''La Grande Galerie de l'Evolution'' of Paris: The only museum in the world entirely devoted to biological evolution

International Nuclear Information System (INIS)

Raulin Cerceau, F.

1995-01-01

The new building called ''Grande Galerie de l'Evolution'' of the national Museum of natural History, in Paris-France, is the first museum in the world exclusively devoted to biological evolution. The Museum is divided in 3 parts (named ''Acts''): The aim of Act 1 is to sensibilize the visitor to the results of 4 billions years of biological evolution. This act shows some examples of biological diversity through few terrestrial and marine environments (deserts, tropical forests, polar habitats, abyssal zones ...). Act 2 is the principal part of the Museum explaining the main processes of evolution. This part shows also the story of life from the first living cells to man. Act 3, the last part offers to visitors a vision of the interactions between man and nature, and of their consequences along millions of years. A special Gallery is entirely devoted to vanished and threatened species, as a nefast consequence of human interaction on biological diversity particularly since the beginning of this century. (Abstract only)

Worldviews and evolution in the biology classroom

NARCIS (Netherlands)

Schilders, M.; Sloep, P.; Peled, E.; Boersma, K.T.

2009-01-01

This study examined what worldviews are present among Dutch students and teachers and how the students cope with scientific knowledge acquired in the biology classroom. Furthermore, we investigated what learning and teaching strategies teachers adopt when they teach about evolution and worldviews.

Biological evolution: Some genetic considerations

Directory of Open Access Journals (Sweden)

Mohammad Saad Zaghloul Salem

2014-01-01

Conclusion: Natural selection might be observed in nature but not in life. The concept of biological evolution is an illogic and insensible hypothesis since it stands in direct contradiction with our current knowledge regarding the behavior as well as the structural and functional characteristics of the human genome and human proteome. Additionally, almost all basic postulations of this concept can neither be tested nor imitated for experimentation, which is a prerequisite for acceptance and validation of any scientific hypotheses.

On the transition period from chemical to biological evolution

International Nuclear Information System (INIS)

Chela-Flores, J.

1991-06-01

We discuss the consequences of the hypothesis that biological evolution was contemporary with an important event in chemical evolution, namely, the induction of a small chiral bias by the electroweak neutral interaction, amplified by the Salam enhancement factor, which we discuss in terms of familiar crystallographic terms. (author). 18 refs, 3 tabs

Biology Students' and Teachers' Religious Beliefs and Attitudes towards Theory of Evolution

Science.gov (United States)

Ozay Kose, Esra

2010-01-01

Evolution has not being well addressed in schools partly because it is a controversial topic in religious views. In the present study, it is explored to what extent Turkish secondary school biology teachers and students accommodate the theory of biological evolution with their religious beliefs. Two-hundred fifty secondary school students and…

Limits in the evolution of biological form: a theoretical morphologic perspective.

Science.gov (United States)

McGhee, George R

2015-12-06

Limits in the evolution of biological form can be empirically demonstrated by using theoretical morphospace analyses, and actual analytic examples are given for univalved ammonoid shell form, bivalved brachiopod shell form and helical bryozoan colony form. Limits in the evolution of form in these animal groups can be shown to be due to functional and developmental constraints on possible evolutionary trajectories in morphospace. Future evolutionary-limit research is needed to analyse the possible existence of temporal constraint in the evolution of biological form on Earth, and in the search for the possible existence of functional alien life forms on Titan and Triton that are developmentally impossible for Earth life.

Evolution of egg coats: linking molecular biology and ecology.

Science.gov (United States)

Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

2015-08-01

One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation. © 2015 John Wiley & Sons Ltd.

The Biological Big Bang model for the major transitions in evolution.

Science.gov (United States)

Koonin, Eugene V

2007-08-20

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal. I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed

Emotional and Spiritual Quotient Approach Improve Biology Education Students’ Acceptance of Evolution Theory

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Darussyamsu, R.; Fadilah, M.; Putri, D. H.

2018-04-01

Emotional and spiritual aspect is one of main factors that influence students’ acceptance of a theory. This study aim to measure university students’ acceptance of evolution by learns evolution using emotional and spiritual quotient (ESQ) approach. This is a quasi-experimental research using one shot case study design with the subject 36 biology educational students at Biology Department, Faculty of Mathematics and Natural Science, Universitas Negeri Padang. Data collected using the MATE instrument by Rutledge and Warden (2000) after the students learn evolution for eight meetings since January until March 2017. The result showed that by learning evolution theory combine with ESQ aspects increase students acceptance from very low become moderate acceptance. It concluded that ESQ aspects can improve students’ acceptance of evolution. Any criteria depend on it are discussed.

[Analysis on property of meridian supramolecules by biological evolution path].

Science.gov (United States)

Deng, Kaiwen; Tao, Yeqin; Tang, Wenhan; He, Fuyuan; Liu, Wenlong; Shi, Jilian; Yang, Yantao; Zhou, Yiqun; Chang, Xiaorong

2017-03-12

With human placed in the whole nature, by following the biologic evolution path, the property of channel structure for "imprinting template" in meridian and zang-fu was explored with supramolecular chemistry. In the history of biologic evolution, each molecule in "molecule society" gradually developed into various highly-ordered supramolecular bodies based on self-identification, self-assembly, self-organization, self-replicating of"imprinting template", and thereby the original biochemical system was established, and finally evolved into human. In the forming process of supramolecular bodies, the channel structure of"imprinting template" in guest supramolecular bodies would be kept by host supramolecular bodies, and communicate with the outside to exchange materials, energy, information, otherwise life phenomenon could not continue, for which it was the chemical nature of biolo-gical supramolecular bodies for body to develop meridian. Therefore, the human was a gigantic and complicated supramolecules body in biological nature, and possessed the supramolecules "imprinting template" at each stage of evolution, for which the meridians were formed. When meridians converged, acupoints appeared; when acupointsconverged, zang-fu appeared. With the promotion of the blood from heart, according to"imprinting template", the guest supramolecular bodies and host meridian produced qi -analysis, which was the qi -phenomenon of guest in meridian. It presented as zang-fu image of physiology and pathology as well as action regularities of medication and acupuncture tolerance, by which current various meridian viewpoints could be explained and propose the hypothesis of meridian supramolecular bodies. The meridian and its phenomenon was decide by its "imprinting template" of supramolecular bodies and self-reaction regularities, which abided through the living nature. This was the substance for meridian biology.

A critical analysis of the new biology and the biological revolution: their impact - from medicine to evolution.

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Dev, Sukhendu B

2010-01-01

In this article, I critically analyze the impact of the new biology and the biological revolution. I argue that indiscriminate use of the words such as 'interdisciplinary,' 'integrative,' and 'revolution' has caused only confusion when applied to biology. The recent debate, especially after the exploding field of systems biology, has brought back the controversy whether molecular biology is reductionist or holistic. I look at the issues involved critically. I discuss the problem of defining the word 'gene' and argue that recent attempts to redefine the central dogma of molecular biology about the information flow from DNA to RNA to protein are not justified. I support my view with comments from the scientist who discovered RNA splicing. Several aspects of evo-devo, a new branch of biology, are discussed. I give examples from this evolution-developmental biology to show how some of Darwin's inspired guesses have had resounding victory when it was found that specific genes during embryonic development of the Galapagos finches decided the size and shape of their beaks. I discuss the recent publications which show that the conditions in the island, such as wet to dry to wet season, can bring about evolutionary changes from year to year. Thus it is essential to monitor both short and long-term evolutionary changes to get the full picture of evolution.

Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution

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Ivan B. Djordjevic

2015-08-01

Full Text Available Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i Markovian classical model, (ii Markovian-like quantum model, and (iii hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage Markov chain-like models of aging, which

Biological Evolution and the History of the Earth Are Foundations of Science

Science.gov (United States)

2008-01-01

AGU affirms the central importance of including scientific theories of Earth history and biological evolution in science education. Within the scientific community, the theory of biological evolution is not controversial, nor have ``alternative explanations'' been found. This is why no competing theories are required by the U.S. National Science Education Standards. Explanations of natural phenomena that appeal to the supernatural or are based on religious doctrine-and therefore cannot be tested through scientific inquiry-are not scientific, and have no place in the science classroom.

A mechano-biological model of multi-tissue evolution in bone

Science.gov (United States)

Frame, Jamie; Rohan, Pierre-Yves; Corté, Laurent; Allena, Rachele

2017-12-01

Successfully simulating tissue evolution in bone is of significant importance in predicting various biological processes such as bone remodeling, fracture healing and osseointegration of implants. Each of these processes involves in different ways the permanent or transient formation of different tissue types, namely bone, cartilage and fibrous tissues. The tissue evolution in specific circumstances such as bone remodeling and fracturing healing is currently able to be modeled. Nevertheless, it remains challenging to predict which tissue types and organization can develop without any a priori assumptions. In particular, the role of mechano-biological coupling in this selective tissue evolution has not been clearly elucidated. In this work, a multi-tissue model has been created which simultaneously describes the evolution of bone, cartilage and fibrous tissues. The coupling of the biological and mechanical factors involved in tissue formation has been modeled by defining two different tissue states: an immature state corresponding to the early stages of tissue growth and representing cell clusters in a weakly neo-formed Extra Cellular Matrix (ECM), and a mature state corresponding to well-formed connective tissues. This has allowed for the cellular processes of migration, proliferation and apoptosis to be described simultaneously with the changing ECM properties through strain driven diffusion, growth, maturation and resorption terms. A series of finite element simulations were carried out on idealized cantilever bending geometries. Starting from a tissue composition replicating a mid-diaphysis section of a long bone, a steady-state tissue formation was reached over a statically loaded period of 10,000 h (60 weeks). The results demonstrated that bone formation occurred in regions which are optimally physiologically strained. In two additional 1000 h bending simulations both cartilaginous and fibrous tissues were shown to form under specific geometrical and loading

The Biological Big Bang model for the major transitions in evolution

Directory of Open Access Journals (Sweden)

Koonin Eugene V

2007-08-01

Full Text Available Abstract Background Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal. Hypothesis I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model

Human evolution, life history theory, and the end of biological reproduction.

