

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Magnetic Field Calculator will calculate the total magnetic field, including components (declination, inclination, horizontal intensity, northerly intensity,...

  19. The rating reliability calculator

    Directory of Open Access Journals (Sweden)

    Solomon David J

    2004-04-01

    Full Text Available Abstract Background Rating scales form an important means of gathering evaluation data. Since important decisions are often based on these evaluations, determining the reliability of rating data can be critical. Most commonly used methods of estimating reliability require a complete set of ratings i.e. every subject being rated must be rated by each judge. Over fifty years ago Ebel described an algorithm for estimating the reliability of ratings based on incomplete data. While his article has been widely cited over the years, software based on the algorithm is not readily available. This paper describes an easy-to-use Web-based utility for estimating the reliability of ratings based on incomplete data using Ebel's algorithm. Methods The program is available public use on our server and the source code is freely available under GNU General Public License. The utility is written in PHP, a common open source imbedded scripting language. The rating data can be entered in a convenient format on the user's personal computer that the program will upload to the server for calculating the reliability and other statistics describing the ratings. Results When the program is run it displays the reliability, number of subject rated, harmonic mean number of judges rating each subject, the mean and standard deviation of the averaged ratings per subject. The program also displays the mean, standard deviation and number of ratings for each subject rated. Additionally the program will estimate the reliability of an average of a number of ratings for each subject via the Spearman-Brown prophecy formula. Conclusion This simple web-based program provides a convenient means of estimating the reliability of rating data without the need to conduct special studies in order to provide complete rating data. I would welcome other researchers revising and enhancing the program.

  20. Completeness theorems in transport theory

    International Nuclear Information System (INIS)

    Zweifel, P.F.

    1984-01-01

    Ever since K. M.; Case's famous 1960 paper, transport theorists have been studying the questions of full- and half-range completeness for various transport type equations. The purpose of this note is to try to define exactly what is meant by completeness as it is needed, and used, in solving transport equations and to discuss some of the various techniques which have been, or might be, used to verify completeness. Attention is restricted to the question of full-range completeness. As a paradigm the generalized form of the transport equation first introduced by Beals is adopted

  1. Social traits, social networks and evolutionary biology.

    Science.gov (United States)

    Fisher, D N; McAdam, A G

    2017-12-01

    The social environment is both an important agent of selection for most organisms, and an emergent property of their interactions. As an aggregation of interactions among members of a population, the social environment is a product of many sets of relationships and so can be represented as a network or matrix. Social network analysis in animals has focused on why these networks possess the structure they do, and whether individuals' network traits, representing some aspect of their social phenotype, relate to their fitness. Meanwhile, quantitative geneticists have demonstrated that traits expressed in a social context can depend on the phenotypes and genotypes of interacting partners, leading to influences of the social environment on the traits and fitness of individuals and the evolutionary trajectories of populations. Therefore, both fields are investigating similar topics, yet have arrived at these points relatively independently. We review how these approaches are diverged, and yet how they retain clear parallelism and so strong potential for complementarity. This demonstrates that, despite separate bodies of theory, advances in one might inform the other. Techniques in network analysis for quantifying social phenotypes, and for identifying community structure, should be useful for those studying the relationship between individual behaviour and group-level phenotypes. Entering social association matrices into quantitative genetic models may also reduce bias in heritability estimates, and allow the estimation of the influence of social connectedness on trait expression. Current methods for measuring natural selection in a social context explicitly account for the fact that a trait is not necessarily the property of a single individual, something the network approaches have not yet considered when relating network metrics to individual fitness. Harnessing evolutionary models that consider traits affected by genes in other individuals (i.e. indirect genetic

  2. EVOLUTIONARY THEORY AND THE MARKET COMPETITION

    Directory of Open Access Journals (Sweden)

    SIRGHI Nicoleta

    2014-12-01

    Full Text Available Evolutionary theory study of processes that transform economy for firms, institutions, industries, employment, production, trade and growth within, through the actions of diverse agents from experience and interactions, using evolutionary methodology. Evolutionary theory analyses the unleashing of a process of technological and institutional innovation by generating and testing a diversity of ideas which discover and accumulate more survival value for the costs incurred than competing alternatives.This paper presents study the behavior of the firms on the market used the evolutionary theory.The paper is to present in full the developments that have led to the re-assessment of theories of firms starting from the criticism on Coase's theory based on the lack of testable hypotheses and on non-operative definition of transaction costs. In the literature in the field studies on firms were allotted a secondary place for a long period of time, to date the new theories of the firm hold a dominant place in the firms’ economic analysis. In an article, published in 1937, Ronald H. Coase identified the main sources of the cost of using the market mechanism. The firms theory represent a issue intensively studied in the literature in the field, regarding the survival, competitiveness and innovation of firm on the market. The research of Nelson and Winter, “An Evolutionary Theory of Economic Change” (1982 is the starting point for a modern literature in the field which considers the approach of the theory of the firm from an evolutionary perspective. Nelson and Winter have shown that the “orthodox” theory, is objectionable primarily by the fact that the hypothesis regarding profit maximization has a normative character and is not valid in any situation. Nelson and Winter reconsidered their microeconomic analysis showing that excessive attention should not be paid to market equilibrium but rather to dynamic processes resulting from irreversible

  3. Evolutionary Computing for Intelligent Power System Optimization and Control

    DEFF Research Database (Denmark)

    This new book focuses on how evolutionary computing techniques benefit engineering research and development tasks by converting practical problems of growing complexities into simple formulations, thus largely reducing development efforts. This book begins with an overview of the optimization the...... theory and modern evolutionary computing techniques, and goes on to cover specific applications of evolutionary computing to power system optimization and control problems....

  4. How to Identify and Interpret Evolutionary Tree Diagrams

    Science.gov (United States)

    Kong, Yi; Anderson, Trevor; Pelaez, Nancy

    2016-01-01

    Evolutionary trees are key tools for modern biology and are commonly portrayed in textbooks to promote learning about biological evolution. However, many people have difficulty in understanding what evolutionary trees are meant to portray. In fact, some ideas that current professional biologists depict with evolutionary trees are neither clearly…

  5. Gender Inequality in Interaction--An Evolutionary Account

    Science.gov (United States)

    Hopcroft, Rosemary L.

    2009-01-01

    In this article I argue that evolutionary theorizing can help sociologists and feminists better understand gender inequality. Evolutionary theory explains why control of the sexuality of young women is a priority across most human societies both past and present. Evolutionary psychology has extended our understanding of male violence against…

  6. Interpreting Evolutionary Diagrams: When Topology and Process Conflict

    Science.gov (United States)

    Catley, Kefyn M.; Novick, Laura R.; Shade, Courtney K.

    2010-01-01

    The authors argue that some diagrams in biology textbooks and the popular press presented as depicting evolutionary relationships suggest an inappropriate (anagenic) conception of evolutionary history. The goal of this research was to provide baseline data that begin to document how college students conceptualize the evolutionary relationships…

  7. Core principles of evolutionary medicine: A Delphi study.

    Science.gov (United States)

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further.

  8. Temporal knowledge and autobiographical memory: an evolutionary perspective

    OpenAIRE

    Skowronski, John J.; Sedikides, Constantine

    2007-01-01

    Section I: Philosophical issues 1. Evolutionary pyschology in the round , Robin Dunbar & Louise Barrett 2. The power of culture , Henry Plotkin 3. Evolution and psychology in philosophical perspective , Matteo Mameli 4. Niche construction, human behavioural ecology and evolutionary psychology , Kevin N Laland 5. Group level evolutionary processes , David Sloan Wilson Section II: The comparative Approach 6. Homologizing the mind , Drew Rendall, Hugh Nottman & John ...

  9. A Note on Evolutionary Algorithms and Its Applications

    Science.gov (United States)

    Bhargava, Shifali

    2013-01-01

    This paper introduces evolutionary algorithms with its applications in multi-objective optimization. Here elitist and non-elitist multiobjective evolutionary algorithms are discussed with their advantages and disadvantages. We also discuss constrained multiobjective evolutionary algorithms and their applications in various areas.

  10. Evolutionary medicine and chronic inflammatory state--known and new concepts in pathophysiology.

    Science.gov (United States)

    Straub, Rainer H

    2012-05-01

    During the last 10 years, a series of exciting observations has led to a new theory of pathophysiology using insights from evolutionary biology and neuroendocrine immunology to understand the sequelae of chronic inflammatory disease. According to this theory, disease sequelae can be explained based on redirection of energy-rich fuels from storage organs to the activated immune system. These disease sequelae are highly diverse and include the following: sickness behavior, anorexia, malnutrition, muscle wasting-cachexia, cachectic obesity, insulin resistance with hyperinsulinemia, dyslipidemia, increase of adipose tissue near inflamed tissue, alterations of steroid hormone axes, elevated sympathetic tone and local sympathetic nerve fiber loss, decreased parasympathetic tone, hypertension, inflammation-related anemia, and osteopenia. Since these disease sequelae can be found in many animal models of chronic inflammatory diseases with mammals (e.g., monkeys, mice, rats, rabbits, etc.), the evolutionary time line goes back at least 70 million years. While the initial version of this theory could explain prominent sequelae of chronic inflammatory disease, it did not however address two features important in the pathogenesis of immune-mediated diseases: the time point when an acute inflammatory disease becomes chronic, and the appearance of hypertension in chronic inflammation. To address these aspects more specifically, a new version of the theory has been developed. This version defines more precisely the moment of transition from acute inflammatory disease to chronic inflammatory disease as a time in which energy stores become empty (complete energy consumption). Depending on the amount of stored energy, this time point can be calculated to be 19-43 days. Second, the revised theory addresses the mechanisms of essential hypertension since, on the basis of water loss, acute inflammatory diseases can stimulate water retention using a positively selected water retention

  11. An Analytical Framework for Runtime of a Class of Continuous Evolutionary Algorithms

    Directory of Open Access Journals (Sweden)

    Yushan Zhang

    2015-01-01

    Full Text Available Although there have been many studies on the runtime of evolutionary algorithms in discrete optimization, relatively few theoretical results have been proposed on continuous optimization, such as evolutionary programming (EP. This paper proposes an analysis of the runtime of two EP algorithms based on Gaussian and Cauchy mutations, using an absorbing Markov chain. Given a constant variation, we calculate the runtime upper bound of special Gaussian mutation EP and Cauchy mutation EP. Our analysis reveals that the upper bounds are impacted by individual number, problem dimension number n, searching range, and the Lebesgue measure of the optimal neighborhood. Furthermore, we provide conditions whereby the average runtime of the considered EP can be no more than a polynomial of n. The condition is that the Lebesgue measure of the optimal neighborhood is larger than a combinatorial calculation of an exponential and the given polynomial of n.