Science.gov (United States)

Last, Cadell

2014-01-01

Throughout primate history there have been three major life history transitions towards increasingly delayed sexual maturation and biological reproduction, as well as towards extended life expectancy. Monkeys reproduce later and live longer than do prosimians, apes reproduce later and live longer than do monkeys, and humans reproduce later and live longer than do apes. These life history transitions are connected to increased encephalization. During the last life history transition from apes to humans, increased encephalization co-evolved with increased dependence on cultural knowledge for energy acquisition. This led to a dramatic pressure for more energy investment in growth over current biological reproduction. Since the industrial revolution socioeconomic development has led to even more energy being devoted to growth over current biological reproduction. I propose that this is the beginning of an ongoing fourth major primate life history transition towards completely delayed biological reproduction and an extension of the evolved human life expectancy. I argue that the only fundamental difference between this primate life history transition and previous life history transitions is that this transition is being driven solely by cultural evolution, which may suggest some deeper evolutionary transition away from biological evolution is already in the process of occurring.

Factors Potentially Influencing Student Acceptance of Biological Evolution

Science.gov (United States)

Wiles, Jason R.

This investigation explored scientific, religious, and otherwise nonscientific factors that may influence student acceptance of biological evolution and related concepts, how students perceived these factors to have influenced their levels of acceptance of evolution and changes therein, and what patterns arose among students' articulations of how their levels of acceptance of evolution may have changed. This exploration also measured the extent to which students' levels of acceptance changed following a treatment designed to address factors identified as potentially affecting student acceptance of evolution. Acceptance of evolution was measured using the MATE instrument (Rutledge and Warden, 1999; Rutledge and Sadler, 2007) among participants enrolled in a secondary-level academic program during the summer prior to their final year of high school and as they transitioned to the post-secondary level. Student acceptance of evolution was measured to be significantly higher than pre-treatment levels both immediately following and slightly over one year after treatment. Qualitative data from informal questionnaires, from formal course evaluations, and from semi-structured interviews of students engaged in secondary level education and former students at various stages of post-secondary education confirmed that the suspected factors were perceived by participants to have influenced their levels of acceptance of evolution. Furthermore, participant reports provided insight regarding the relative effects they perceived these factors to have had on their evolution acceptance levels. Additionally, many participants reported that their science teachers in public schools had avoided, omitted, or denigrated evolution during instruction, and several of these students expressed frustration regarding what they perceived to have been a lack of education of an important scientific principle. Finally, no students expressed feelings of being offended by having been taught about

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

Evolution and Personal Religious Belief: Christian University Biology-Related Majors' Search for Reconciliation

Science.gov (United States)

Winslow, Mark W.; Staver, John R.; Scharmann, Lawrence C.

2011-01-01

The goal of this study was to explore Christian biology-related majors' perceptions of conflicts between evolution and their religious beliefs. This naturalistic study utilized a case study design of 15 undergraduate biology-related majors at or recent biology-related graduates from a mid-western Christian university. The broad sources of data…

Lack of Evolution Acceptance Inhibits Students' Negotiation of Biology-Based Socioscientific Issues

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Fowler, S. R.; Zeidler, D. L.

2016-01-01

The purpose of this study was to explore science content used during college students' negotiation of biology-based socioscientific issues (SSI) and examine how it related to students' conceptual understanding and acceptance of biological evolution. The Socioscientific Issues Questionnaire (SSI-Q) was developed to measure depth of evolutionary…

Does the nature of science influence college students' learning of biological evolution?

Science.gov (United States)

Butler, Wilbert, Jr.

This quasi-experimental, mixed-methods study assessed the influence of the nature of science (NOS) instruction on college students' learning of biological evolution. In this research, conducted in two introductory biology courses, in each course the same instruction was employed, with one important exception: in the experimental section students were involved in an explicit, reflective treatment of the nature of science (Explicit, reflective NOS), in the traditional treatment section, NOS was implicitly addressed (traditional treatment). In both sections, NOS aspects of science addressed included is tentative, empirically based, subjective, inferential, and based on relationship between scientific theories and laws. Students understanding of evolution, acceptance of evolution, and understanding of the nature of science were assessed before, during and after instruction. Data collection entailed qualitative and quantitative methods including Concept Inventory for Natural Selection (CINS), Measure of Acceptance of the Theory of Evolution (MATE) survey, Views of nature of Science (VNOS-B survey), as well as interviews, classroom observations, and journal writing to address understand students' views of science and understanding and acceptance of evolution. The quantitative data were analyzed via inferential statistics and the qualitative data were analyzed using grounded theory. The data analysis allowed for the construction and support for four assertions: Assertion 1: Students engaged in explicit and reflective NOS specific instruction significantly improved their understanding of the nature of science concepts. Alternatively, students engaged in instruction using an implicit approach to the nature of science did not improve their understanding of the nature of science to the same degree. The VNOS-B results indicated that students in the explicit, reflective NOS class showed the better understanding of the NOS after the course than students in the implicit NOS class

Quantum information and the problem of mechanisms of biological evolution.

Science.gov (United States)

Melkikh, Alexey V

2014-01-01

One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Evolution in health and medicine Sackler colloquium: 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

2010-01-26

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.

Trace elements at the intersection of marine biological and geochemical evolution

Science.gov (United States)

Robbins, Leslie J.; Lalonde, Stefan V.; Planavsky, Noah J.; Partin, Camille A.; Reinhard, Christopher T.; Kendall, Brian; Scott, Clinton T.; Hardisty, Dalton S.; Gill, Benjamin C.; Alessi, Daniel S.; Dupont, Christopher L.; Saito, Mak A.; Crowe, Sean A.; Poulton, Simon W.; Bekker, Andrey; Lyons, Timothy W.; Konhauser, Kurt O.

2016-01-01

Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages has yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth's ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies.

[Around biological evolution. Reflections of a physicist].

Science.gov (United States)

Sanchez-Palencia, Evariste

2016-01-01

This text is the written version of a talk at the Société de Biologie on February 17, 2016. It contains reflections of a non-biologist scientist on general problems of biological evolution, including the kind of causality involved, the ideas emerging from it, in particular the constructive and structuring character of phenomena such as predation, the role of stability and attractors. This leads to a larger reflection on dialectics, the general framework of evolving processes, which overpasses formal logic and instantaneousness. © Société de Biologie, 2016.

Three Southern high school biology teachers' perspectives on teaching evolution: Sociocultural influences

Science.gov (United States)

Kyzer, Peggy Mckewen

Organizations in science and science education call for students to have a thorough understanding of the theory of evolution. Yet many high school biology teachers do not teach evolution and/or include creationism in their instruction (National Academy of Science, 1998). Historically, the controversy surrounding evolution has created tension for teachers. This case study explored the sociocultural influences related to teaching evolution in three Southern 10th-grade public high school biology classrooms. It also explored the socially and culturally embedded influences on teachers' instructional goals and personal perspectives toward evolution as well as modification of instruction when evolution is taught. Theoretically framed using symbolic interactionism and sociocultural theory, data were collected between October 2003 and April 2004 and included classroom observations two to three times per week, artifacts, and in-depth interviews of the participating teachers, their science department chairpersons, their students, and a Protestant minister. The classroom teachers were unaware of the focus of the study until after evolution was taught. The analysis used in this study was an inductive, interpretative approach that allowed exploration of the sociocultural influences that affect how teachers teach evolution. The sociocultural influences and the lived experiences of each teacher created a continuum for teaching evolution. One of the participating teachers who was heavily involved in the community and one of its fundamentalist churches elected to avoid teaching evolution. Another participating teacher at the same school integrated the theory of evolution in every unit. The third teacher who taught in another school elected to teach evolution in a superficial manner to avoid conflict. The data revealed that the participating teachers' sociocultural situatedness influenced their decisions and instruction on evolution. The influence of strong religious beliefs within

Taiwan High School Biology Teachers' Acceptance and Understanding of Evolution and the Nature of Science

Science.gov (United States)

Chen, Li-Hua

2015-01-01

Evolution is the cornerstone of biological sciences, but anti-evolution teaching has become a global controversy since the introduction of evolutionary ideas into the United States high school science curricula in 1914. It is suggested that teachers' attitude toward and acceptance of the theory of evolution will influence their effect of teaching…

Biological information systems: Evolution as cognition-based information management.

Science.gov (United States)

Miller, William B

2018-05-01

An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reconstructing Anaximander's biological model unveils a theory of evolution akin to Darwin's, though centuries before the birth of science.

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Trevisanato, Siro Igino

2016-08-01

Anaximander's fragments on biology report a theory of evolution, which, unlike the development of other biological systems in the ancient Aegean, is naturalistic and is not based on metaphysics. According to Anaximander, evolution affected all living beings, including humans. The first biological systems formed in an aquatic environment, and were encased in a rugged and robust envelope. Evolution progressed with modifications that enabled the formation of more dynamic biological systems. For instance, after reaching land, the robust armors around aquatic beings dried up, and became brittle, This led to the loss of the armor and the development of more mobile life forms. Anaximander's theory combines observations of animals with speculations, and as such mirrors the more famous theory of evolution by Charles Darwin expressed 24 centuries later. The poor reception received by Anaximander's model in his time, illustrates a zeitgeist that would explain the contemporary lag phase in the development of biology and, as a result, medicine, in the ancient western world.

Breeding biology and the evolution of dynamic sexual dichromatism in frogs.

Science.gov (United States)

Bell, R C; Webster, G N; Whiting, M J

2017-12-01

Dynamic sexual dichromatism is a temporary colour change between the sexes and has evolved independently in a wide range of anurans, many of which are explosive breeders wherein males physically compete for access to females. Behavioural studies in a few species indicate that dynamic dichromatism functions as a visual signal in large breeding aggregations; however, the prevalence of this trait and the social and environmental factors underlying its expression are poorly understood. We compiled a database of 178 anurans with dynamic dichromatism that include representatives from 15 families and subfamilies. Dynamic dichromatism is common in two of the three subfamilies of hylid treefrogs. Phylogenetic comparative analyses of 355 hylid species (of which 95 display dynamic dichromatism) reveal high transition rates between dynamic dichromatism, ontogenetic (permanent) dichromatism and monochromatism reflecting the high evolutionary lability of this trait. Correlated evolution in hylids between dynamic dichromatism and forming large breeding aggregations indicates that the evolution of large breeding aggregations precedes the evolution of dynamic dichromatism. Multivariate phylogenetic logistic regression recovers the interaction between biogeographic distribution and forming breeding aggregations as a significant predictor of dynamic dichromatism in hylids. Accounting for macroecological differences between temperate and tropical regions, such as seasonality and the availability of breeding sites, may improve our understanding of ecological contexts in which dynamic dichromatism is likely to arise in tropical lineages and why it is retained in some temperate species and lost in others. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Without it no music: cognition, biology and evolution of musicality

Science.gov (United States)

Honing, Henkjan; ten Cate, Carel; Peretz, Isabelle; Trehub, Sandra E.

2015-01-01

Musicality can be defined as a natural, spontaneously developing trait based on and constrained by biology and cognition. Music, by contrast, can be defined as a social and cultural construct based on that very musicality. One critical challenge is to delineate the constituent elements of musicality. What biological and cognitive mechanisms are essential for perceiving, appreciating and making music? Progress in understanding the evolution of music cognition depends upon adequate characterization of the constituent mechanisms of musicality and the extent to which they are present in non-human species. We argue for the importance of identifying these mechanisms and delineating their functions and developmental course, as well as suggesting effective means of studying them in human and non-human animals. It is virtually impossible to underpin the evolutionary role of musicality as a whole, but a multicomponent perspective on musicality that emphasizes its constituent capacities, development and neural cognitive specificity is an excellent starting point for a research programme aimed at illuminating the origins and evolution of musical behaviour as an autonomous trait. PMID:25646511

Elastic Multi-scale Mechanisms: Computation and Biological Evolution.

Science.gov (United States)

Diaz Ochoa, Juan G

2018-01-01

Explanations based on low-level interacting elements are valuable and powerful since they contribute to identify the key mechanisms of biological functions. However, many dynamic systems based on low-level interacting elements with unambiguous, finite, and complete information of initial states generate future states that cannot be predicted, implying an increase of complexity and open-ended evolution. Such systems are like Turing machines, that overlap with dynamical systems that cannot halt. We argue that organisms find halting conditions by distorting these mechanisms, creating conditions for a constant creativity that drives evolution. We introduce a modulus of elasticity to measure the changes in these mechanisms in response to changes in the computed environment. We test this concept in a population of predators and predated cells with chemotactic mechanisms and demonstrate how the selection of a given mechanism depends on the entire population. We finally explore this concept in different frameworks and postulate that the identification of predictive mechanisms is only successful with small elasticity modulus.

Darwin's legacy: why biology is not physics, or why evolution has not become a common sense.

Science.gov (United States)

Singh, Rama S

2011-10-01

Cosmology and evolution together have enabled us to look deep into the past and comprehend evolution-from the big bang to the cosmos, from molecules to humans. Here, I compare the nature of theories in biology and physics and ask why physical theories get accepted by the public without necessarily comprehending them but biological theories do not. Darwin's theory of natural selection, utterly simple in its premises but profound in its consequences, is not accepted widely. Organized religions, and creationists in particularly, have been the major critic of evolution, but not all opposition to evolution comes from organized religions. A great many people, between evolutionary biologists on one hand and creationists on the other, many academics included, who may not be logically opposed to evolution nevertheless do not accept it. This is because the process of and the evidence for evolution are invisible to a nonspecialist, or the theory may look too simple to explain complex traits to some, or because people compare evolution against God and find evolutionary explanations threatening to their beliefs. Considering how evolution affects our lives, including health and the environment to give just two examples, a basic course in evolution should become a required component of all our college and university educational systems.

Without it no music: cognition, biology and evolution of musicality.

Science.gov (United States)

Honing, Henkjan; ten Cate, Carel; Peretz, Isabelle; Trehub, Sandra E

2015-03-19

Musicality can be defined as a natural, spontaneously developing trait based on and constrained by biology and cognition. Music, by contrast, can be defined as a social and cultural construct based on that very musicality. One critical challenge is to delineate the constituent elements of musicality. What biological and cognitive mechanisms are essential for perceiving, appreciating and making music? Progress in understanding the evolution of music cognition depends upon adequate characterization of the constituent mechanisms of musicality and the extent to which they are present in non-human species. We argue for the importance of identifying these mechanisms and delineating their functions and developmental course, as well as suggesting effective means of studying them in human and non-human animals. It is virtually impossible to underpin the evolutionary role of musicality as a whole, but a multicomponent perspective on musicality that emphasizes its constituent capacities, development and neural cognitive specificity is an excellent starting point for a research programme aimed at illuminating the origins and evolution of musical behaviour as an autonomous trait. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Use of the "Tree" Analogy in Evolution Teaching by Biology Teachers

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Marcelos, Maria Fatima; Nagem, Ronaldo Luiz

2012-01-01

This work discusses the use of Darwin's "Tree of Life" as a didactic analogy and metaphor in teaching evolution. It investigates whether biology teachers of pupils from 17 to 18 years old know Darwin's text "Tree of Life". In addition, it examines whether those teachers systematically employ either the analogies present in that…

MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution

Directory of Open Access Journals (Sweden)

Xia Xuhua

2005-03-01

Full Text Available Abstract Background MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. Results We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. Conclusion MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454.

Use of the "Tree" Analogy in Evolution Teaching by Biology Teachers

Science.gov (United States)

Marcelos, Maria Fátima; Nagem, Ronaldo Luiz

2012-04-01

This work discusses the use of Darwin's `Tree of Life' as a didactic analogy and metaphor in teaching evolution. It investigates whether biology teachers of pupils from 17 to 18 years old know Darwin's text `Tree of Life'. In addition, it examines whether those teachers systematically employ either the analogies present in that text or other analogies between the tree and evolution, and whether they adopt a specific methodology for teaching with analogies and metaphors (A&M). The academic training of teachers regarding use of A&M is review briefly. A diagnostic study was carried out with biology teachers in a public school in the town of Contagem in the state of Minas Gerais in Brazil. The data were obtained through direct observation, questionnaires and a focus group. The teachers pointed out in the questionnaires that some details of Darwin's analogy are utilized as a resource. However, analysis of the data indicates that the `Tree of Life' text is not known or utilized in class. At the same time, the teachers state that they use aspects of the tree as a didactic resource to teach evolution and that its use facilitates the learning of content. The teachers have little knowledge of specific methodologies of teaching with analogies and metaphors, revealing that their training is incomplete in this area.

Biological adaptations for functional features of language in the face of cultural evolution.

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Christiansen, Morten H; Reali, Florencia; Chater, Nick

2011-04-01

Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

[Historic and functional biology: the inadequacy of a system theory of evolution].

Science.gov (United States)

Regelmann, J P

1982-01-01

In the first half of the 20th century neo-Kantianism in a broad sense proved itself the main conceptual and methodological background of the central European biology. As such it contributed much to the victory on the typological, idealistic-morphological and psycho-vitalistic interpretations of life. On the other hand it could not give tools to the biologists for working out a strictly darwinian evolution theory. Kant's theory of organism was conceived without evolution as a theory of the internal functionality of the organism. There was only some 'play' with the evolutionary differentiation of the species. Since then the disputes around the work of August Weismann, a synthetical evolution theory which is now behind time, arose. This theory developed from coinciding claims, elaborated by geneticists, mathematicians, and by biologists studying development, natural history and systematics. This was done under a strong influence of marxist ideas. Through the interweaving of such different approaches it was possible for this evolutionary synthesis to influence successfully the development of evolution research during more than 40 years. Philosophically speaking modern evolution theory means therefore an aversion, even a positive abolition of Kantian positions. A number of biologists however--as L. von Bertalanffy--refused to adhere to a misinterpreted Kantian methodology and oriented themselves to an approach via system theory, which obtained a place in evolution research. In fact this is a Kantian approach as well. They only repeated the Kantian dilemma of the evolution which can also be found in Lamarck and Hegel. The system theory of the functionality of the organism never reaches to the level of the evolving species, but remains always on the level of epigenetic thinking, because of its philosophical origin. This paper points out the consequences of this still current dilemma. At the same time an all-enclosing reflection on the methodological, epistemological and

Biomimicry, Biofabrication, and Biohybrid Systems: The Emergence and Evolution of Biological Design.

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Raman, Ritu; Bashir, Rashid

2017-10-01

The discipline of biological design has a relatively short history, but has undergone very rapid expansion and development over that time. This Progress Report outlines the evolution of this field from biomimicry to biofabrication to biohybrid systems' design, showcasing how each subfield incorporates bioinspired dynamic adaptation into engineered systems. Ethical implications of biological design are discussed, with an emphasis on establishing responsible practices for engineering non-natural or hypernatural functional behaviors in biohybrid systems. This report concludes with recommendations for implementing biological design into educational curricula, ensuring effective and responsible practices for the next generation of engineers and scientists. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Student world view as a framework for learning genetics and evolution in high school biology

Science.gov (United States)

McCoy, Roger Wesley

Statement of the problem. Few studies in biology education have examined the underlying presuppositions which guide thinking and concept learning in adolescents. The purpose of this study was to describe and understand the biological world views of a variety of high school students before they take biology courses. Specifically, the study examined student world views in the domains of Classification, Relationship and Causation related to the concepts of heredity, evolution and biotechnology. The following served as guiding questions: (1) What are the personal world views of high school students entering biology classes, related to the domain of Classification, Relationship and Causality? (2) How do these student world views confound or enhance the learning of basic concepts in genetics and evolution? Methods. An interpretive method was chosen for this study. The six student participants were ninth graders and represented a wide range of world view backgrounds. A series of three interviews was conducted with each participant, with a focus group used for triangulation of data. The constant comparative method was used to categorize the data and facilitate the search for meaningful patterns. The analysis included a thick description of each student's personal views of classification, evolution and the appropriate use of biotechnology. Results. The study demonstrates that world view is the basis upon which students build knowledge in biology. The logic of their everyday thinking may not match that of scientists. The words they use are sometimes inconsistent with scientific terminology. This study provides evidence that students voice different opinions depending on the social situation, since they are strongly influenced by peers. Students classify animals based on behaviors. They largely believe that the natural world is unpredictable, and that humans are not really part of that world. Half are unlikely to accept the evolution of humans, but may accept it in other

A Novel Application of Synthetic Biology and Directed Evolution to Engineer Phage-based Antibiotics

Energy Technology Data Exchange (ETDEWEB)

Wu, Meiye [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

2014-09-01

The emergence of multiple drug resistant bacteria poses threats to human health, agriculture and food safety. Annually over 100,000 deaths and up to $20 billion loss to the U.S. economy are attributed to multiple drug resistant bacteria. With only four new chemical antibiotics in the drug development pipeline, we are in dire need of new solutions to address the emerging threat of multiple drug resistance. We propose a paradigm-changing approach to address the multi-drug resistant bacteria problem by utilizing Synthetic Biology (SynBio) methodologies to create and evolve “designer” bacteriophages or phages – viruses that specifically infect bacteria – to infect and kill newly emerging pathogenic bacterial strains WITHOUT the need for chemical antibiotics. A major advantage of using phage to combat pathogenic bacteria is that phages can co-evolve with their bacterial host, and Sandia can be the first in the world to establish an industrial scale Synthetic Biology pipeline for phage directed evolution for safe, targeted, customizable solution to bacterial drug resistance. Since there is no existing phage directed evolution effort within or outside of Sandia, this proposal is suitable as a high-risk LDRD effort to create the first pipeline for such an endeavor. The high potential reward nature of this proposal will be the immediate impact in decontamination and restoration of surfaces and infrastructure, with longer term impact in human or animal therapeutics. The synthetic biology and screening approaches will lead to fundamental knowledge of phage/bacteria co-evolution, making Sandia a world leader in directed evolution of bacteriophages.