  12. Latino College Completion: New York

    Science.gov (United States)

    Excelencia in Education (NJ1), 2012

    2012-01-01

    In 2009, Excelencia in Education launched the Ensuring America's Future initiative to inform, organize, and engage leaders in a tactical plan to increase Latino college completion. An executive summary of Latino College Completion in 50 states synthesizes information on 50 state factsheets and builds on the national benchmarking guide. Each…

  13. Latino College Completion: United States

    Science.gov (United States)

    Excelencia in Education (NJ1), 2012

    2012-01-01

    In 2009, Excelencia in Education launched the Ensuring America's Future initiative to inform, organize, and engage leaders in a tactical plan to increase Latino college completion. An executive summary of Latino College Completion in 50 states synthesizes information on 50 state factsheets and builds on the national benchmarking guide. Each…

  14. Latino College Completion: South Dakota

    Science.gov (United States)

    Excelencia in Education (NJ1), 2012

    2012-01-01

    In 2009, Excelencia in Education launched the Ensuring America's Future initiative to inform, organize, and engage leaders in a tactical plan to increase Latino college completion. An executive summary of Latino College Completion in 50 states synthesizes information on 50 state factsheets and builds on the national benchmarking guide. Each…

  15. Latino College Completion: North Dakota

    Science.gov (United States)

    Excelencia in Education (NJ1), 2012

    2012-01-01

    In 2009, Excelencia in Education launched the Ensuring America's Future initiative to inform, organize, and engage leaders in a tactical plan to increase Latino college completion. An executive summary of Latino College Completion in 50 states synthesizes information on 50 state factsheets and builds on the national benchmarking guide. Each…

  16. Latino College Completion: New Mexico

    Science.gov (United States)

    Excelencia in Education (NJ1), 2012

    2012-01-01

    In 2009, Excelencia in Education launched the Ensuring America's Future initiative to inform, organize, and engage leaders in a tactical plan to increase Latino college completion. An executive summary of Latino College Completion in 50 states synthesizes information on 50 state factsheets and builds on the national benchmarking guide. Each…

  17. Evolutionary computation techniques a comparative perspective

    CERN Document Server

    Cuevas, Erik; Oliva, Diego

    2017-01-01

    This book compares the performance of various evolutionary computation (EC) techniques when they are faced with complex optimization problems extracted from different engineering domains. Particularly focusing on recently developed algorithms, it is designed so that each chapter can be read independently. Several comparisons among EC techniques have been reported in the literature, however, they all suffer from one limitation: their conclusions are based on the performance of popular evolutionary approaches over a set of synthetic functions with exact solutions and well-known behaviors, without considering the application context or including recent developments. In each chapter, a complex engineering optimization problem is posed, and then a particular EC technique is presented as the best choice, according to its search characteristics. Lastly, a set of experiments is conducted in order to compare its performance to other popular EC methods.

  18. A brief introduction to continuous evolutionary optimization

    CERN Document Server

    Kramer, Oliver

    2014-01-01

    Practical optimization problems are often hard to solve, in particular when they are black boxes and no further information about the problem is available except via function evaluations. This work introduces a collection of heuristics and algorithms for black box optimization with evolutionary algorithms in continuous solution spaces. The book gives an introduction to evolution strategies and parameter control. Heuristic extensions are presented that allow optimization in constrained, multimodal, and multi-objective solution spaces. An adaptive penalty function is introduced for constrained optimization. Meta-models reduce the number of fitness and constraint function calls in expensive optimization problems. The hybridization of evolution strategies with local search allows fast optimization in solution spaces with many local optima. A selection operator based on reference lines in objective space is introduced to optimize multiple conflictive objectives. Evolutionary search is employed for learning kernel ...

  19. Synthesis of logic circuits with evolutionary algorithms

    Energy Technology Data Exchange (ETDEWEB)

    JONES,JAKE S.; DAVIDSON,GEORGE S.

    2000-01-26

    In the last decade there has been interest and research in the area of designing circuits with genetic algorithms, evolutionary algorithms, and genetic programming. However, the ability to design circuits of the size and complexity required by modern engineering design problems, simply by specifying required outputs for given inputs has as yet eluded researchers. This paper describes current research in the area of designing logic circuits using an evolutionary algorithm. The goal of the research is to improve the effectiveness of this method and make it a practical aid for design engineers. A novel method of implementing the algorithm is introduced, and results are presented for various multiprocessing systems. In addition to evolving standard arithmetic circuits, work in the area of evolving circuits that perform digital signal processing tasks is described.

  20. Evolutionary Games with Randomly Changing Payoff Matrices

    Science.gov (United States)

    Yakushkina, Tatiana; Saakian, David B.; Bratus, Alexander; Hu, Chin-Kun

    2015-06-01

    Evolutionary games are used in various fields stretching from economics to biology. In most of these games a constant payoff matrix is assumed, although some works also consider dynamic payoff matrices. In this article we assume a possibility of switching the system between two regimes with different sets of payoff matrices. Potentially such a model can qualitatively describe the development of bacterial or cancer cells with a mutator gene present. A finite population evolutionary game is studied. The model describes the simplest version of annealed disorder in the payoff matrix and is exactly solvable at the large population limit. We analyze the dynamics of the model, and derive the equations for both the maximum and the variance of the distribution using the Hamilton-Jacobi equation formalism.

  1. Is Exercise Really Medicine? An Evolutionary Perspective.

    Science.gov (United States)

    Lieberman, Daniel E

    2015-01-01

    An evolutionary perspective helps evaluate the extent to which exercise is medicine and to explain the exercise paradox: why people tend to avoid exercise despite its benefits. Many lines of evidence indicate that humans evolved to be adapted for regular, moderate amounts of endurance physical activity into late age. However, because energy from food was limited, humans also were selected to avoid unnecessary exertion, and most anatomical and physiological systems evolved to require stimuli from physical activity to adjust capacity to demand. Consequently, selection never operated to cope with the long-term effects of chronic inactivity. However, because all adaptations involve trade-offs, there is no evolutionary-determined dose or type of physical activity that will optimize health. Furthermore, because humans evolved to be active for play or necessity, efforts to promote exercise will require altering environments in ways that nudge or even compel people to be active and to make exercise fun.

  2. Applying evolutionary biology to address global challenges

    Science.gov (United States)

    Carroll, Scott P.; Jørgensen, Peter Søgaard; Kinnison, Michael T.; Bergstrom, Carl T.; Denison, R. Ford; Gluckman, Peter; Smith, Thomas B.; Strauss, Sharon Y.; Tabashnik, Bruce E.

    2014-01-01

    Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens and pests that evolve too quickly, and the second from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This review highlights both progress and gaps in genetic, developmental and environmental manipulations across the life sciences that either target the rate and direction of evolution, or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development. PMID:25213376

  3. An evolutionary approach to financial history.

    Science.gov (United States)

    Ferguson, N

    2009-01-01

    Financial history is not conventionally thought of in evolutionary terms, but it should be. Traditional ways of thinking about finance, dating back to Hilferding, emphasize the importance of concentration and economies of scale. But these approaches overlook the rich "biodiversity" that characterizes the financial world. They also overlook the role of natural selection. To be sure, natural selection in the financial world is not exactly analogous to the processes first described by Darwin and elaborated on by modern biologists. There is conscious adaptation as well as random mutation. Moreover, there is something resembling "intelligent design" in finance, whereby regulators and legislators act in a quasidivine capacity, putting dinosaurs on life support. The danger is that such interventions in the natural processes of the market may ultimately distort the evolutionary process, by getting in the way of Schumpeter's "creative destruction."

  4. Evolutionary ethics from Darwin to Moore.

    Science.gov (United States)

    Allhoff, Fritz

    2003-01-01

    Evolutionary ethics has a long history, dating all the way back to Charles Darwin. Almost immediately after the publication of the Origin, an immense interest arose in the moral implications of Darwinism and whether the truth of Darwinism would undermine traditional ethics. Though the biological thesis was certainly exciting, nobody suspected that the impact of the Origin would be confined to the scientific arena. As one historian wrote, 'whether or not ancient populations of armadillos were transformed into the species that currently inhabit the new world was certainly a topic about which zoologists could disagree. But it was in discussing the broader implications of the theory...that tempers flared and statements were made which could transform what otherwise would have been a quiet scholarly meeting into a social scandal' (Farber 1994, 22). Some resistance to the biological thesis of Darwinism sprung from the thought that it was incompatible with traditional morality and, since one of them had to go, many thought that Darwinism should be rejected. However, some people did realize that a secular ethics was possible so, even if Darwinism did undermine traditional religious beliefs, it need not have any effects on moral thought. Before I begin my discussion of evolutionary ethics from Darwin to Moore, I would like to make some more general remarks about its development. There are three key events during this history of evolutionary ethics. First, Charles Darwin published On the Origin of the Species (Darwin 1859). Since one did not have a fully developed theory of evolution until 1859, there exists little work on evolutionary ethics until then. Shortly thereafter, Herbert Spencer (1898) penned the first systematic theory of evolutionary ethics, which was promptly attacked by T.H. Huxley (Huxley 1894). Second, at about the turn of the century, moral philosophers entered the fray and attempted to demonstrate logical errors in Spencer's work; such errors were alluded

  5. The Asian Future of Evolutionary Psychology

    Directory of Open Access Journals (Sweden)

    Geoffrey Miller

    2006-01-01

    Full Text Available Asia's population, wealth, cognitive capital, and scientific influence are growing quickly. Reasonable demographic, economic, and psychometric projections suggest that by the mid-21st century, most of the world's psychology will be done in Asia, by Asians. Even if evolutionary psychology wins the battles for academic respectability in the United States and European Union, if it ignores the rise of Asian psychology, it will fail to have any serious, long-term, global influence in the behavioral sciences after the current generations of researchers are dead. I outline a ‘marketing strategy’ for promoting evolutionary psychology in the current Asian powers (Japan, South Korea, Taiwan, Hong Kong, Singapore, the new Asian mega-powers (China, India, and other developing Asia countries (e.g. Vietnam, Thailand, Malaysia, in a way that takes advantage of Asia's relative secularism, freedom from political correctness, sex-positive social attitudes, and intellectual traditions of Hinduism, Buddhism, and Confucianism.

  6. Evolution of microbes and viruses: A paradigm shift in evolutionary biology?

    Directory of Open Access Journals (Sweden)

    Eugene V. Koonin

    2012-09-01

    Full Text Available When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain ‘ribosomal Tree of Life’ that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: i pervasive horizontal gene transfer (HGT, in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment of the Tree of Life concept, ii Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and iii evolution of evolvability, i.e. dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary

  7. Codon usage is associated with the evolutionary age of genes in metazoan genomes

    Directory of Open Access Journals (Sweden)

    Linial Nathan

    2009-12-01

    Full Text Available Abstract Background Codon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes. Results We assign an evolutionary age to a gene based on the relative positions of its identified homologues in a standard phylogenetic tree. This yields a classification of all genes in a genome to several evolutionary age classes. The present study starts from the observation that each age class of genes has a unique codon usage and proceeds to provide a quantitative analysis of the codon usage in these classes. This observation is made for the genomes of Homo sapiens, Mus musculus, and Drosophila melanogaster. It is even more remarkable that the differences between codon usages in different age groups exhibit similar and consistent behavior in various organisms. While we find that GC content and gene length are also associated with the evolutionary age of genes, they can provide only a partial explanation for the observed codon usage. Conclusion While factors such as GC content, mutational bias, and selection shape the codon usage in a genome, the evolutionary history of an organism over hundreds of millions of years is an overlooked property that is strongly linked to GC content, protein length, and, even more significantly, to the codon usage of metazoan genomes.

  8. Structure completion for facade layouts

    KAUST Repository

    Fan, Lubin

    2014-11-18

    (Figure Presented) We present a method to complete missing structures in facade layouts. Starting from an abstraction of the partially observed layout as a set of shapes, we can propose one or multiple possible completed layouts. Structure completion with large missing parts is an ill-posed problem. Therefore, we combine two sources of information to derive our solution: the observed shapes and a database of complete layouts. The problem is also very difficult, because shape positions and attributes have to be estimated jointly. Our proposed solution is to break the problem into two components: a statistical model to evaluate layouts and a planning algorithm to generate candidate layouts. This ensures that the completed result is consistent with the observation and the layouts in the database.

  9. Is evolutionary psychology a metatheory for psychology? A discussion of four major issues in psychology from an evolutionary developmental perspective

    NARCIS (Netherlands)

    Ploeger, A.; van der Maas, H.L.J.; Raijmakers, M.E.J.

    2008-01-01

    Evolutionary psychology has been proposed as a metatheoretical framework for psychology. We argue that evolutionary psychology should be expanded if it is to offer new insights regarding the major issues in psychology. Evolutionary developmental biology can provide valuable new insights into issues

  10. Massively parallel evolutionary computation on GPGPUs

    CERN Document Server

    Tsutsui, Shigeyoshi

    2013-01-01

    Evolutionary algorithms (EAs) are metaheuristics that learn from natural collective behavior and are applied to solve optimization problems in domains such as scheduling, engineering, bioinformatics, and finance. Such applications demand acceptable solutions with high-speed execution using finite computational resources. Therefore, there have been many attempts to develop platforms for running parallel EAs using multicore machines, massively parallel cluster machines, or grid computing environments. Recent advances in general-purpose computing on graphics processing units (GPGPU) have opened u

  11. Probability Weighting as Evolutionary Second-best

    OpenAIRE

    Herold, Florian; Netzer, Nick

    2011-01-01

    The economic concept of the second-best involves the idea that multiple simultaneous deviations from a hypothetical first-best optimum may be optimal once the first-best itself can no longer be achieved, since one distortion may partially compensate for another. Within an evolutionary framework, we translate this concept to behavior under uncertainty. We argue that the two main components of prospect theory, the value function and the probability weighting function, are complements in the sec...

  12. Conversion Rate Optimization through Evolutionary Computation

    OpenAIRE

    Miikkulainen, Risto; Iscoe, Neil; Shagrin, Aaron; Cordell, Ron; Nazari, Sam; Schoolland, Cory; Brundage, Myles; Epstein, Jonathan; Dean, Randy; Lamba, Gurmeet

    2017-01-01

    Conversion optimization means designing a web interface so that as many users as possible take a desired action on it, such as register or purchase. Such design is usually done by hand, testing one change at a time through A/B testing, or a limited number of combinations through multivariate testing, making it possible to evaluate only a small fraction of designs in a vast design space. This paper describes Sentient Ascend, an automatic conversion optimization system that uses evolutionary op...

  13. Evolutionary dynamics on infinite strategy spaces

    OpenAIRE

    Oechssler, Jörg; Riedel, Frank

    1998-01-01

    The study of evolutionary dynamics was so far mainly restricted to finite strategy spaces. In this paper we show that this unsatisfying restriction is unnecessary. We specify a simple condition under which the continuous time replicator dynamics are well defined for the case of infinite strategy spaces. Furthermore, we provide new conditions for the stability of rest points and show that even strict equilibria may be unstable. Finally, we apply this general theory to a number of applications ...

  14. The Evolutionary Psychology of Envy and Jealousy

    Science.gov (United States)

    Ramachandran, Vilayanur S.; Jalal, Baland

    2017-01-01

    The old dogma has always been that the most complex aspects of human emotions are driven by culture; Germans and English are thought to be straight-laced whereas Italians and Indians are effusive. Yet in the last two decades there has been a growing realization that even though culture plays a major role in the final expression of human nature, there must be a basic scaffolding specified by genes. While this is recognized to be true for simple emotions like anger, fear, and joy, the relevance of evolutionary arguments for more complex nuances of emotion have been inadequately explored. In this paper, we consider envy or jealousy as an example; the feeling evoked when someone is better off than you. Our approach is broadly consistent with traditional evolutionary psychology (EP) approaches, but takes it further by exploring the complexity and functional logic of the emotion – and the precise social triggers that elicit them – by using deliberately farfetched, and contrived “thought experiments” that the subject is asked to participate in. When common sense (e.g., we should be jealous of Bill Gates – not of our slightly richer neighbor) appears to contradict observed behavior (i.e., we are more envious of our neighbor) the paradox can often be resolved by evolutionary considerations which h predict the latter. Many – but not all – EP approaches fail because evolution and common sense do not make contradictory predictions. Finally, we briefly raise the possibility that gaining deeper insight into the evolutionary origins of certain undesirable emotions or behaviors can help shake them off, and may therefore have therapeutic utility. Such an approach would complement current therapies (such as cognitive behavior therapies, psychoanalysis, psychopharmacologies, and hypnotherapy), rather than negate them. PMID:28970815

  15. Evolutionary modelling of transitions to sustainable development

    International Nuclear Information System (INIS)

    Safarzynska, K.

    2010-01-01

    This thesis has examined how evolutionary economics can contribute to modelling the micromechanisms that underlie transitions towards sustainable development. In general, transitions are fundamental or structural system changes. They involve, or even require, escaping lock-in of dominant, environmentally unsustainable technologies, introducing major technical or social innovations, and changing prevailing social practices and structures. Due to the complexity of socioeconomic interactions, it is not always possible to identify, and thus target with appropriate policy instruments, causes of specific unsustainable patterns of behaviour. Formal modelling exercises can help improve our understanding of the interaction of various transition mechanisms which are otherwise difficult to grasp intuitively. They allow exploring effects of policy interventions in complex systems. However, existing models of transitions focus on social phenomena and seldom address economic problems. As opposed, mainstream (neoclassical) economic models of technological change do not account for social interactions, and changing heterogeneity of users and their perspectives - even though all of these can influence the direction of innovations and patterns of socio-technological development. Evolutionary economics offers an approach that goes beyond neoclassical economics - in the sense of employing more realistic assumptions regarding the behaviour and heterogeneity of consumers, firms and investors. It can complement current transition models by providing them with a better understanding of associated economic dynamics. In this thesis, formal models were proposed to illustrate the usefulness of a range of evolutionary-economic techniques for modelling transitions. Modelling exercises aimed to explain the core properties of socio-economic systems, such as lock-in, path-dependence, coevolution, group selection and recombinant innovation. The studies collected in this dissertation illustrate that

  16. Evolutionary problems in non-reflexive spaces

    Czech Academy of Sciences Publication Activity Database

    Kružík, Martin; Zimmer, J.

    2010-01-01

    Roč. 16, č. 1 (2010), s. 1-22 ISSN 1262-3377 R&D Projects: GA AV ČR IAA1075402 Institutional research plan: CEZ:AV0Z10750506 Keywords : concentrations * energetic solution * energies with linear growth * oscillations * relaxation Subject RIV: BA - General Mathematics Impact factor: 1.084, year: 2009 http://library.utia.cas.cz/separaty/2008/MTR/kruzik-evolutionary problems in non-reflexive spaces.pdf

  17. Compassion: An Evolutionary Analysis and Empirical Review

    OpenAIRE

    Goetz, Jennifer L.; Keltner, Dacher; Simon-Thomas, Emiliana

    2010-01-01

    What is compassion? And how did it evolve? In this review, we integrate three evolutionary arguments that converge on the hypothesis that compassion evolved as a distinct affective experience whose primary function is to facilitate cooperation and protection of the weak and those who suffer. Our empirical review reveals compassion to have distinct appraisal processes attuned to undeserved suffering, distinct signaling behavior related to caregiving patterns of touch, posture, and vocalization...

  18. Prospective Algorithms for Quantum Evolutionary Computation

    OpenAIRE

    Sofge, Donald A.

    2008-01-01

    This effort examines the intersection of the emerging field of quantum computing and the more established field of evolutionary computation. The goal is to understand what benefits quantum computing might offer to computational intelligence and how computational intelligence paradigms might be implemented as quantum programs to be run on a future quantum computer. We critically examine proposed algorithms and methods for implementing computational intelligence paradigms, primarily focused on ...

  19. Software testing for evolutionary iterative rapid prototyping

    OpenAIRE

    Davis, Edward V., Jr.

    1990-01-01

    Approved for public release; distribution unlimited. Rapid prototyping is emerging as a promising software development paradigm. It provides a systematic and automatable means of developing a software system under circumstances where initial requirements are not well known or where requirements change frequently during development. To provide high software quality assurance requires sufficient software testing. The unique nature of evolutionary iterative prototyping is not well-suited for ...

  20. Evolutionary Algorithm for Optimal Vaccination Scheme

    International Nuclear Information System (INIS)

    Parousis-Orthodoxou, K J; Vlachos, D S

    2014-01-01

    The following work uses the dynamic capabilities of an evolutionary algorithm in order to obtain an optimal immunization strategy in a user specified network. The produced algorithm uses a basic genetic algorithm with crossover and mutation techniques, in order to locate certain nodes in the inputted network. These nodes will be immunized in an SIR epidemic spreading process, and the performance of each immunization scheme, will be evaluated by the level of containment that provides for the spreading of the disease

  1. The Evolutionary Psychology of Envy and Jealousy

    Directory of Open Access Journals (Sweden)

    Vilayanur S. Ramachandran

    2017-09-01

    Full Text Available The old dogma has always been that the most complex aspects of human emotions are driven by culture; Germans and English are thought to be straight-laced whereas Italians and Indians are effusive. Yet in the last two decades there has been a growing realization that even though culture plays a major role in the final expression of human nature, there must be a basic scaffolding specified by genes. While this is recognized to be true for simple emotions like anger, fear, and joy, the relevance of evolutionary arguments for more complex nuances of emotion have been inadequately explored. In this paper, we consider envy or jealousy as an example; the feeling evoked when someone is better off than you. Our approach is broadly consistent with traditional evolutionary psychology (EP approaches, but takes it further by exploring the complexity and functional logic of the emotion – and the precise social triggers that elicit them – by using deliberately farfetched, and contrived “thought experiments” that the subject is asked to participate in. When common sense (e.g., we should be jealous of Bill Gates – not of our slightly richer neighbor appears to contradict observed behavior (i.e., we are more envious of our neighbor the paradox can often be resolved by evolutionary considerations which h predict the latter. Many – but not all – EP approaches fail because evolution and common sense do not make contradictory predictions. Finally, we briefly raise the possibility that gaining deeper insight into the evolutionary origins of certain undesirable emotions or behaviors can help shake them off, and may therefore have therapeutic utility. Such an approach would complement current therapies (such as cognitive behavior therapies, psychoanalysis, psychopharmacologies, and hypnotherapy, rather than negate them.

  2. EVOLUTIONARY ASPECTS OF LOVE AND EMPATHY

    OpenAIRE

    Allott, Robin

    1992-01-01

    Love has always been a central preoccupation in individual human lives, but there has been little consideration of it by psychologists or other scientists and little attempt to explain it as an evolutionary phenomenon. There are various possible behavioral precursors of love: animal "love", empathy, group feeling, sexuality, the mother/infant bond. The principal candidates are sexuality and the mother/infant bond. Sexuality has been favored as an origin by those few writers who have discussed...

  3. Evolutionary Economics and Moral Relativism - Some Thoughts

    OpenAIRE

    Binder, Martin

    2006-01-01

    Doubts about the decidability of moral questions have often been used as an excuse for economists to eschew any normative propositions. Evolutionary economics, still lacking a well-developed normative branch, gives rise to a form of descriptive moral relativism. This paper wants to explore the consequences of adopting a form of meta-ethical and normative moral relativism as well. It develops a normative position called ‘naturalistic relativism’, which is a naturalistically reconstructed neo-p...

  4. An evolutionary behaviorist perspective on orgasm

    Science.gov (United States)

    Fleischman, Diana S.