Life’s a Gas: A Thermodynamic Theory of Biological Evolution

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Keith R. Skene

2015-07-01

Full Text Available This paper outlines a thermodynamic theory of biological evolution. Beginning with a brief summary of the parallel histories of the modern evolutionary synthesis and thermodynamics, we use four physical laws and processes (the first and second laws of thermodynamics, diffusion and the maximum entropy production principle to frame the theory. Given that open systems such as ecosystems will move towards maximizing dispersal of energy, we expect biological diversity to increase towards a level, Dmax, representing maximum entropic production (Smax. Based on this theory, we develop a mathematical model to predict diversity over the last 500 million years. This model combines diversification, post-extinction recovery and likelihood of discovery of the fossil record. We compare the output of this model with that of the observed fossil record. The model predicts that life diffuses into available energetic space (ecospace towards a dynamic equilibrium, driven by increasing entropy within the genetic material. This dynamic equilibrium is punctured by extinction events, which are followed by restoration of Dmax through diffusion into available ecospace. Finally we compare and contrast our thermodynamic theory with the MES in relation to a number of important characteristics of evolution (progress, evolutionary tempo, form versus function, biosphere architecture, competition and fitness.

The Origin and Evolution of Complex Enough Systems in Biology

OpenAIRE

Brändas, Erkki

2017-01-01

Recent criticisms of Neo-Darwinism are considered and disputed within the setting of recent advances in chemical physics. A related query, viz., the ontological thesis, that everything is physical, confronts a crucial test on the validity of reductionism as a fundamental approach to science.  While traditional ‘physicalism’ interprets evolution as a sequence of physical accidents governed by the second law of thermodynamics, the concepts of biology concern processes that owe their goal-direct...

Science for Survival: The Modern Synthesis of Evolution and The Biological Sciences Curriculum Study

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Green, Lisa Anne

In this historical dissertation, I examined the process of curriculum development in the Biological Sciences Curriculum Study (BSCS) in the United States during the period 1959-1963. The presentation of evolution in the high school texts was based on a more robust form of Darwinian evolution which developed during the 1930s and 1940s called "the modern synthesis of evolution." Building primarily on the work of historians Vassiliki Smocovitis and John L. Rudolph, I used the archival papers and published writings of the four architects of the modern synthesis and the four most influential leaders of the BSCS in regards to evolution to investigate how the modern synthetic theory of evolution shaped the BSCS curriculum. The central question was "Why was evolution so important to the BSCS to make it the central theme of the texts?" Important answers to this question had already been offered in the historiography, but it was still not clear why every citizen in the world needed to understand evolution. I found that the emphasis on natural selection in the modern synthesis shifted the focus away from humans as passive participants to the recognition that humans are active agents in their own cultural and biological evolution. This required re-education of the world citizenry, which was accomplished in part by the BSCS textbooks. I also found that BSCS leaders Grobman, Glass, and Muller had serious concerns regarding the effects of nuclear radiation on the human gene pool, and were actively involved in informing th public. Lastly, I found that concerns of 1950s reform eugenicists were addressed in the BSCS textbooks, without mentioning eugenics by name. I suggest that the leaders of the BSCS, especially Bentley Glass and Hermann J. Muller, thought that students needed to understand genetics and evolution to be able to make some of the tough choices they might be called on to make as the dominant species on earth and the next reproductive generation in the nuclear age. This

Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process

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James A. Shapiro

2016-06-01

Full Text Available The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.

The relative importance of physical and biological energy in landscape evolution

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Turowski, J. M.; Schwanghart, W.

2017-12-01

Landscapes are formed by the interplay of uplift and geomorphic processes, including interacting and competing physical and biological processes. For example, roots re-inforce soil and thereby stabilize hillslopes and the canopy cover of the forest may mediate the impact of precipitation. Furthermore, plants and animals act as geomorphic agents, directly altering landscape response and dynamics by their actions: tree roots may crack rocks, thus changing subsurface water flows and exposing fresh material for denudation; fungi excrete acids that accelerate rates of chemical weathering, and burrowing animals displace soil and rocks while digging holes for shelter or in search of food. Energetically, landscapes can be viewed as open systems in which topography stores potential energy above a base level. Tectonic processes add energy to the system by uplift and mechanically altering rock properties. Especially in unvegetated regions, erosion and transport by wind can be an important geomorphic process. Advection of atmospheric moisture in high altitudes provides potential energy that is converted by water fluxes through catchments. At the same time, the conversion of solar energy through atmospheric and biological processes drives primary production of living organisms. If we accept that biota influence geomorphic processes, then what is their energetic contribution to landscape evolution relative to physical processes? Using two case studies, we demonstrate that all components of energy input are negligible apart from biological production, quantified by net primary productivity (NPP) and potential energy conversion by water that is placed high up in the landscape as rainfall and leaves it as runoff. Assuming that the former is representative for biological energy and the latter for physical energy, we propose that the ratio of these two values can be used as a proxy for the relative importance of biological and physical processes in landscape evolution. All necessary

Biological evolution of replicator systems: towards a quantitative approach.

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Martin, Osmel; Horvath, J E

2013-04-01

The aim of this work is to study the features of a simple replicator chemical model of the relation between kinetic stability and entropy production under the action of external perturbations. We quantitatively explore the different paths leading to evolution in a toy model where two independent replicators compete for the same substrate. To do that, the same scenario described originally by Pross (J Phys Org Chem 17:312-316, 2004) is revised and new criteria to define the kinetic stability are proposed. Our results suggest that fast replicator populations are continually favored by the effects of strong stochastic environmental fluctuations capable to determine the global population, the former assumed to be the only acting evolution force. We demonstrate that the process is continually driven by strong perturbations only, and that population crashes may be useful proxies for these catastrophic environmental fluctuations. As expected, such behavior is particularly enhanced under very large scale perturbations, suggesting a likely dynamical footprint in the recovery patterns of new species after mass extinction events in the Earth's geological past. Furthermore, the hypothesis that natural selection always favors the faster processes may give theoretical support to different studies that claim the applicability of maximum principles like the Maximum Metabolic Flux (MMF) or Maximum Entropy Productions Principle (MEPP), seen as the main goal of biological evolution.

Towards a Universal Biology: Is the Origin and Evolution of Life Predictable?

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Rothschild, Lynn J.

2017-01-01

The origin and evolution of life seems an unpredictable oddity, based on the quirks of contingency. Celebrated by the late Stephen Jay Gould in several books, "evolution by contingency" has all the adventure of a thriller, but lacks the predictive power of the physical sciences. Not necessarily so, replied Simon Conway Morris, for convergence reassures us that certain evolutionary responses are replicable. The outcome of this debate is critical to Astrobiology. How can we understand where we came from on Earth without prophesy? Further, we cannot design a rational strategy for the search for life elsewhere - or to understand what the future will hold for life on Earth and beyond - without extrapolating from pre-biotic chemistry and evolution. There are several indirect approaches to understanding, and thus describing, what life must be. These include philosophical approaches to defining life (is there even a satisfactory definition of life?), using what we know of physics, chemistry and life to imagine alternate scenarios, using different approaches that life takes as pseudoreplicates (e.g., ribosomal vs non-ribosomal protein synthesis), and experimental approaches to understand the art of the possible. Given that: (1) Life is a process based on physical components rather than simply an object; (2). Life is likely based on organic carbon and needs a solvent for chemistry, most likely water, and (3) Looking for convergence in terrestrial evolution we can predict certain tendencies, if not quite "laws", that provide predictive power. Biological history must obey the laws of physics and chemistry, the principles of natural selection, the constraints of an evolutionary past, genetics, and developmental biology. This amalgam creates a surprising amount of predictive power in the broad outline. Critical is the apparent prevalence of organic chemistry, and uniformity in the universe of the laws of chemistry and physics. Instructive is the widespread occurrence of

Quantum selfish gene (biological evolution in terms of quantum mechanics)

OpenAIRE

Ozhigov, Yuri I.

2013-01-01

I propose to treat the biological evolution of genoms by means of quantum mechanical tools. We start with the concept of meta- gene, which specifies the "selfish gene" of R.Dawkins. Meta- gene encodes the abstract living unity, which can live relatively independently of the others, and can contain a few real creatures. Each population of living creatures we treat as the wave function on meta- genes, which module squared is the total number of creatures with the given meta-gene, and the phase ...

The genome sequence of taurine cattle: A window to ruminant biology and evolution

Science.gov (United States)

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (ma...

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

Science.gov (United States)

Currin, Andrew; Swainston, Neil; Day, Philip J.

2015-01-01

The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the ‘search space’ of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (K d) and catalytic (k cat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving k cat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the ‘best’ amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

OpenAIRE

Mi, Huaiyu; Guo, Nan; Kejariwal, Anish; Thomas, Paul D.

2006-01-01

PANTHER is a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles. Since 2005, there have been three main improvements to PANTHER. First, the sequences used to create evolutionary trees are carefully selected to provide coverage of phylogenetic as well as functional information. Second, PANTHER is now a member of the InterPro Consortium, and the PANTHER hidden markov Models (HMMs) are distri...

Time-evolution of the entropy of fluctuations in some biological systems as investigated by NMR

International Nuclear Information System (INIS)

Lenk, R.

1979-01-01

A simple expression for the entropy of fluctuations has been developed, using the tunnelling-effect model. This gives the possibility to estimate the changes and evolution of entropy in non-crystalline and biological samples by NMR investigations. On the other hand, the oscillatory character of the time-evolution of some properties, experimentally found in the investigated samples of plants, is interpreted in terms of the generalized master equation with an exponential memory function. (Auth.)

The evolution of fairness in a biological market.

Science.gov (United States)

André, Jean-Baptiste; Baumard, Nicolas

2011-05-01

Human beings universally express a concern for the fairness of social interactions, and it remains an open question that which ultimate factors led to the evolution of this preference. Here, we present a model accounting for the evolution of fairness on the basis of individual selection alone. We consider a simple social interaction based on the Dictator Game. Two individuals, a "proposer" and a "responder," have an opportunity to split a resource. When they have no choice but to interact together, the most powerful (here the proposer) reaps all the profits and fairness cannot evolve. Partner choice is the key lever to overcome this difficulty. Rather than just two individuals, we consider a population composed of two classes of individuals (either proposers or responders), and we allow the responders to choose their partner. In such a "biological market," fairness evolves as an "equilibrium price," resulting from an ecological equivalent of the law of supply and demand. If a class is disadvantaged by the chosen resource partition (i.e., if it frequently receives less than half of the resource), it is outcompeted by the other one, and automatically becomes rarer. This rarity grants it an advantage on the market, which yields in turn to the evolution of a more favorable partition. Splitting the resource into two identical halves, or more generally in a way that equalizes the payoffs of the two classes, is then the only evolutionarily stable outcome. Beyond human fairness, this mechanism also opens up new ways of explaining the distribution of benefits in many mutualistic interactions. No Claim to original U.S. government works.

Evolution of bow-tie architectures in biology.

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Tamar Friedlander

2015-03-01

Full Text Available Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal determines the size of the narrowest part of the network-that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.

Formation of dominant mode by evolution in biological systems

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Furusawa, Chikara; Kaneko, Kunihiko

2018-04-01

A reduction in high-dimensional phenotypic states to a few degrees of freedom is essential to understand biological systems. Here, we show evolutionary robustness causes such reduction which restricts possible phenotypic changes in response to a variety of environmental conditions. First, global protein expression changes in Escherichia coli after various environmental perturbations were shown to be proportional across components, across different types of environmental conditions. To examine if such dimension reduction is a result of evolution, we analyzed a cell model—with a huge number of components, that reproduces itself via a catalytic reaction network—and confirmed that common proportionality in the concentrations of all components is shaped through evolutionary processes. We found that the changes in concentration across all components in response to environmental and evolutionary changes are constrained to the changes along a one-dimensional major axis, within a huge-dimensional state space. On the basis of these observations, we propose a theory in which such constraints in phenotypic changes are achieved both by evolutionary robustness and plasticity and formulate this proposition in terms of dynamical systems. Accordingly, broad experimental and numerical results on phenotypic changes caused by evolution and adaptation are coherently explained.

Learning bias, cultural evolution of language, and the biological evolution of the language faculty.

Science.gov (United States)

Smith, Kenny

2011-04-01

The biases of individual language learners act to determine the learnability and cultural stability of languages: learners come to the language learning task with biases which make certain linguistic systems easier to acquire than others. These biases are repeatedly applied during the process of language transmission, and consequently should effect the types of languages we see in human populations. Understanding the cultural evolutionary consequences of particular learning biases is therefore central to understanding the link between language learning in individuals and language universals, common structural properties shared by all the world’s languages. This paper reviews a range of models and experimental studies which show that weak biases in individual learners can have strong effects on the structure of socially learned systems such as language, suggesting that strong universal tendencies in language structure do not require us to postulate strong underlying biases or constraints on language learning. Furthermore, understanding the relationship between learner biases and language design has implications for theories of the evolution of those learning biases: models of gene-culture coevolution suggest that, in situations where a cultural dynamic mediates between properties of individual learners and properties of language in this way, biological evolution is unlikely to lead to the emergence of strong constraints on learning.

A Course in Evolutionary Biology: Engaging Students in the "Practice" of Evolution. Research Report.

Science.gov (United States)

Passmore, Cynthia; Stewart, James

Recent education reform documents emphasize the need for students to develop a rich understanding of evolution's power to integrate knowledge of the natural world. This paper describes a nine-week high school course designed to help students understand evolutionary biology by engaging them in developing, elaborating, and using Charles Darwin's…

Can Man Control His Biological Evolution? A Symposium on Genetic Engineering. Man's Responsibility to His Future

Science.gov (United States)

Hoagland, Hudson

1972-01-01

Biological evolution can be carried out in the laboratory. With new knowledge available in genetics, possibilities are raised that genetic characters can be transferred in the future to embryos according to a predetermined plan. (PS)

The Effect of Using Evolution Textbook Based on ICT and Metacognitive on Cognitive Competence of Biology Students at State University of Padang

Science.gov (United States)

Helendra, H.; Fadilah, M.; Arsih, F.

2018-04-01

Implementation of evolution lectures at Biology Department Faculty of Mathematics and Natural Sciences State University of Padang has been considered not optimal. The reasons are the limited availability of textbooks and students' learning attitudes. Because currently the students are very familiar with the internet and even has become a necessity, it has developed textbooks of evolution based on ICT and metacognitive. Selection of ICT based is in order to optimize the utilization of multimedia, and this is very compatible with the development of learning technology. While metacognitive based is in order to train students' learning attitudes to be able to think analysis, creative and evaluative. The aim of this study is to determine the effect of the use of evolution textbooks based on ICT and metacognitive to the cognitive competence of students of Biology Department State University of Padang. The data of this research is students' cognitive competence obtained from the implementation of effectiveness test of evolution textbook in the form of student learning outcomes. The research instrument is a learning result test designed to determine students’ cognitive competence. The subject of the study is a group of students in evolution course consisting of 33 students. Lectures are conducted through face-to-face and online lectures on Edmodo’s platform. The result of data analysis shows that there is an increase of cognitive competence of biology students after learning using ICT and metacognitive based evolution textbook, where average achievement is 77.72 with Percentage of achievement of criteria mastery is 81.25%. Therefore, it can be concluded that the evolution textbook based on ICT and metacognitive is effective in improving cognitive competence of students of Biology Department, Universitas Negeri Padang.

Mutation rules and the evolution of sparseness and modularity in biological systems.

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Tamar Friedlander

Full Text Available Biological systems exhibit two structural features on many levels of organization: sparseness, in which only a small fraction of possible interactions between components actually occur; and modularity--the near decomposability of the system into modules with distinct functionality. Recent work suggests that modularity can evolve in a variety of circumstances, including goals that vary in time such that they share the same subgoals (modularly varying goals, or when connections are costly. Here, we studied the origin of modularity and sparseness focusing on the nature of the mutation process, rather than on connection cost or variations in the goal. We use simulations of evolution with different mutation rules. We found that commonly used sum-rule mutations, in which interactions are mutated by adding random numbers, do not lead to modularity or sparseness except for in special situations. In contrast, product-rule mutations in which interactions are mutated by multiplying by random numbers--a better model for the effects of biological mutations--led to sparseness naturally. When the goals of evolution are modular, in the sense that specific groups of inputs affect specific groups of outputs, product-rule mutations also lead to modular structure; sum-rule mutations do not. Product-rule mutations generate sparseness and modularity because they tend to reduce interactions, and to keep small interaction terms small.

Evolution across the Curriculum: Microbiology

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Burmeister, Alita R.; Smith, James J.

2016-01-01

An integrated understanding of microbiology and evolutionary biology is essential for students pursuing careers in microbiology and healthcare fields. In this Perspective, we discuss the usefulness of evolutionary concepts and an overall evolutionary framework for students enrolled in microbiology courses. Further, we propose a set of learning goals for students studying microbial evolution concepts. We then describe some barriers to microbial evolution teaching and learning and encourage the continued incorporation of evidence-based teaching practices into microbiology courses at all levels. Next, we review the current status of microbial evolution assessment tools and describe some education resources available for teaching microbial evolution. Successful microbial evolution education will require that evolution be taught across the undergraduate biology curriculum, with a continued focus on applications and applied careers, while aligning with national biology education reform initiatives. Journal of Microbiology & Biology Education PMID:27158306

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

OpenAIRE

Elsik, Christine G.; Tellam, Ross L.; Worley, Kim C.; Gibbs, Richard A.; Abatepaulo, Antonio R. R.; Abbey, Colette A.; Adelson, David L.; Aerts, Jan; Ahola, Virpi; Alexander, Lee; Alioto, Tyler; Almeida, Iassudara G.; Amadio, Ariel F.; Anatriello, Elen; Antonarakis, Stylianos E.

2009-01-01

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specifi...

THE EVOLUTION OF THE KREBS CYCLE: A PROMISING THEME FOR MEANINGFUL BIOCHEMISTRY LEARNING IN BIOLOGY

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C. Costa

2015-08-01

Full Text Available INTRODUCTION: Evolution has been recognized as a key concept for biologists. In order to motivate biology undergraduates for contents of central energetic metabolism, we addressed the Krebs cycle structure and functions to an evolutionary view. To this end, we created a study guide which contextualizes the emergence of the cyclic pathway, in light of the prokaryotic influence since early Earth anaerobic condition to oxygen rise in atmosphere. OBJECTIVES: The main goal is to highlight the educational potential of the material whose subject is scarcely covered in biochemistry textbooks. MATERIALS AND METHODS: The study guide is composed by three interrelated sections, the problem (Section 1, designed to arouse curiosity, inform and motivate students; an introductory text (Section 2 about life evolution, including early micro-organisms and Krebs cycle emergence, and questions (Section 3 for debate. The activity consisted on a peer discussion session, with instructors tutoring. The questions were designed to foster exchange of ideas in an ever-increasing level of complexity, and cover subjects from early atmospheric conditions to organization of the metabolism along the subsequent geological ages. RESULTS AND DISCUSSION: We noticed that students were engaged and motivated by the task, especially during group discussion. Based on students’ feedbacks and class observations, we learned that the material raised curiosity and stimulated discussion among peers. It brought a historical and purposeful way of dealing with difficult biochemical concepts. CONCLUSIONS: The whole experience suggests that the study guide was a stimulus for broadening comprehension of the Krebs cycle, reinforcing the evolutionary stance as an important theme for biology and biochemistry understanding. On the other hand, we do not underestimate the fact that approaching Krebs cycle from an evolutionary standpoint is a quite complex discussion for the majority of students

Controversy in Biology Classrooms—Citizen Science Approaches to Evolution and Applications to Climate Change Discussions

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Rachel A. Yoho

2015-11-01

Full Text Available The biological sciences encompass topics considered controversial by the American public, such as evolution and climate change. We believe that the development of climate change education in the biology classroom is better informed by an understanding of the history of the teaching of evolution. A common goal for science educators should be to engender a greater respect for and appreciation of science among students while teaching specific content knowledge. Citizen science has emerged as a viable yet underdeveloped method for engaging students of all ages in key scientific issues that impact society through authentic data-driven scientific research. Where successful, citizen science may open avenues of communication and engagement with the scientific process that would otherwise be more difficult to achieve. Citizen science projects demonstrate versatility in education and the ability to test hypotheses by collecting large amounts of often publishable data. We find a great possibility for science education research in the incorporation of citizen science projects in curriculum, especially with respect to “hot topics” of socioscientific debate based on our review of the findings of other authors.