    2016-01-01

    Evolutionary explanations for sexual behavior and orgasm most often posit facilitating reproduction as the primary function (i.e. greater rate of fertilization). Other reproductive benefits of sexual pleasure and orgasm such as improved bonding of parents have also been discussed but not thoroughly. Although sex is known to be highly reinforcing, behaviorist principles are rarely invoked alongside evolutionary psychology in order to account for human sexual and social behavior. In this paper, I will argue that intense sexual pleasure, especially orgasm, can be understood as a primary reinforcer shaped by evolution to reinforce behavior that facilitates reproductive success (i.e. conception through copulation). Next, I will describe an evolutionary account of social shaping. In particular, I will focus on how humans evolved to use orgasm and sexual arousal to shape the social behavior and emotional states of others through both classical and operant conditioning and through both reproductive and non-reproductive forms of sexual behavior. Finally, I will describe how orgasm is a signal of sensitivity to reinforcement that is itself reinforcing. PMID:27799083

  5. Investigating intertemporal choice through experimental evolutionary robotics.

    Science.gov (United States)

    Paglieri, Fabio; Parisi, Domenico; Patacchiola, Massimiliano; Petrosino, Giancarlo

    2015-06-01

    In intertemporal choices, subjects face a trade-off between value and delay: achieving the most valuable outcome requires a longer time, whereas the immediately available option is objectively poorer. Intertemporal choices are ubiquitous, and comparative studies reveal commonalities and differences across species: all species devalue future rewards as a function of delay (delay aversion), yet there is a lot of inter-specific variance in how rapidly such devaluation occurs. These differences are often interpreted in terms of ecological rationality, as depending on environmental factors (e.g., feeding ecology) and the physiological and morphological constraints of different species (e.g., metabolic rate). Evolutionary hypotheses, however, are hard to verify in vivo, since it is difficult to observe precisely enough real environments, not to mention ancestral ones. In this paper, we discuss the viability of an approach based on evolutionary robotics: in Study 1, we evolve robots without a metabolism in five different ecologies; in Study 2, we evolve metabolic robots (i.e., robots that consume energy over time) in three different ecologies. The intertemporal choices of the robots are analyzed both in their ecology and under laboratory conditions. Results confirm the generality of delay aversion and the usefulness of studying intertemporal choice through experimental evolutionary robotics. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. On the Existence of Evolutionary Learning Equilibriums

    Directory of Open Access Journals (Sweden)

    Masudul Alam Choudhury

    2011-12-01

    Full Text Available The usual kinds of Fixed-Point Theorems formalized on the existence of competitive equilibrium that explain much of economic theory at the core of economics can operate only on bounded and closed sets with convex mappings. But these conditions are hardly true of the real world of economic and financial complexities and perturbations. The category of learning sets explained by continuous fields of interactive, integrative and evolutionary behaviour caused by dynamic preferences at the individual and institutional and social levels cannot maintain the assumption of closed, bounded and convex sets. Thus learning sets and multi-system inter-temporal relations explained by pervasive complementarities and  participation between variables and entities, and evolution by learning, have evolutionary equilibriums. Such a study requires a new methodological approach. This paper formalizes such a methodology for evolutionary equilibriums in learning spaces. It briefly points out the universality of learning equilibriums in all mathematical structures. For a particular case though, the inter-systemic interdependence between sustainable development and ethics and economics in the specific understanding of learning domain is pointed out.

  7. Cryptic Genetic Variation in Evolutionary Developmental Genetics

    Directory of Open Access Journals (Sweden)

    Annalise B. Paaby

    2016-06-01

    Full Text Available Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits.

  8. Evolutionary plant physiology: Charles Darwin's forgotten synthesis

    Science.gov (United States)

    Kutschera, Ulrich; Niklas, Karl J.

    2009-11-01

    Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin’s son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin’s work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.

  9. Helminths and Cancers From the Evolutionary Perspective.

    Science.gov (United States)

    Scholte, Larissa L S; Pascoal-Xavier, Marcelo A; Nahum, Laila A

    2018-01-01

    Helminths include free-living and parasitic Platyhelminthes and Nematoda which infect millions of people worldwide. Some Platyhelminthes species of blood flukes ( Schistosoma haematobium, Schistosoma japonicum , and Schistosoma mansoni ) and liver flukes ( Clonorchis sinensis and Opisthorchis viverrini ) are known to be involved in human cancers. Other helminths are likely to be carcinogenic. Our main goals are to summarize the current knowledge of human cancers caused by Platyhelminthes, point out some helminth and human biomarkers identified so far, and highlight the potential contributions of phylogenetics and molecular evolution to cancer research. Human cancers caused by helminth infection include cholangiocarcinoma, colorectal hepatocellular carcinoma, squamous cell carcinoma, and urinary bladder cancer. Chronic inflammation is proposed as a common pathway for cancer initiation and development. Furthermore, different bacteria present in gastric, colorectal, and urogenital microbiomes might be responsible for enlarging inflammatory and fibrotic responses in cancers. Studies have suggested that different biomarkers are involved in helminth infection and human cancer development; although, the detailed mechanisms remain under debate. Different helminth proteins have been studied by different approaches. However, their evolutionary relationships remain unsolved. Here, we illustrate the strengths of homology identification and function prediction of uncharacterized proteins from genome sequencing projects based on an evolutionary framework. Together, these approaches may help identifying new biomarkers for disease diagnostics and intervention measures. This work has potential applications in the field of phylomedicine (evolutionary medicine) and may contribute to parasite and cancer research.

  10. Evolutionary game theory: cells as players.

    Science.gov (United States)

    Hummert, Sabine; Bohl, Katrin; Basanta, David; Deutsch, Andreas; Werner, Sarah; Theissen, Günter; Schroeter, Anja; Schuster, Stefan

    2014-12-01

    In two papers we review game theory applications in biology below the level of cognitive living beings. It can be seen that evolution and natural selection replace the rationality of the actors appropriately. Even in these micro worlds, competing situations and cooperative relationships can be found and modeled by evolutionary game theory. Also those units of the lowest levels of life show different strategies for different environmental situations or different partners. We give a wide overview of evolutionary game theory applications to microscopic units. In this first review situations on the cellular level are tackled. In particular metabolic problems are discussed, such as ATP-producing pathways, secretion of public goods and cross-feeding. Further topics are cyclic competition among more than two partners, intra- and inter-cellular signalling, the struggle between pathogens and the immune system, and the interactions of cancer cells. Moreover, we introduce the theoretical basics to encourage scientists to investigate problems in cell biology and molecular biology by evolutionary game theory.

  11. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Science.gov (United States)

    Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

    2017-01-01

    For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683

  12. Evolutionary hotspots in the Mojave Desert

    Science.gov (United States)

    Vandergast, Amy G.; Inman, Richard D.; Barr, Kelly R.; Nussear, Kenneth E.; Esque, Todd C.; Hathaway, Stacie A.; Wood, Dustin A.; Medica, Philip A.; Breinholt, Jesse W.; Stephen, Catherine L.; Gottscho, Andrew D.; Marks, Sharyn B.; Jennings, W. Bryan; Fisher, Robert N.

    2013-01-01

    Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

  13. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Graziele Pereira Oliveira

    2017-01-01

    Full Text Available For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV, raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’ that could be evolved gradually by nucleotides’ gain and loss and point mutations.

  14. Helminths and Cancers From the Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Larissa L. S. Scholte

    2018-04-01

    Full Text Available Helminths include free-living and parasitic Platyhelminthes and Nematoda which infect millions of people worldwide. Some Platyhelminthes species of blood flukes (Schistosoma haematobium, Schistosoma japonicum, and Schistosoma mansoni and liver flukes (Clonorchis sinensis and Opisthorchis viverrini are known to be involved in human cancers. Other helminths are likely to be carcinogenic. Our main goals are to summarize the current knowledge of human cancers caused by Platyhelminthes, point out some helminth and human biomarkers identified so far, and highlight the potential contributions of phylogenetics and molecular evolution to cancer research. Human cancers caused by helminth infection include cholangiocarcinoma, colorectal hepatocellular carcinoma, squamous cell carcinoma, and urinary bladder cancer. Chronic inflammation is proposed as a common pathway for cancer initiation and development. Furthermore, different bacteria present in gastric, colorectal, and urogenital microbiomes might be responsible for enlarging inflammatory and fibrotic responses in cancers. Studies have suggested that different biomarkers are involved in helminth infection and human cancer development; although, the detailed mechanisms remain under debate. Different helminth proteins have been studied by different approaches. However, their evolutionary relationships remain unsolved. Here, we illustrate the strengths of homology identification and function prediction of uncharacterized proteins from genome sequencing projects based on an evolutionary framework. Together, these approaches may help identifying new biomarkers for disease diagnostics and intervention measures. This work has potential applications in the field of phylomedicine (evolutionary medicine and may contribute to parasite and cancer research.

  15. Ecological interactions drive evolutionary loss of traits.

    Science.gov (United States)

    Ellers, Jacintha; Kiers, E Toby; Currie, Cameron R; McDonald, Bradon R; Visser, Bertanne

    2012-10-01

    Loss of traits can dramatically alter the fate of species. Evidence is rapidly accumulating that the prevalence of trait loss is grossly underestimated. New findings demonstrate that traits can be lost without affecting the external phenotype, provided the lost function is compensated for by species interactions. This is important because trait loss can tighten the ecological relationship between partners, affecting the maintenance of species interactions. Here, we develop a new perspective on so-called `compensated trait loss' and how this type of trait loss may affect the evolutionary dynamics between interacting organisms. We argue that: (1) the frequency of compensated trait loss is currently underestimated because it can go unnoticed as long as ecological interactions are maintained; (2) by analysing known cases of trait loss, specific factors promoting compensated trait loss can be identified and (3) genomic sequencing is a key way forwards in detecting compensated trait loss. We present a comprehensive literature survey showing that compensated trait loss is taxonomically widespread, can involve essential traits, and often occurs as replicated evolutionary events. Despite its hidden nature, compensated trait loss is important in directing evolutionary dynamics of ecological relationships and has the potential to change facultative ecological interactions into obligatory ones. © 2012 Blackwell Publishing Ltd/CNRS.

  16. Multiscale structure in eco-evolutionary dynamics

    Science.gov (United States)

    Stacey, Blake C.

    In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

  17. On the evolutionary origins of equity.

    Directory of Open Access Journals (Sweden)

    Stéphane Debove

    Full Text Available Equity, defined as reward according to contribution, is considered a central aspect of human fairness in both philosophical debates and scientific research. Despite large amounts of research on the evolutionary origins of fairness, the evolutionary rationale behind equity is still unknown. Here, we investigate how equity can be understood in the context of the cooperative environment in which humans evolved. We model a population of individuals who cooperate to produce and divide a resource, and choose their cooperative partners based on how they are willing to divide the resource. Agent-based simulations, an analytical model, and extended simulations using neural networks provide converging evidence that equity is the best evolutionary strategy in such an environment: individuals maximize their fitness by dividing benefits in proportion to their own and their partners' relative contribution. The need to be chosen as a cooperative partner thus creates a selection pressure strong enough to explain the evolution of preferences for equity. We discuss the limitations of our model, the discrepancies between its predictions and empirical data, and how interindividual and intercultural variability fit within this framework.

  18. Diabetes and Obesity—An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Sylvia Kirchengast

    2017-01-01

    Full Text Available Obesity and type II diabetes belong to the most serious public health challenges of the 21st century. Initially both diseases were typical of affluent societies. Currently both conditions however are increasingly found in low and middle income countries. In future obesity and diabetes are expected to reach epidemic proportions and affect developing countries to a greater extent than developed ones. A globalization of obesity and diabetes is observable. Recently prevalence rates increased, especially in Asia, the Near and Middle East, the Western Pacific region and even in Sub-Saharan Africa. Evolutionary Anthropology tries to understand the evolutionary mechanisms promoting rising obesity and diabetes type II rates. Homo sapiens evolved in an environment quite different from our recent one. Profound changes in physical activity patterns and nutritional habits during the last 10,000 years and increasingly during the last 200 years increased the risk of obesity and diabetes type II. Consequently our recent environment is called “obesogenic”. This mismatch has been recently observable among societies experiencing rapid cultural changes characterized by Westernization and modernization. This review focuses on obesity and type II diabetes from the viewpoint of evolutionary anthropology.

  19. Evolutionary plant physiology: Charles Darwin's forgotten synthesis.

    Science.gov (United States)

    Kutschera, Ulrich; Niklas, Karl J

    2009-11-01

    Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin's son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin's work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.