The evolution of the Faculty of Language from a Chomskyan perspective: bridging linguistics and biology.

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Longa, Victor Manuel

2013-01-01

While language was traditionally considered a purely cultural trait, the advent of Noam Chomsky's Generative Grammar in the second half of the twentieth century dramatically challenged that view. According to that theory, language is an innate feature, part of the human biological endowment. If language is indeed innate, it had to biologically evolve. This review has two main objectives: firstly, it characterizes from a Chomskyan perspective the evolutionary processes by which language could have come into being. Secondly, it proposes a new method for interpreting the archaeological record that radically differs from the usual types of evidence Paleoanthropology has concentrated on when dealing with language evolution: while archaeological remains have usually been regarded from the view of the behavior they could be associated with, the paper will consider archaeological remains from the view of the computational processes and capabilities at work for their production. This computational approach, illustrated with a computational analysis of prehistoric geometric engravings, will be used to challenge the usual generative thinking on language evolution, based on the high specificity of language. The paper argues that the biological machinery of language is neither specifically linguistic nor specifically human, although language itself can still be considered a species-specific innate trait. From such a view, language would be one of the consequences of a slight modification operated on an ancestral architecture shared with vertebrates.

Colloquium paper: uniquely human evolution of sialic acid genetics and biology.

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Varki, Ajit

2010-05-11

Darwinian evolution of humans from our common ancestors with nonhuman primates involved many gene-environment interactions at the population level, and the resulting human-specific genetic changes must contribute to the "Human Condition." Recent data indicate that the biology of sialic acids (which directly involves less than 60 genes) shows more than 10 uniquely human genetic changes in comparison with our closest evolutionary relatives. Known outcomes are tissue-specific changes in abundant cell-surface glycans, changes in specificity and/or expression of multiple proteins that recognize these glycans, and novel pathogen regimes. Specific events include Alu-mediated inactivation of the CMAH gene, resulting in loss of synthesis of the Sia N-glycolylneuraminic acid (Neu5Gc) and increase in expression of the precursor N-acetylneuraminic acid (Neu5Ac); increased expression of alpha2-6-linked Sias (likely because of changed expression of ST6GALI); and multiple changes in SIGLEC genes encoding Sia-recognizing Ig-like lectins (Siglecs). The last includes binding specificity changes (in Siglecs -5, -7, -9, -11, and -12); expression pattern changes (in Siglecs -1, -5, -6, and -11); gene conversion (SIGLEC11); and deletion or pseudogenization (SIGLEC13, SIGLEC14, and SIGLEC16). A nongenetic outcome of the CMAH mutation is human metabolic incorporation of foreign dietary Neu5Gc, in the face of circulating anti-Neu5Gc antibodies, generating a novel "xeno-auto-antigen" situation. Taken together, these data suggest that both the genes associated with Sia biology and the related impacts of the environment comprise a relative "hot spot" of genetic and physiological changes in human evolution, with implications for uniquely human features both in health and disease.

A hypothesis on the biological origins and social evolution of music and dance

Directory of Open Access Journals (Sweden)

Tianyan eWang

2015-02-01

Full Text Available The origins of music and musical emotions is still an enigma, here I propose a comprehensive hypothesis on the origins and evolution of music, dance and speech from a biological and sociological perspective. I suggest that every pitch interval between neighboring notes in music represents corresponding movement pattern through interpreting the Doppler effect of sound, which not only provides a possible explanation to the transposition invariance of music, but also integrates music and dance into a common form—rhythmic movements. Accordingly, investigating the origins of music poses the question: why do humans appreciate rhythmic movements? I suggest that human appreciation of rhythmic movements and rhythmic events developed from the natural selection of organisms adapting to the internal and external rhythmic environments. The perception and production of, as well as synchronization with external and internal rhythms are so vital for an organism’s survival and reproduction, that animals have a rhythm-related reward and emotion (RRRE system. The RRRE system enables the appreciation of rhythmic movements and events, and is integral to the origination of music, dance and speech. The first type of rewards and emotions (rhythm-related rewards and emotions, RRREs are evoked by music and dance, and have biological and social functions, which in turn, promote the evolution of music, dance and speech. These functions also evoke a second type of rewards and emotions, which I name society-related rewards and emotions (SRREs. The neural circuits of RRREs and SRREs develop in species formation and personal growth, with congenital and acquired characteristics, respectively, namely music is the combination of nature and culture. This hypothesis provides probable selection pressures and outlines the evolution of music, dance and speech. The links between the Doppler effect and the RRREs and SRREs can be empirically tested, making the current hypothesis

A hypothesis on the biological origins and social evolution of music and dance.

Science.gov (United States)

Wang, Tianyan

2015-01-01

The origins of music and musical emotions is still an enigma, here I propose a comprehensive hypothesis on the origins and evolution of music, dance, and speech from a biological and sociological perspective. I suggest that every pitch interval between neighboring notes in music represents corresponding movement pattern through interpreting the Doppler effect of sound, which not only provides a possible explanation for the transposition invariance of music, but also integrates music and dance into a common form-rhythmic movements. Accordingly, investigating the origins of music poses the question: why do humans appreciate rhythmic movements? I suggest that human appreciation of rhythmic movements and rhythmic events developed from the natural selection of organisms adapting to the internal and external rhythmic environments. The perception and production of, as well as synchronization with external and internal rhythms are so vital for an organism's survival and reproduction, that animals have a rhythm-related reward and emotion (RRRE) system. The RRRE system enables the appreciation of rhythmic movements and events, and is integral to the origination of music, dance and speech. The first type of rewards and emotions (rhythm-related rewards and emotions, RRREs) are evoked by music and dance, and have biological and social functions, which in turn, promote the evolution of music, dance and speech. These functions also evoke a second type of rewards and emotions, which I name society-related rewards and emotions (SRREs). The neural circuits of RRREs and SRREs develop in species formation and personal growth, with congenital and acquired characteristics, respectively, namely music is the combination of nature and culture. This hypothesis provides probable selection pressures and outlines the evolution of music, dance, and speech. The links between the Doppler effect and the RRREs and SRREs can be empirically tested, making the current hypothesis scientifically

Adaptability and evolution.

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Bateson, Patrick

2017-10-06

The capacity of organisms to respond in their own lifetimes to new challenges in their environments probably appeared early in biological evolution. At present few studies have shown how such adaptability could influence the inherited characteristics of an organism's descendants. In part, this has been because organisms have been treated as passive in evolution. Nevertheless, their effects on biological evolution are likely to have been important and, when they occurred, accelerated the pace of evolution. Ways in which this might have happened have been suggested many times since the 1870s. I review these proposals and discuss their relevance to modern thought.

Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes.

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Kang, Zhen; Zhang, Junli; Jin, Peng; Yang, Sen

2015-01-01

Owing to our limited understanding of the relationship between sequence and function and the interaction between intracellular pathways and regulatory systems, the rational design of enzyme-coding genes and de novo assembly of a brand-new artificial genome for a desired functionality or phenotype are difficult to achieve. As an alternative approach, directed evolution has been widely used to engineer genomes and enzyme-coding genes. In particular, significant developments toward DNA synthesis, DNA assembly (in vitro or in vivo), recombination-mediated genetic engineering, and high-throughput screening techniques in the field of synthetic biology have been matured and widely adopted, enabling rapid semi-rational genome engineering to generate variants with desired properties. In this commentary, these novel tools and their corresponding applications in the directed evolution of genomes and enzymes are discussed. Moreover, the strategies for genome engineering and rapid in vitro enzyme evolution are also proposed.

Developing biology teachers' pedagogical content knowledge through learning study: the case of teaching human evolution

Science.gov (United States)

Bravo, Paulina; Cofré, Hernán

2016-11-01

This work explores how pedagogical content knowledge (PCK) on evolution was modified by two biology teachers who participated in a professional development programme (PDP) that included a subsequent follow-up in the classroom. The PDP spanned a semester and included activities such as content updates, collaborative lesson planning, and the presentation of planned lessons. In the follow-up part, the lessons were videotaped and analysed, identifying strategies, activities, and conditions based on student learning about the theory of evolution. Data were collected in the first round with an interview before the training process, identifying these teachers' initial content representation (CoRe) for evolution. Then, a group interview was conducted after the lessons, and, finally, an interview of stimulated recall with each teacher was conducted regarding the subject taught to allow teachers to reflect on their practice (final CoRe). This information was analysed by the teachers and the researchers, reflecting on the components of the PCK, possible changes, and the rationale behind their actions. The results show that teachers changed their beliefs and knowledge about the best methods and strategies to teach evolution, and about students' learning obstacles and misconceptions on evolution. They realised how a review of their own practices promotes this transformation.

Evolution across the Curriculum: Microbiology

Directory of Open Access Journals (Sweden)

Alita R. Burmeister

2016-05-01

Full Text Available An integrated understanding of microbiology and evolutionary biology is essential for students pursuing careers in microbiology and healthcare fields. In this Perspective, we discuss the usefulness of evolutionary concepts and an overall evolutionary framework for students enrolled in microbiology courses. Further, we propose a set of learning goals for students studying microbial evolution concepts. We then describe some barriers to microbial evolution teaching and learning and encourage the continued incorporation of evidence-based teaching practices into microbiology courses at all levels. Next, we review the current status of microbial evolution assessment tools and describe some education resources available for teaching microbial evolution. Successful microbial evolution education will require that evolution be taught across the undergraduate biology curriculum, with a continued focus on applications and applied careers, while aligning with national biology education reform initiatives.

Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity.

Science.gov (United States)

Barrera-Redondo, Josué; Ramírez-Barahona, Santiago; Eguiarte, Luis E

2018-05-01

Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population-level factors to better understand the processes affecting the tempo of evolution at the molecular level. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Proceedings of Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2015

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Silver, Pamela [Harvard Univ., Cambridge, MA (United States); SEED 2015 Conference Chair; Flach, Evan [American Institute of Chemical Engineers; SEED 2015 Conference Organizer

2016-10-27

Synthetic Biology is an emerging discipline that seeks to accelerate the process of engineering biology. As such, the tools are broadly applicable to application areas, including chemicals and biofuels, materials, medicine and agriculture. A characteristic of the field is to look holistically at cellular design, from sensing and genetic circuitry to the manipulation of cellular processes and actuators, to controlling metabolism, to programming multicellular behaviors. Further, the types of cells that are manipulated are broad, from in vitro systems to microbes and fungi to mammalian and plant cells and living animals. Many of the projects in synthetic biology seek to move biochemical functions across organisms. The field is highly interdisciplinary with faculty and students spread across departments that focus on engineering (biological, chemical, electrical, mechanical, civil, computer science) and basic science (biology and systems biology, chemistry, physics). While there have been many one-off workshops and meeting on synthetic biology, the 2014 Synthetic Biology: Engineering, Evolution and Design (SEED) was the first of an annual conference series that serves as a reliable place to pull together the involved disciplines in order to organize and exchange advances in the science and technology in the field. Further, the SEED conferences have a strong focus on industry, with many companies represented and actively participating. A number of these companies have started major efforts in synthetic biology including large companies (e.g., Pfizer, Novartis, Dow, Dupont, BP, Total), smaller companies have recently gone public (e.g., Amyris, Gevo, Intrexon), and many start-ups (e.g., Teslagen, Refactored Materials, Pivot, Genomatica). There are a number of loosely affiliated Synthetic Biology Centers, including ones at MIT, Boston University, UCSD, UCSF, UC-Berkeley, Imperial College, Oxford, and ETH. SEED 2015 will serve as the primary meeting at which international

Neutral Evolution in a Biological Population as Diffusion in Phenotype Space: Reproduction with Local Mutation but without Selection

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Lawson, Daniel John; Jensen, Henrik Jeldtoft

2007-03-01

The process of “evolutionary diffusion,” i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.

Should We Add History of Science to Provide Nature of Science into Vietnamese Biology Textbook: A Case of Evolution and Genetics Teaching?

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Diem, Huynh Thi Thuy; Yuenyong, Chokchai

2018-01-01

History of science (HOS) plays a substantial role in the enhancement of rooted understanding in science teaching and learning. HOS of evolution and genetics has not been included in Vietnamese biology textbooks. This study aims to investigate the necessity of introducing evolution and genetics HOS into Vietnamese textbooks. A case study approach…

Biological evolution: Some genetic considerations

African Journals Online (AJOL)

Mohammad Saad Zaghloul Salem

2013-12-08

Dec 8, 2013 ... cept of evolution, viz. genetic memory and evolutionary variations, genomic adaptations to stress .... or codons, along the transcript without giving attention to whether they are ... They do not affect the genome in a straightfor-.

A comparison of biological and cultural evolution

Indian Academy of Sciences (India)

2016-08-26

Aug 26, 2016 ... fitness; information; language; learning; teaching. ... Further, conditions for cultural evolution are proposed, including a suggestion for language being the cultural replicator corresponding to the concept of the gene in ... The importance of language as a necessary condition for cultural evolution is stressed.

Stability-based sorting: The forgotten process behind (not only) biological evolution.

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Toman, Jan; Flegr, Jaroslav

2017-12-21

Natural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more general persistence principle, whose temporal consequences we propose to name "stability-based sorting" (SBS). Sorting based on static stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities. Sorted entities could originate independently from each other, are not required to propagate and need not exhibit heredity. Natural selection is a specific form of SBS-sorting based on dynamic stability. It requires some form of heredity and is based on competition for the largest difference between the speed of generating its own copies and their expiration. SBS in its strict sense and selection thus have markedly different evolutionary consequences that are stressed in this paper. In contrast to selection, which is opportunistic, SBS is able to accumulate even momentarily detrimental characters that are advantageous for the long-term persistence of sorted entities. However, it lacks the amplification effect based on the preferential propagation of holders of advantageous characters. Thus, it works slower than selection and normally is unable to create complex adaptations. From a long-term perspective, SBS is a decisive force in evolution-especially macroevolution. SBS offers a new explanation for numerous evolutionary phenomena, including broad distribution and persistence of sexuality, altruistic behaviour, horizontal gene transfer, patterns of evolutionary stasis, planetary homeostasis, increasing ecosystem resistance to disturbances, and the universal decline of disparity in the evolution of metazoan lineages. SBS acts on all levels in

The Relationship between Biology Teachers' Understanding of the Nature of Science and the Understanding and Acceptance of the Theory of Evolution

Science.gov (United States)

Cofré, Hernán; Cuevas, Emilia; Becerra, Beatriz

2017-01-01

Despite the importance of the theory of evolution (TE) to scientific knowledge, a number of misconceptions continue to be found among biology teachers. In this context, the first objective of this study was to identify the impact of professional development programme (PDP) on teachers' understanding of nature of science (NOS) and evolution and on…

Teaching evolution (and all of biology) more effectively: Strategies for engagement, critical reasoning, and confronting misconceptions.

Science.gov (United States)

Nelson, Craig E

2008-08-01

The strength of the evidence supporting evolution has increased markedly since the discovery of DNA but, paradoxically, public resistance to accepting evolution seems to have become stronger. A key dilemma is that science faculty have often continued to teach evolution ineffectively, even as the evidence that traditional ways of teaching are inferior has become stronger and stronger. Three pedagogical strategies that together can make a large difference in students' understanding and acceptance of evolution are extensive use of interactive engagement, a focus on critical thinking in science (especially on comparisons and explicit criteria) and using both of these in helping the students actively compare their initial conceptions (and publicly popular misconceptions) with more fully scientific conceptions. The conclusion that students' misconceptions must be dealt with systematically can be difficult for faculty who are teaching evolution since much of the students' resistance is framed in religious terms and one might be reluctant to address religious ideas in class. Applications to teaching evolution are illustrated with examples that address criteria and critical thinking, standard geology versus flood geology, evolutionary developmental biology versus organs of extreme perfection, and the importance of using humans as a central example. It is also helpful to bridge the false dichotomy, seen by many students, between atheistic evolution versus religious creationism. These applications are developed in detail and are intended to be sufficient to allow others to use these approaches in their teaching. Students and other faculty were quite supportive of these approaches as implemented in my classes.

Space biology research development

Science.gov (United States)

Bonting, Sjoerd L.

1993-01-01

The purpose of the Search for Extraterrestrial Intelligence (SETI) Institute is to conduct and promote research related activities regarding the search for extraterrestrial life, particularly intelligent life. Such research encompasses the broad discipline of 'Life in the Universe', including all scientific and technological aspects of astronomy and the planetary sciences, chemical evolution, the origin of life, biological evolution, and cultural evolution. The primary purpose was to provide funding for the Principal Investigator to collaborate with the personnel of the SETI Institute and the NASA-Ames Research center in order to plan and develop space biology research on and in connection with Space Station Freedom; to promote cooperation with the international partners in the space station; to conduct a study on the use of biosensors in space biology research and life support system operation; and to promote space biology research through the initiation of an annual publication 'Advances in Space Biology and Medicine'.

Darwinian evolution

NARCIS (Netherlands)

Jagers op Akkerhuis, Gerard A.J.M.; Spijkerboer, Hendrik Pieter; Koelewijn, Hans Peter

2016-01-01

Darwinian evolution is a central tenet in biology. Conventionally, the defi nition of Darwinian evolution is linked to a population-based process that can be measured by focusing on changes in DNA/allele frequencies. However, in some publications it has been suggested that selection represents a

Can Chimpanzee Biology Highlight Human Origin and Evolution?

Directory of Open Access Journals (Sweden)

Itai Roffman

2010-07-01

Full Text Available The closest living relatives of humans are their chimpanzee/bonobo (Pan sister species, members of the same subfamily “Homininae”. This classification is supported by over 50 years of research in the fields of chimpanzee cultural diversity, language competency, genomics, anatomy, high cognition, psychology, society, self-consciousness and relation to others, tool use/production, as well as Homo level emotions, symbolic competency, memory recollection, complex multifaceted problem-solving capabilities, and interspecies communication. Language competence and symbolism can be continuously bridged from chimpanzee to man. Emotions, intercommunity aggression, body language, gestures, facial expressions, and vocalization of intonations seem to parallel between the sister taxa Homo and Pan. The shared suite of traits between Pan and Homo genus demonstrated in this article integrates old and new information on human–chimpanzee evolution, bilateral informational and cross-cultural exchange, promoting the urgent need for Pan cultures in the wild to be protected, as they are part of the cultural heritage of mankind. Also, we suggest that bonobos, Pan paniscus, based on shared traits with Australopithecus, need to be included in Australopithecine’s subgenus, and may even represent living-fossil Australopithecines. Unfolding bonobo and chimpanzee biology highlights our common genetic and cultural evolutionary origins.

Introductory Biology Labs... They Just Aren't Sexy Enough!

Science.gov (United States)

Cotner, Sehoya; Gallup, Gordon G., Jr.

2011-01-01

The typical introductory biology curriculum includes the nature of science, evolution and genetics. Laboratory activities are designed to engage students in typical subject areas ranging from cell biology and physiology, to ecology and evolution. There are few, if any, laboratory classes exploring the biology and evolution of human sexual…

Evolution, Entropy, & Biological Information

Science.gov (United States)

Peterson, Jacob

2014-01-01

A logical question to be expected from students: "How could life develop, that is, change, evolve from simple, primitive organisms into the complex forms existing today, while at the same time there is a generally observed decline and disorganization--the second law of thermodynamics?" The explanations in biology textbooks relied upon by…

The role of biology in planetary evolution: cyanobacterial primary production in low?oxygen Proterozoic oceans

OpenAIRE

Hamilton, Trinity L.; Bryant, Donald A.; Macalady, Jennifer L.