  20. Evolutionary Dynamics and Diversity in Microbial Populations

    Science.gov (United States)

    Thompson, Joel; Fisher, Daniel

    2013-03-01

    Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

  1. An Evolutionary Perspective on Toxic Leadership

    Directory of Open Access Journals (Sweden)

    Lucia Ovidia VREJA

    2016-12-01

    Full Text Available Charles Darwin’s prediction from 1859, that future psychology was going to be built on principles derived from evolutionary theory came at last to be fulfilled. Nowadays, there are at least four disciplines that attempt to explain human behaviours as evolutionary adaptations (or maladaptations to the natural and/or social environment: human sociobiology, human behavioural ecology, evolutionary psychology, memetics and gene–culture coevolution theory (in our view, the most adequate of all. According to gene–culture coevolution theory, articulated language was the singular phenomenon that permitted humans to become a cultural species, and from that moment on culture become itself a selection factor. Culture means transmission of information from one generation to the next and learning from other individuals’ experiences, trough language. So, it is of critical importance to have good criteria for the selection of those individuals from whom we should learn. Yet when humans also choose their leaders from among those role-models, according to the same criteria, this mechanism can become a maladaptation and the result can be toxic leadership.

  2. Resistance and relatedness on an evolutionary graph

    Science.gov (United States)

    Maciejewski, Wes

    2012-01-01

    When investigating evolution in structured populations, it is often convenient to consider the population as an evolutionary graph—individuals as nodes, and whom they may act with as edges. There has, in recent years, been a surge of interest in evolutionary graphs, especially in the study of the evolution of social behaviours. An inclusive fitness framework is best suited for this type of study. A central requirement for an inclusive fitness analysis is an expression for the genetic similarity between individuals residing on the graph. This has been a major hindrance for work in this area as highly technical mathematics are often required. Here, I derive a result that links genetic relatedness between haploid individuals on an evolutionary graph to the resistance between vertices on a corresponding electrical network. An example that demonstrates the potential computational advantage of this result over contemporary approaches is provided. This result offers more, however, to the study of population genetics than strictly computationally efficient methods. By establishing a link between gene transfer and electric circuit theory, conceptualizations of the latter can enhance understanding of the former. PMID:21849384

  3. Evolutionary games on multilayer networks: a colloquium

    Science.gov (United States)

    Wang, Zhen; Wang, Lin; Szolnoki, Attila; Perc, Matjaž

    2015-05-01

    Networks form the backbone of many complex systems, ranging from the Internet to human societies. Accordingly, not only is the range of our interactions limited and thus best described and modeled by networks, it is also a fact that the networks that are an integral part of such models are often interdependent or even interconnected. Networks of networks or multilayer networks are therefore a more apt description of social systems. This colloquium is devoted to evolutionary games on multilayer networks, and in particular to the evolution of cooperation as one of the main pillars of modern human societies. We first give an overview of the most significant conceptual differences between single-layer and multilayer networks, and we provide basic definitions and a classification of the most commonly used terms. Subsequently, we review fascinating and counterintuitive evolutionary outcomes that emerge due to different types of interdependencies between otherwise independent populations. The focus is on coupling through the utilities of players, through the flow of information, as well as through the popularity of different strategies on different network layers. The colloquium highlights the importance of pattern formation and collective behavior for the promotion of cooperation under adverse conditions, as well as the synergies between network science and evolutionary game theory.

  4. Toward a general evolutionary theory of oncogenesis.

    Science.gov (United States)

    Ewald, Paul W; Swain Ewald, Holly A

    2013-01-01

    We propose an evolutionary framework, the barrier theory of cancer, which is based on the distinction between barriers to oncogenesis and restraints. Barriers are defined as mechanisms that prevent oncogenesis. Restraints, which are more numerous, inhibit but do not prevent oncogenesis. Processes that compromise barriers are essential causes of cancer; those that interfere with restraints are exacerbating causes. The barrier theory is built upon the three evolutionary processes involved in oncogenesis: natural selection acting on multicellular organisms to mold barriers and restraints, natural selection acting on infectious organisms to abrogate these protective mechanisms, and oncogenic selection which is responsible for the evolution of normal cells into cancerous cells. The barrier theory is presented as a first step toward the development of a general evolutionary theory of cancer. Its attributes and implications for intervention are compared with those of other major conceptual frameworks for understanding cancer: the clonal diversification model, the stem cell theory and the hallmarks of cancer. The barrier theory emphasizes the practical value of distinguishing between essential and exacerbating causes. It also stresses the importance of determining the scope of infectious causation of cancer, because individual pathogens can be responsible for multiple essential causes in infected cells.

  5. Spatial evolutionary epidemiology of spreading epidemics.

    Science.gov (United States)

    Lion, S; Gandon, S

    2016-10-26

    Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

  6. Evolutionary perspectives into placental biology and disease

    Directory of Open Access Journals (Sweden)

    Edward B. Chuong

    2013-12-01

    Full Text Available In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal–fetal conflict shapes both basic placental and reproductive biology – in all species – will provide key insights into diseases of pregnancy.

  7. Complexity of Products of Some Complete and Complete Bipartite Graphs

    Directory of Open Access Journals (Sweden)

    S. N. Daoud

    2013-01-01

    Full Text Available The number of spanning trees in graphs (networks is an important invariant; it is also an important measure of reliability of a network. In this paper, we derive simple formulas of the complexity, number of spanning trees, of products of some complete and complete bipartite graphs such as cartesian product, normal product, composition product, tensor product, and symmetric product, using linear algebra and matrix analysis techniques.

  8. CO2 flowrate calculator

    International Nuclear Information System (INIS)

    Carossi, Jean-Claude

    1969-02-01

    A CO 2 flowrate calculator has been designed for measuring and recording the gas flow in the loops of Pegase reactor. The analog calculator applies, at every moment, Bernoulli's formula to the values that characterize the carbon dioxide flow through a nozzle. The calculator electronics is described (it includes a sampling calculator and a two-variable function generator), with its amplifiers, triggers, interpolator, multiplier, etc. Calculator operation and setting are presented

  9. Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention

    OpenAIRE

    Williams, Ben; Johnston, Iain

    2016-01-01

    Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modelling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondri...

  10. Trend of Complete Hydatidiform Mole

    Directory of Open Access Journals (Sweden)

    K Thapa

    2010-03-01

    Full Text Available INTRODUCTION: Complete Hydatidiform mole is one of the most frequent abnormal pregnancies. This review studies the trend of complete mole in Paropakar Maternity and Women's hospital and clinical ability to detect it. METHODS: This is a retrospective study of 504 cases of complete hydatidiform mole recorded at Paropakar maternity and women's hospital, Kathmandu, during 2058-2065 B.S. Medical records were reviewed and incidence, clinical presentation and method of diagnosis were studied. RESULTS: During the study period, there were 13,9117 births and 504 complete moles, 12 partial moles, 48 persistent gestational tumours, six choriocarcinoma and four invasive moles recorded in the hospital. The incidence of complete mole was one per 276 births. It was prevalent among women younger than 29 years (80% and among the primigravidae (36.7%. More than 90% women presented in the first half of their pregnancy and vaginal bleeding was the main complaint (68.3%. Suction evacuation, dilation and evacuation followed by sharp curettage and abdominal hysterectomy were performed in 80.6%, 17.6% and 1.2% of the women respectively. Persistent mole and choriocarcinoma developed in 9.5% and 0.4% respectively. CONCLUSIONS: Complete mole has the highest incidence. It affects mostly younger women and presents with vaginal bleeding most of the time, usually in the first half of their pregnancy. Keywords: complete hydatidiform mole, gestational trophoblastic disease, persistent gestational tumours.

  11. Incorporating evolutionary principles into environmental management and policy

    DEFF Research Database (Denmark)

    Lankau, Richard; Jørgensen, Peter Søgaard; Harris, David J.

    2011-01-01

    As policymakers and managers work to mitigate the effects of rapid anthropogenic environmental changes, they need to consider organisms’ responses. In light of recent evidence that evolution can be quite rapid, this now includes evolutionary responses. Evolutionary principles have a long history...... in conservation biology, and the necessary next step for the field is to consider ways in which conservation policy makers and managers can proactively manipulate evolutionary processes to achieve their goals. In this review, we aim to illustrate the potential conservation benefits of an increased understanding...... of evolutionary history and prescriptive manipulation of three basic evolutionary factors: selection, variation, and gene flow. For each, we review and propose ways that policy makers and managers can use evolutionary thinking to preserve threatened species, combat pest species, or reduce undesirable evolutionary...

  12. Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management.

    Science.gov (United States)

    Laugen, Ane T; Engelhard, Georg H; Whitlock, Rebecca; Arlinghaus, Robert; Dankel, Dorothy J; Dunlop, Erin S; Eikeset, Anne M; Enberg, Katja; Jørgensen, Christian; Matsumura, Shuichi; Nusslé, Sébastien; Urbach, Davnah; Baulier, Loїc; Boukal, David S; Ernande, Bruno; Johnston, Fiona D; Mollet, Fabian; Pardoe, Heidi; Therkildsen, Nina O; Uusi-Heikkilä, Silva; Vainikka, Anssi; Heino, Mikko; Rijnsdorp, Adriaan D; Dieckmann, Ulf

    2014-03-01

    Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.

  13. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

    Science.gov (United States)

    Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

    2011-01-01

    Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

  14. Where Evolutionary Psychology Meets Cognitive Neuroscience: A Précis to Evolutionary Cognitive Neuroscience1

    Directory of Open Access Journals (Sweden)

    Austen L. Krill

    2007-01-01

    Full Text Available Cognitive neuroscience, the study of brain-behavior relationships, has long attempted to map the brain. The discipline is flourishing, with an increasing number of functional neuroimaging studies appearing in the scientific literature daily. Unlike biology and even psychology, the cognitive neurosciences have only recently begun to apply evolutionary meta-theory and methodological guidance. Approaching cognitive neuroscience from an evolutionary perspective allows scientists to apply biologically based theoretical guidance to their investigations and can be conducted in both humans and nonhuman animals. In fact, several investigations of this sort are underway in laboratories around the world. This paper and two new volumes (Platek, Keenan, and Shackelford [Eds.], 2007; Platek and Shackelford [Eds.], under contract represent the first formal attempts to document the burgeoning field of evolutionary cognitive neuroscience. Here, we briefly review the current state of the science of evolutionary cognitive neuroscience, the methods available to the evolutionary cognitive neuroscientist, and what we foresee as the future directions of the discipline.

  15. Reactor plant for Belene NPP completion

    International Nuclear Information System (INIS)

    Dragunov, Yu. G.; Ryzhov, S. B.; Ermakov, D. N.; Repin, A. I.

    2004-01-01

    Construction of 'Belene' NPP was started at the end of 80-ties using project U-87 with V-320 reactor plant, general designer of this plant is OKB 'Gidropress'. At the beginning of 90-ties, on completing the considerable number of deliveries and performance of civil engineering work at the site the NPP construction was suspended. Nowadays, considering the state of affairs at the site and the work performed by Bulgarian Party on preservation of the equipment delivered, the most perspective is supposed to be implementation of the following versions in completing 'Belene' NPP: for completion of Unit 1 - reactor plant VVER-1000 on the basis of V-320 reactor with the maximum use of the delivered equipment (V-320M) having the extended service life and safety improvement; for Unit 2 - advanced reactor plant VVER-1000. For the upgraded reactor plant V-230M the basic solutions and characteristics are presented, as well as the calculated justification of strength and safety analyses, design of the reactor core and fuel cycle, instrumentation and control systems, application of the 'leak-before break' in the project and implementation of safety measures. For the modernised reactor plant V-392M the main characteristics and basic changes are presented, concerning reactor pressure vessel, steam generator, reactor coolant pump set. Design of NPP with the modernized reactor plant V-320M meets the up-to-date requirements and can be licensed for completion and operation. In the design of NPP with the advanced reactor plant the basic solutions and the equipment are used that are similar to those used in standard reactor plant V-320 and new one with VVER-1000 under construction and completion in Russia, and abroad. Compliance of reactor design with the up-to-date international requirements, considering the extended service life of the main equipment, shows its rather high potential for implementation during completion of 'Belene' NPP

  16. The complete chloroplast genome sequence of Abies nephrolepis (Pinaceae: Abietoideae

    Directory of Open Access Journals (Sweden)

    Dong-Keun Yi

    2016-06-01

    Full Text Available The plant chloroplast (cp genome has maintained a relatively conserved structure and gene content throughout evolution. Cp genome sequences have been used widely for resolving evolutionary and phylogenetic issues at various taxonomic levels of plants. Here, we report the complete cp genome of Abies nephrolepis. The A. nephrolepis cp genome is 121,336 base pairs (bp in length including a pair of short inverted repeat regions (IRa and IRb of 139 bp each separated by a small single copy (SSC region of 54,323 bp (SSC and a large single copy region of 66,735 bp (LSC. It contains 114 genes, 68 of which are protein coding genes, 35 tRNA and four rRNA genes, six open reading frames, and one pseudogene. Seventeen repeat units and 64 simple sequence repeats (SSR have been detected in A. nephrolepis cp genome. Large IR sequences locate in 42-kb inversion points (1186 bp. The A. nephrolepis cp genome is identical to Abies koreana’s which is closely related to taxa. Pairwise comparison between two cp genomes revealed 140 polymorphic sites in each. Complete cp genome sequence of A. nephrolepis has a significant potential to provide information on the evolutionary pattern of Abietoideae and valuable data for development of DNA markers for easy identification and classification.

  17. Large Hadron Collider nears completion

    CERN Multimedia

    2008-01-01

    Installation of the final component of the Large Hadron Collider particle accelerator is under way along the Franco-Swiss border near Geneva, Switzerland. When completed this summer, the LHC will be the world's largest and most complex scientific instrument.

  18. Complete Blood Count (For Parents)

    Science.gov (United States)

    ... Kids Deal With Injections and Blood Tests Blood Culture Anemia Blood Test: Basic Metabolic Panel (BMP) Blood Test: Hemoglobin Basic Blood Chemistry Tests Word! Complete Blood Count (CBC) Medical Tests and Procedures ( ...

  19. Monitoring Completed Navigation Projects Program

    National Research Council Canada - National Science Library

    Bottin, Jr., Robert R

    2001-01-01

    ... (MCNP) Program. The program was formerly known as the Monitoring Completed Coastal Projects Program, but was modified in the late 1990s to include all navigation projects, inland as well as coastal...

  20. Complete colonic duplication in children.

    Science.gov (United States)

    Khaleghnejad Tabari, Ahmad; Mirshemirani, Alireza; Khaleghnejad Tabari, Nasibeh

    2012-01-01

    Complete colonic duplication is a very rare congenital anomaly that may have different presentations according to its location and size. Complete colonic duplication can occur in 15% of gastrointestinal duplication. We report two cases of complete colonic duplications, and their characteristics. We present two patients with complete colonic duplication with different types and presentations. Case 1: A 2- year old boy presented to the clinic with abdominal protrusion, difficulty to defecate, chronic constipation and mucosal prolaps covered bulging (rectocele) since he was 6 months old. The patient had palpable pelvic mass with doughy consistency. Rectal exam confirmed perirectal mass with soft consistency. The patient underwent a surgical operation that had total tubular colorectal duplication with one blind end and was treated with simple fenestration of distal end, and was discharged without complication. After two years follow up, he had normal defecation and good weight gain. Case 2: A 2 -day old infant was referred with imperforate anus and complete duplication of recto-sigmoid colon, diphallus, double bladder, and hypospadiasis. After clinical and paraclinical investigations, he underwent operations in several stages in different periods, and was discharged without complications. After four years follow up, he led a normal life. The patients with complete duplication have to be examined carefully because of the high incidence of other systemic anomalies. Treatment includes simple resection of distal common wall, fenestration, and repair other associated anomalies.

  1. A Self-adaptive Dynamic Evaluation Model for Diabetes Mellitus, Based on Evolutionary Strategies

    Directory of Open Access Journals (Sweden)

    An-Jiang Lu

    2016-03-01

    Full Text Available In order to evaluate diabetes mellitus objectively and accurately, this paper builds a self-adaptive dynamic evaluation model for diabetes mellitus, based on evolutionary strategies. First of all, on the basis of a formalized description of the evolutionary process of diabetes syndromes, using a state transition function, it judges whether a disease is evolutionary, through an excitation parameter. It then, provides evidence for the rebuilding of the evaluation index system. After that, by abstracting and rebuilding the composition of evaluation indexes, it makes use of a heuristic algorithm to determine the composition of the evolved evaluation index set of diabetes mellitus, It then, calculates the weight of each index in the evolved evaluation index set of diabetes mellitus by building a dependency matrix and realizes the self-adaptive dynamic evaluation of diabetes mellitus under an evolutionary environment. Using this evaluation model, it is possible to, quantify all kinds of diagnoses and treatment experiences of diabetes and finally to adopt ideal diagnoses and treatment measures for different patients with diabetics.

  2. Distribution of Marburg virus in Africa: An evolutionary approach.

    Science.gov (United States)

    Zehender, Gianguglielmo; Sorrentino, Chiara; Veo, Carla; Fiaschi, Lisa; Gioffrè, Sonia; Ebranati, Erika; Tanzi, Elisabetta; Ciccozzi, Massimo; Lai, Alessia; Galli, Massimo

    2016-10-01

    The aim of this study was to investigate the origin and geographical dispersion of Marburg virus, the first member of the Filoviridae family to be discovered. Seventy-three complete genome sequences of Marburg virus isolated from animals and humans were retrieved from public databases and analysed using a Bayesian phylogeographical framework. The phylogenetic tree of the Marburg virus data set showed two significant evolutionary lineages: Ravn virus (RAVV) and Marburg virus (MARV). MARV divided into two main clades; clade A included isolates from Uganda (five from the European epidemic in 1967), Kenya (1980) and Angola (from the epidemic of 2004-2005); clade B included most of the isolates obtained during the 1999-2000 epidemic in the Democratic Republic of the Congo (DRC) and a group of Ugandan isolates obtained in 2007-2009. The estimated mean evolutionary rate of the whole genome was 3.3×10(-4) substitutions/site/year (credibility interval 2.0-4.8). The MARV strain had a mean root time of the most recent common ancestor of 177.9years ago (YA) (95% highest posterior density 87-284), thus indicating that it probably originated in the mid-XIX century, whereas the RAVV strain had a later origin dating back to a mean 33.8 YA. The most probable location of the MARV ancestor was Uganda (state posterior probability, spp=0.41), whereas that of the RAVV ancestor was Kenya (spp=0.71). There were significant migration rates from Uganda to the DRC (Bayes Factor, BF=42.0) and in the opposite direction (BF=5.7). Our data suggest that Uganda may have been the cradle of Marburg virus in Africa. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Evolutionary relationships and functional diversity of plant sulfate transporters

    Directory of Open Access Journals (Sweden)

    Hideki eTakahashi

    2012-01-01

    Full Text Available Sulfate is an essential nutrient cycled in nature. Ion transporters that specifically facilitate the transport of sulfate across the membranes are found ubiquitously in living organisms. The phylogenetic analysis of known sulfate transporters and their homologous proteins from eukaryotic organisms indicate two evolutionarily distinct groups of sulfate transport systems. One major group named Tribe 1 represents yeast and fungal SUL, plant SULTR and animal SLC26 families. The evolutionary origin of SULTR family members in land plants and green algae is suggested to be common with yeast and fungal sulfate transporters (SUL and animal anion exchangers (SLC26. The lineage of plant SULTR family is expanded into four subfamilies (SULTR1 to SULTR4 in land plant species. By contrast, the putative SULTR homologues from Chlorophyte green algae are in two separate lineages; one with the subfamily of plant tonoplast-localized sulfate transporters (SULTR4, and the other diverged before the appearance of lineages for SUL, SULTR and SLC26. There also was a group of yet undefined members of putative sulfate transporters in yeast and fungi divergent from these major lineages in Tribe 1. The other distinct group is Tribe 2, primarily composed of animal sodium-dependent sulfate/carboxylate transporters (SLC13 and plant tonoplast-localized dicarboxylate transporters (TDT. The putative sulfur-sensing protein (SAC1 and SAC1-like transporters (SLT of Chlorophyte green algae, bryophyte and lycophyte show low degrees of sequence similarities with SLC13 and TDT. However, the phylogenetic relationship between SAC1/SLT and the other two families, SLC13 and TDT in Tribe 2, is not clearly supported. In addition, the SAC1/SLT family is completely absent in the angiosperm species analyzed. The present study suggests distinct evolutionary trajectories of sulfate transport systems for land plants and green algae.

  4. The Algorithm for Algorithms: An Evolutionary Algorithm Based on Automatic Designing of Genetic Operators

    Directory of Open Access Journals (Sweden)

    Dazhi Jiang

    2015-01-01

    Full Text Available At present there is a wide range of evolutionary algorithms available to researchers and practitioners. Despite the great diversity of these algorithms, virtually all of the algorithms share one feature: they have been manually designed. A fundamental question is “are there any algorithms that can design evolutionary algorithms automatically?” A more complete definition of the question is “can computer construct an algorithm which will generate algorithms according to the requirement of a problem?” In this paper, a novel evolutionary algorithm based on automatic designing of genetic operators is presented to address these questions. The resulting algorithm not only explores solutions in the problem space like most traditional evolutionary algorithms do, but also automatically generates genetic operators in the operator space. In order to verify the performance of the proposed algorithm, comprehensive experiments on 23 well-known benchmark optimization problems are conducted. The results show that the proposed algorithm can outperform standard differential evolution algorithm in terms of convergence speed and solution accuracy which shows that the algorithm designed automatically by computers can compete with the algorithms designed by human beings.

  5. A dynamic parking charge optimal control model under perspective of commuters' evolutionary game behavior

    Science.gov (United States)

    Lin, XuXun; Yuan, PengCheng

    2018-01-01

    In this research we consider commuters' dynamic learning effect by modeling the trip mode choice behavior from a new perspective of dynamic evolutionary game theory. We explore the behavior pattern of different types of commuters and study the evolution path and equilibrium properties under different traffic conditions. We further establish a dynamic parking charge optimal control (referred to as DPCOC) model to alter commuters' trip mode choice while minimizing the total social cost. Numerical tests show. (1) Under fixed parking fee policy, the evolutionary results are completely decided by the travel time and the only method for public transit induction is to increase the parking charge price. (2) Compared with fixed parking fee policy, DPCOC policy proposed in this research has several advantages. Firstly, it can effectively turn the evolutionary path and evolutionary stable strategy to a better situation while minimizing the total social cost. Secondly, it can reduce the sensitivity of trip mode choice behavior to traffic congestion and improve the ability to resist interferences and emergencies. Thirdly, it is able to control the private car proportion to a stable state and make the trip behavior more predictable for the transportation management department. The research results can provide theoretical basis and decision-making references for commuters' mode choice prediction, dynamic setting of urban parking charge prices and public transit induction.

  6. Heterogeneous Calculation of {epsilon}

    Energy Technology Data Exchange (ETDEWEB)

    Jonsson, Alf

    1961-02-15

    A heterogeneous method of calculating the fast fission factor given by Naudet has been applied to the Carlvik - Pershagen definition of {epsilon}. An exact calculation of the collision probabilities is included in the programme developed for the Ferranti - Mercury computer.

  7. Heterogeneous Calculation of ε

    International Nuclear Information System (INIS)

    Jonsson, Alf

    1961-02-01

    A heterogeneous method of calculating the fast fission factor given by Naudet has been applied to the Carlvik - Pershagen definition of ε. An exact calculation of the collision probabilities is included in the programme developed for the Ferranti - Mercury computer

  8. Making evolutionary biology a basic science for medicine

    Science.gov (United States)

    Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

    2010-01-01

    New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

  9. The fate of completed intentions.

    Science.gov (United States)

    Anderson, Francis T; Einstein, Gilles O

    2017-04-01

    The goal of this research was to determine whether and how people deactivate prospective memory (PM) intentions after they have been completed. One view proposes that PM intentions can be deactivated after completion, such that they no longer come to mind and interfere with current tasks. Another view is that now irrelevant completed PM intentions exhibit persisting activation, and continue to be retrieved. In Experiment 1, participants were given a PM intention embedded within the ongoing task during Phase 1, after which participants were told either that the PM task had been completed or suspended until later. During Phase 2, participants were instructed to perform only the ongoing task and were periodically prompted to report their thoughts. Critically, the PM targets from Phase 1 reappeared in Phase 2. All of our measures, including thoughts reported about the PM task, supported the existence of persisting activation. In Experiment 2, we varied conditions that were expected to mitigate persisting activation. Despite our best attempts to promote deactivation, we found evidence for the persistence of spontaneous retrieval in all groups after intentions were completed. The theoretical and practical implications of this potential dark side to spontaneous retrieval are discussed.

  10. Self-organized modularization in evolutionary algorithms.

    Science.gov (United States)

    Dauscher, Peter; Uthmann, Thomas

    2005-01-01

    The principle of modularization has proven to be extremely successful in the field of technical applications and particularly for Software Engineering purposes. The question to be answered within the present article is whether mechanisms can also be identified within the framework of Evolutionary Computation that cause a modularization of solutions. We will concentrate on processes, where modularization results only from the typical evolutionary operators, i.e. selection and variation by recombination and mutation (and not, e.g., from special modularization operators). This is what we call Self-Organized Modularization. Based on a combination of two formalizations by Radcliffe and Altenberg, some quantitative measures of modularity are introduced. Particularly, we distinguish Built-in Modularity as an inherent property of a genotype and Effective Modularity, which depends on the rest of the population. These measures can easily be applied to a wide range of present Evolutionary Computation models. It will be shown, both theoretically and by simulation, that under certain conditions, Effective Modularity (as defined within this paper) can be a selection factor. This causes Self-Organized Modularization to take place. The experimental observations emphasize the importance of Effective Modularity in comparison with Built-in Modularity. Although the experimental results have been obtained using a minimalist toy model, they can lead to a number of consequences for existing models as well as for future approaches. Furthermore, the results suggest a complex self-amplification of highly modular equivalence classes in the case of respected relations. Since the well-known Holland schemata are just the equivalence classes of respected relations in most Simple Genetic Algorithms, this observation emphasizes the role of schemata as Building Blocks (in comparison with arbitrary subsets of the search space).

  11. Extrapolating Weak Selection in Evolutionary Games

    Science.gov (United States)

    Wu, Bin; García, Julián; Hauert, Christoph; Traulsen, Arne

    2013-01-01

    In evolutionary games, reproductive success is determined by payoffs. Weak selection means that even large differences in game outcomes translate into small fitness differences. Many results have been derived using weak selection approximations, in which perturbation analysis facilitates the derivation of analytical results. Here, we ask whether results derived under weak selection are also qualitatively valid for intermediate and strong selection. By “qualitatively valid” we mean that the ranking of strategies induced by an evolutionary process does not change when the intensity of selection increases. For two-strategy games, we show that the ranking obtained under weak selection cannot be carried over to higher selection intensity if the number of players exceeds two. For games with three (or more) strategies, previous examples for multiplayer games have shown that the ranking of strategies can change with the intensity of selection. In particular, rank changes imply that the most abundant strategy at one intensity of selection can become the least abundant for another. We show that this applies already to pairwise interactions for a broad class of evolutionary processes. Even when both weak and strong selection limits lead to consistent predictions, rank changes can occur for intermediate intensities of selection. To analyze how common such games are, we show numerically that for randomly drawn two-player games with three or more strategies, rank changes frequently occur and their likelihood increases rapidly with the number of strategies . In particular, rank changes are almost certain for , which jeopardizes the predictive power of results derived for weak selection. PMID:24339769

  12. Exercise, Affect, and Adherence: An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Harold Lee

    2016-08-01

    Full Text Available The low rates of regular exercise and overall physical activity (PA in the general population represent a significant public health challenge. Previous research suggests that, for many people, exercise leads to a negative affective response and, in turn, reduced likelihood of future exercise. The purpose of this paper is to examine this exercise-affect-adherence relationship from an evolutionary perspective. Specifically, we argue that low rates of physical exercise in the general population are a function of the evolved human tendency to avoid unnecessary physical exertion. This innate tendency evolved because it allowed our evolutionary ancestors to conserve energy for physical activities that had immediate adaptive utility such as pursuing prey, escaping predators, and engaging in social and reproductive behaviors. The commonly observed negative affective response to exercise is an evolved proximate psychological mechanism through which humans avoid unnecessary energy expenditure. The fact that the human tendencies toward negative affective response to and avoidance of unnecessary physical activities are innate does not mean that they are unchangeable. Indeed, it is only because of human-engineered changes in our environmental conditions (i.e., it is no longer necessary for us to work for our food that our predisposition to avoid unnecessary physical exertion has become a liability. Thus, it is well within our capabilities to reengineer our environments to once again make PA necessary or, at least, to serve an immediate functional purpose. We propose a two-pronged approach to PA promotion based on this evolutionary functional perspective: First, to promote exercise and other physical activities that are perceived to have an immediate purpose, and second, to instill greater perceived purpose for a wider range of physical activities. We posit that these strategies are more likely to result in more positive (or at least less negative affective

  13. Occult hepatitis B infection: an evolutionary scenario

    Directory of Open Access Journals (Sweden)

    Lukashov Vladimir V

    2008-12-01

    Full Text Available Abstract Background Occult or latent hepatitis B virus (HBV infection is defined as infection with detectable HBV DNA and undetectable surface antigen (HBsAg in patients' blood. The cause of an overt HBV infection becoming an occult one is unknown. To gain insight into the mechanism of the development of occult infection, we compared the full-length HBV genome from a blood donor carrying an occult infection (d4 with global genotype D genomes. Results The phylogenetic analysis of polymerase, core and X protein sequences did not distinguish d4 from other genotype D strains. Yet, d4 surface protein formed the evolutionary outgroup relative to all other genotype D strains. Its evolutionary branch was the only one where accumulation of substitutions suggests positive selection (dN/dS = 1.3787. Many of these substitutiions accumulated specifically in regions encoding the core/surface protein interface, as revealed in a 3D-modeled protein complex. We identified a novel RNA splicing event (deleting nucleotides 2986-202 that abolishes surface protein gene expression without affecting polymerase, core and X-protein related functions. Genotype D strains differ in their ability to perform this 2986-202 splicing. Strains prone to 2986-202 splicing constitute a separate clade in a phylogenetic tree of genotype D HBVs. A single substitution (G173T that is associated with clade membership alters the local RNA secondary structure and is proposed to affect splicing efficiency at the 202 acceptor site. Conclusion We propose an evolutionary scenario for occult HBV infection, in which 2986-202 splicing generates intracellular virus particles devoid of surface protein, which subsequently accumulates mutations due to relaxation of coding constraints. Such viruses are deficient of autonomous propagation and cannot leave the host cell until it is lysed.

  14. Evolutionary Computing Methods for Spectral Retrieval

    Science.gov (United States)

    Terrile, Richard; Fink, Wolfgang; Huntsberger, Terrance; Lee, Seugwon; Tisdale, Edwin; VonAllmen, Paul; Tinetti, Geivanna

    2009-01-01

    A methodology for processing spectral images to retrieve information on underlying physical, chemical, and/or biological phenomena is based on evolutionary and related computational methods implemented in software. In a typical case, the solution (the information that one seeks to retrieve) consists of parameters of a mathematical model that represents one or more of the phenomena of interest. The methodology was developed for the initial purpose of retrieving the desired information from spectral image data acquired by remote-sensing instruments aimed at planets (including the Earth). Examples of information desired in such applications include trace gas concentrations, temperature profiles, surface types, day/night fractions, cloud/aerosol fractions, seasons, and viewing angles. The methodology is also potentially useful for retrieving information on chemical and/or biological hazards in terrestrial settings. In this methodology, one utilizes an iterative process that minimizes a fitness function indicative of the degree of dissimilarity between observed and synthetic spectral and angular data. The evolutionary computing methods that lie at the heart of this process yield a population of solutions (sets of the desired parameters) within an accuracy represented by a fitness-function value specified by the user. The evolutionary computing methods (ECM) used in this methodology are Genetic Algorithms and Simulated Annealing, both of which are well-established optimization techniques and have also been described in previous NASA Tech Briefs articles. These are embedded in a conceptual framework, represented in the architecture of the implementing software, that enables automatic retrieval of spectral and angular data and analysis of the retrieved solutions for uniqueness.

  15. The evolutionary sequence: origin and emergences

    Science.gov (United States)

    Fox, S. W.

    1986-01-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

  16. Advances of evolutionary computation methods and operators

    CERN Document Server

    Cuevas, Erik; Oliva Navarro, Diego Alberto

    2016-01-01

    The goal of this book is to present advances that discuss alternative Evolutionary Computation (EC) developments and non-conventional operators which have proved to be effective in the solution of several complex problems. The book has been structured so that each chapter can be read independently from the others. The book contains nine chapters with the following themes: 1) Introduction, 2) the Social Spider Optimization (SSO), 3) the States of Matter Search (SMS), 4) the collective animal behavior (CAB) algorithm, 5) the Allostatic Optimization (AO) method, 6) the Locust Search (LS) algorithm, 7) the Adaptive Population with Reduced Evaluations (APRE) method, 8) the multimodal CAB, 9) the constrained SSO method.

  17. Application of evolutionary games to modeling carcinogenesis.

    Science.gov (United States)

    Swierniak, Andrzej; Krzeslak, Michal

    2013-06-01

    We review a quite large volume of literature concerning mathematical modelling of processes related to carcinogenesis and the growth of cancer cell populations based on the theory of evolutionary games. This review, although partly idiosyncratic, covers such major areas of cancer-related phenomena as production of cytotoxins, avoidance of apoptosis, production of growth factors, motility and invasion, and intra- and extracellular signaling. We discuss the results of other authors and append to them some additional results of our own simulations dealing with the possible dynamics and/or spatial distribution of the processes discussed.

  18. Statistical mechanics of spatial evolutionary games

    International Nuclear Information System (INIS)

    Miekisz, Jacek

    2004-01-01

    We discuss the long-run behaviour of stochastic dynamics of many interacting players in spatial evolutionary games. In particular, we investigate the effect of the number of players and the noise level on the stochastic stability of Nash equilibria. We discuss similarities and differences between systems of interacting players maximizing their individual payoffs and particles minimizing their interaction energy. We use concepts and techniques of statistical mechanics to study game-theoretic models. In order to obtain results in the case of the so-called potential games, we analyse the thermodynamic limit of the appropriate models of interacting particles

  19. Evolutionary tracks of the terrestrial planets

    International Nuclear Information System (INIS)

    Matsui, Takafumi; Abe, Yutaka

    1987-01-01

    On the basis of the model proposed by Matsui and Abe, the authors show that two major factors - distance from the Sun and the efficiency of retention of accretional energy - control the early evolution of the terrestrial planets. A diagram of accretional energy versus the optical depth of a proto-atmosphere provides a means to follow the evolutionary track of surface temperature of the terrestrial planets and an explanation for why the third planet in our solar system is an 'aqua'-planet. 15 refs; 3 figs

  20. Can evolutionary convergence be tested on Europa?

    Energy Technology Data Exchange (ETDEWEB)

    Chela-Flores, Julian [Instituto de Estudios Avanzados, Caracas (Venezuela); [Abdus Salam International Centre for Theoretical Physics, Trieste (Italy)]. E-mail: chelaf@ictp.trieste.it

    2002-09-01

    A major objective in solar system exploration has to be the insertion of appropriate biology-oriented experiments in future missions. We discuss various reasons for suggesting that this type of research be considered a high priority for feasibility studies and, subsequently, for technological development of appropriate melters and submersibles. With the assumption that Darwin's theory is valid for the evolution of life anywhere in the universe, various degrees of convergent phenomena argue in favor of the conjecture that universal evolution of intelligent behavior is just a matter of time and preservation of steady planetary conditions. A preliminary test of this conjecture is feasible with experiments involving evolutionary biosignatures on Europa. (author)

  1. The evolutionary sequence: origin and emergences.

    Science.gov (United States)

    Fox, S W

    1986-03-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

  2. Religion and psychosis: a common evolutionary trajectory?

    Science.gov (United States)

    Dein, Simon; Littlewood, Roland

    2011-07-01

    In this article we propose that schizophrenia and religious cognition engage cognate mental modules in the over-attribution of agency and the overextension of theory of mind. We argue similarities and differences between assumptions of ultrahuman agents with omniscient minds and certain ''pathological'' forms of thinking in schizophrenia: thought insertion, withdrawal and broadcasting, and delusions of reference. In everyday religious cognition agency detection and theory of mind modules function ''normally,'' whereas in schizophrenia both modules are impaired. It is suggested that religion and schizophrenia have perhaps had a related evolutionary trajectory.

  3. The evolutionary status of symbiotic stars

    International Nuclear Information System (INIS)

    Rudak, B.

    1982-01-01

    The evolutionary relations between symbiotic stars and cataclysmic variables are presented. The symbiotic stars are assumed to be long period detached binaries containing a carbon-oxygen degenerate primary and a red giant losing its mass through a spherically symmetric wind. Such systems can be obtained in Case C evolution, provided a common envelope during a rapid mass transfer phase was not formed. The same way recurrent novae containing a red giant as a secondary component may be produced. The factors influencing the differences between symbiotic stars and nova-type stars are discussed. (Auth.)

  4. Completing the Heterocubane Family [Cp*AlE]4 (E = O, S, Se, and Te) by Selective Oxygenation and Sulfuration of [Cp*Al]4: Density Functional Theory Calculations of [Cp*AlE]4 and Reactivity of [Cp*AlO]4 toward Hydrolysis.

    Science.gov (United States)

    Stelzer, Adrian C; Hrobárik, Peter; Braun, Thomas; Kaupp, Martin; Braun-Cula, Beatrice

    2016-05-16

    The subvalent aluminum compound [Cp*Al]4 (1) reacts with dioxygen, N2O, or sulfur to yield the heterocubane complexes [Cp*AlX]4 [X = O (2) and S (3)]. Treatment of [Cp*AlO]4 (2) with (tBuO)3SiOH gave [(tBuO)3SiOAlO]4 (6) and Cp*H. The structures and spectroscopic data of the Al clusters are supported by density functional theory (DFT) calculations, which also demonstrate the importance of noncovalent interactions (NCI) in oligomeric Al(I) complexes as well as in [Cp*AlS]4 and the heavier homologues of Se and Te. The computed (27)Al NMR shifts indicate a deshielding at the Al centers with increasing electronegativity of the chalcogen atom as well as significant spin-orbit shielding effects within the heavier heterocubane [Al4E4] cores. Further hydrolysis of 6 with an additional amount of silanol in the presence of water resulted in the formation of [Al4(OH)6(OH2)2(OSiOtBu3)6] (7), which shows a structural motif found in boehmite and diaspore.

  5. Why is economic geography not an evolutionary science? : towards an evolutionary economic geography

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.; Martin, R.

    2008-01-01

    The paper explains the commonalities and differences between neoclassical, institutional and evolutionary approaches that have been influential in economic geography during the last couple of decades. By separating the three approaches in terms of theoretical content and research methodology, we can

  6. Expanding Evolutionary Theory beyond Darwinism with Elaborating, Self-Organizing, and Fractionating Complex Evolutionary Systems

    Science.gov (United States)

    Fichter, Lynn S.; Pyle, E. J.; Whitmeyer, S. J.

    2010-01-01

    Earth systems increase in complexity, diversity, and interconnectedness with time, driven by tectonic/solar energy that keeps the systems far from equilibrium. The evolution of Earth systems is facilitated by three evolutionary mechanisms: "elaboration," "fractionation," and "self-organization," that share…

  7. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes.

    Science.gov (United States)

    Novák, Lukáš; Zubáčová, Zuzana; Karnkowska, Anna; Kolisko, Martin; Hroudová, Miluše; Stairs, Courtney W; Simpson, Alastair G B; Keeling, Patrick J; Roger, Andrew J; Čepička, Ivan; Hampl, Vladimír

    2016-10-06

    Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.

  8. Evolutionary dynamics with fluctuating population sizes and strong mutualism

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R.

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  9. Evolutionary engineering of industrial microorganisms-strategies and applications.

    Science.gov (United States)

    Zhu, Zhengming; Zhang, Juan; Ji, Xiaomei; Fang, Zhen; Wu, Zhimeng; Chen, Jian; Du, Guocheng

    2018-06-01

    Microbial cells have been widely used in the industry to obtain various biochemical products, and evolutionary engineering is a common method in biological research to improve their traits, such as high environmental tolerance and improvement of product yield. To obtain better integrate functions of microbial cells, evolutionary engineering combined with other biotechnologies have attracted more attention in recent years. Classical laboratory evolution has been proven effective to letting more beneficial mutations occur in different genes but also has some inherent limitations such as a long evolutionary period and uncontrolled mutation frequencies. However, recent studies showed that some new strategies may gradually overcome these limitations. In this review, we summarize the evolutionary strategies commonly used in industrial microorganisms and discuss the combination of evolutionary engineering with other biotechnologies such as systems biology and inverse metabolic engineering. Finally, we prospect the importance and application prospect of evolutionary engineering as a powerful tool especially in optimization of industrial microbial cell factories.

  10. Evolutionary dynamics with fluctuating population sizes and strong mutualism.

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  11. Structural Completeness in Fuzzy Logics

    Czech Academy of Sciences Publication Activity Database

    Cintula, Petr; Metcalfe, G.

    2009-01-01

    Roč. 50, č. 2 (2009), s. 153-183 ISSN 0029-4527 R&D Projects: GA MŠk(CZ) 1M0545 Institutional research plan: CEZ:AV0Z10300504 Keywords : structral logics * fuzzy logics * structural completeness * admissible rules * primitive variety * residuated lattices Subject RIV: BA - General Mathematics

  12. Quantum space and quantum completeness

    Science.gov (United States)

    Jurić, Tajron

    2018-05-01

    Motivated by the question whether quantum gravity can "smear out" the classical singularity we analyze a certain quantum space and its quantum-mechanical completeness. Classical singularity is understood as a geodesic incompleteness, while quantum completeness requires a unique unitary time evolution for test fields propagating on an underlying background. Here the crucial point is that quantum completeness renders the Hamiltonian (or spatial part of the wave operator) to be essentially self-adjoint in order to generate a unique time evolution. We examine a model of quantum space which consists of a noncommutative BTZ black hole probed by a test scalar field. We show that the quantum gravity (noncommutative) effect is to enlarge the domain of BTZ parameters for which the relevant wave operator is essentially self-adjoint. This means that the corresponding quantum space is quantum complete for a larger range of BTZ parameters rendering the conclusion that in the quantum space one observes the effect of "smearing out" the singularity.

  13. Program Costs and Student Completion

    Science.gov (United States)

    Manning, Terri M.; Crosta, Peter M.

    2014-01-01

    Community colleges are under pressure to increase completion rates, prepare students for the workplace, and contain costs. Colleges need to know the financial implications of what are often perceived as routine decisions: course scheduling, program offerings, and the provision of support services. This chapter presents a methodology for estimating…

  14. Globals of Completely Regular Monoids

    Institute of Scientific and Technical Information of China (English)

    Wu Qian-qian; Gan Ai-ping; Du Xian-kun

    2015-01-01

    An element of a semigroup S is called irreducible if it cannot be expressed as a product of two elements in S both distinct from itself. In this paper we show that the class C of all completely regular monoids with irreducible identity elements satisfies the strong isomorphism property and so it is globally determined.

  15. Complete nitrification by Nitrospira bacteria

    DEFF Research Database (Denmark)

    Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra

    2015-01-01

    Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetic...

  16. The Completeness Theorem of Godel

    Indian Academy of Sciences (India)

    GENERAL I ARTICLE. The Completeness Theorem of Godel. 2. Henkin's Proof for First Order Logic. S M Srivastava is with the. Indian Statistical,. Institute, Calcutta. He received his PhD from the Indian Statistical. Institute in 1980. His research interests are in descriptive set theory. I Part 1. An Introduction to Math- ematical ...

  17. Spring valve for well completion

    Energy Technology Data Exchange (ETDEWEB)

    Gorbatov, P T

    1966-07-22

    A spring-loaded valve for well completion consists of a housing with a spring-loaded closing element. In order to protect the closing element from corrosion which might lower the pressure drop, the closing element is made in the form of a piston. It is tightly connected with sealing elements. The housing has orifices, overlapping the piston in the initial position.

  18. Largest particle detector nearing completion

    CERN Multimedia

    2006-01-01

    "Construction of another part of the Large Hadron Collider (LHC), the worl's largest particle accelerator at CERN in Switzerland, is nearing completion. The Compact Muon Solenoid (CMS) is oner of the LHC project's four large particle detectors. (1/2 page)

  19. YB0 SERVICES INSTALLATION COMPLETED

    CERN Document Server

    The beauty of the completed YB0 was briefly visible at P5 as preparations continue for Tracker installation. A tremendous effort, lasting 7 months and involving more than 100 workers on the busiest days, resulted in 5700 electrical cables, 780 optical cables with 65k fibre channels, and 550 pipes laid on YB0 for HB, EB and Tracker.

  20. A multilevel evolutionary framework for sustainability analysis

    Directory of Open Access Journals (Sweden)

    Timothy M. Waring

    2015-06-01

    Full Text Available Sustainability theory can help achieve desirable social-ecological states by generalizing lessons across contexts and improving the design of sustainability interventions. To accomplish these goals, we argue that theory in sustainability science must (1 explain the emergence and persistence of social-ecological states, (2 account for endogenous cultural change, (3 incorporate cooperation dynamics, and (4 address the complexities of multilevel social-ecological interactions. We suggest that cultural evolutionary theory broadly, and cultural multilevel selection in particular, can improve on these fronts. We outline a multilevel evolutionary framework for describing social-ecological change and detail how multilevel cooperative dynamics can determine outcomes in environmental dilemmas. We show how this framework complements existing sustainability frameworks with a description of the emergence and persistence of sustainable institutions and behavior, a means to generalize causal patterns across social-ecological contexts, and a heuristic for designing and evaluating effective sustainability interventions. We support these assertions with case examples from developed and developing countries in which we track cooperative change at multiple levels of social organization as they impact social-ecological outcomes. Finally, we make suggestions for further theoretical development, empirical testing, and application.