2015-01-01

Summary Understanding the role of biology in planetary evolution remains an outstanding challenge to geobiologists. Progress towards unravelling this puzzle for Earth is hindered by the scarcity of well?preserved rocks from the Archean (4.0 to 2.5?Gyr ago) and Proterozoic (2.5 to 0.5?Gyr ago) Eons. In addition, the microscopic life that dominated Earth's biota for most of its history left a poor fossil record, consisting primarily of lithified microbial mats, rare microbial body fossils and m...

Alfred Russel Wallace (1823-1913): the forgotten co-founder of the Neo-Darwinian theory of biological evolution.

Science.gov (United States)

Kutschera, Ulrich; Hossfeld, Uwe

2013-12-01

The British naturalist Alfred Russel Wallace (1823-1913), who had to leave school aged 14 and never attended university, did extensive fieldwork, first in the Amazon River basin (1848-1852) and then in Southeast Asia (1854-1862). Based on this experience, and after reading the corresponding scientific literature, Wallace postulated that species were not created, but are modified descendants of pre-existing varieties (Sarawak Law paper, 1855). Evolution is brought about by a struggle for existence via natural selection, which results in the adaptation of those individuals in variable populations who survive and reproduce (Ternate essay, 1858). In his monograph Darwinism (1889), and in subsequent publications, Wallace extended the contents of Darwin's Origin of Species (1859) into the Neo-Darwinian theory of biological evolution, with reference to the work of August Weismann (1834-1914). Wallace also became the (co)-founder of biogeography, biodiversity research, astrobiology and evolutionary anthropology. Moreover, he envisioned what was later called the anthropocene (i.e., the age of human environmental destructiveness). However, since Wallace believed in atheistic spiritualism and mixed up scientific facts and supernatural speculations in some of his writings, he remains a controversial figure in the history of biology.

Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology.

Science.gov (United States)

Pandey, Ramesh Prasad; Parajuli, Prakash; Koffas, Mattheos A G; Sohng, Jae Kyung

2016-01-01

In this review, we address recent advances made in pathway engineering, directed evolution, and systems/synthetic biology approaches employed in the production and modification of flavonoids from microbial cells. The review is divided into two major parts. In the first, various metabolic engineering and system/synthetic biology approaches used for production of flavonoids and derivatives are discussed broadly. All the manipulations/engineering accomplished on the microorganisms since 2000 are described in detail along with the biosynthetic pathway enzymes, their sources, structures of the compounds, and yield of each product. In the second part of the review, post-modifications of flavonoids by four major reactions, namely glycosylations, methylations, hydroxylations and prenylations using recombinant strains are described. Copyright © 2016 Elsevier Inc. All rights reserved.

A timeless biology.

Science.gov (United States)

Tozzi, Arturo; Peters, James F; Chafin, Clifford; De Falco, Domenico; Torday, John S

2018-05-01

Contrary to claims that physics is timeless while biology is time-dependent, we take the opposite standpoint: physical systems' dynamics are constrained by the arrow of time, while living assemblies are time-independent. Indeed, the concepts of "constraints" and "displacements" shed new light on the role of continuous time flow in life evolution, allowing us to sketch a physical gauge theory for biological systems in long timescales. In the very short timescales of biological systems' individual lives, time looks like "frozen" and "fixed", so that the second law of thermodynamics is momentarily wrecked. The global symmetries (standing for biological constrained trajectories, i.e. the energetic gradient flows dictated by the second law of thermodynamics in long timescales) are broken by local "displacements" where time is held constant, i.e., modifications occurring in living systems. Such displacements stand for brief local forces, able to temporarily "break" the cosmic increase in entropy. The force able to restore the symmetries (called "gauge field") stands for the very long timescales of biological evolution. Therefore, at the very low speeds of life evolution, time is no longer one of the four phase space coordinates of a spacetime Universe: it becomes just a gauge field superimposed to three-dimensional biological systems. We discuss the implications in biology: when assessing living beings, the underrated role of isolated "spatial" modifications needs to be emphasized, living apart the evolutionary role of time. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology.

Science.gov (United States)

Pazos, Florencio; Chagoyen, Monica

2018-01-16

Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of >5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the 'trendy' subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server 'death', which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mass extinctions vs. uniformitarianism in biological evolution

Energy Technology Data Exchange (ETDEWEB)

Bak, P.; Paczuski, M.

1995-12-31

It is usually believed that Darwin`s theory leads to a smooth gradual evolution, so that mass extinctions must be caused by external shocks. However, it has recently been argued that mass extinctions arise from the intrinsic dynamics of Darwinian evolution. Species become extinct when swept by intermittent avalanches propagating through the global ecology. These ideas are made concrete through studies of simple mathematical models of co-evolving species. The models exhibit self-organized criticality and describe some general features of the extinction pattern in the fossil record.

Chemical Evolution and the Evolutionary Definition of Life.

Science.gov (United States)

Higgs, Paul G

2017-06-01

Darwinian evolution requires a mechanism for generation of diversity in a population, and selective differences between individuals that influence reproduction. In biology, diversity is generated by mutations and selective differences arise because of the encoded functions of the sequences (e.g., ribozymes or proteins). Here, I draw attention to a process that I will call chemical evolution, in which the diversity is generated by random chemical synthesis instead of (or in addition to) mutation, and selection acts on physicochemical properties, such as hydrolysis, photolysis, solubility, or surface binding. Chemical evolution applies to short oligonucleotides that can be generated by random polymerization, as well as by template-directed replication, and which may be too short to encode a specific function. Chemical evolution is an important stage on the pathway to life, between the stage of "just chemistry" and the stage of full biological evolution. A mathematical model is presented here that illustrates the differences between these three stages. Chemical evolution leads to much larger differences in molecular concentrations than can be achieved by selection without replication. However, chemical evolution is not open-ended, unlike biological evolution. The ability to undergo Darwinian evolution is often considered to be a defining feature of life. Here, I argue that chemical evolution, although Darwinian, does not quite constitute life, and that a good place to put the conceptual boundary between non-life and life is between chemical and biological evolution.

Formal Definitions of Unbounded Evolution and Innovation Reveal Universal Mechanisms for Open-Ended Evolution in Dynamical Systems.

Science.gov (United States)

Adams, Alyssa; Zenil, Hector; Davies, Paul C W; Walker, Sara Imari

2017-04-20

Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an isolated system, and innovation as trajectories not observed in isolated systems. As a case study, we implement novel variants of cellular automata (CA) where the update rules are allowed to vary with time in three alternative ways. Each is capable of generating conditions for open-ended evolution, but vary in their ability to do so. We find that state-dependent dynamics, regarded as a hallmark of life, statistically out-performs other candidate mechanisms, and is the only mechanism to produce open-ended evolution in a scalable manner, essential to the notion of ongoing evolution. This analysis suggests a new framework for unifying mechanisms for generating OEE with features distinctive to life and its artifacts, with broad applicability to biological and artificial systems.

Human evolution: humanistic selection and looking to the future.

Science.gov (United States)

Krsiak, Miloslav

2006-10-01

Cultural evolution has predominated over biological evolution in modern man (Homo sapiens sapiens). Cultural evolution differs from biological evolution not only by inheritance of acquired characteristics but also, as is proposed in the present essay, by another kind of selection mechanism. Whereas selection in biological evolution is executed according to a criterion of reproductive success (the natural selection), selection in cultural evolution appears to be carried out according to human and humanistic criteria (success or fitness in meeting human needs, interests and humanistic values--"humanistic selection"). Many humanistic needs or values do not seem to be prerequisite for reproductive success, yet some of them (e.g. a need for freedom) seem to be inborn. Innateness, humanistic selection (decisive at a community level) and hierarchy of some human needs, interests and values appear to give cultural evolution a generally upward trend although long periods of stagnation or even regression may occur. Modern humans appear to be still at the early stage of their cultural evolution. A further cultural evolution of man appears to be, in contrast to biological evolution, predictable (with an optimistic outlook) and testable. The problem is that the hopeful result of this test will probably be known only in the fairly remote future provided that this species will not become extinct before that.

Evolution of meanings of the concept of gen in students of higher education in the teaching of biology

Directory of Open Access Journals (Sweden)

Dalia Diez de Tancredi

2012-01-01

Full Text Available The aim of the study was to identify initial meanings of the concept of the gene among 50 students from the career training of teachers of biology at the University Pedagogical Experimental Libertador (UPEL, Pedagogical Institute of Caracas, who enrolled in Cell Biology (BC and General Genetics (GG, as well as those built from a didactic intervention that formed part of Participatory Action Research (PAR. The work is based on the Theory of Meaningful Learning of Ausubel, on the principles of critical meaningful learning facilitators of Moreira, and on elements of the educational act of Novak. To investigate the evolution of meaning of this concept were used: questionnaires, interviews, maps and graphic representations of concepts developed by students. The data analysis provides a differentiated evolution of the meaning of the gene in the students, which corresponds to the didactic intervention and teachers, actions in both courses. It shows the importance of organizing the teaching in a potentially meaningful way to reflect on the content and learning, so that abstract concepts such as gene, must be presented with a critical and reflexive epistemology.

The sociobiology of genes: the gene's eye view as a unifying behavioural-ecological framework for biological evolution.

Science.gov (United States)

De Tiège, Alexis; Van de Peer, Yves; Braeckman, Johan; Tanghe, Koen B

2017-11-22

Although classical evolutionary theory, i.e., population genetics and the Modern Synthesis, was already implicitly 'gene-centred', the organism was, in practice, still generally regarded as the individual unit of which a population is composed. The gene-centred approach to evolution only reached a logical conclusion with the advent of the gene-selectionist or gene's eye view in the 1960s and 1970s. Whereas classical evolutionary theory can only work with (genotypically represented) fitness differences between individual organisms, gene-selectionism is capable of working with fitness differences among genes within the same organism and genome. Here, we explore the explanatory potential of 'intra-organismic' and 'intra-genomic' gene-selectionism, i.e., of a behavioural-ecological 'gene's eye view' on genetic, genomic and organismal evolution. First, we give a general outline of the framework and how it complements the-to some extent-still 'organism-centred' approach of classical evolutionary theory. Secondly, we give a more in-depth assessment of its explanatory potential for biological evolution, i.e., for Darwin's 'common descent with modification' or, more specifically, for 'historical continuity or homology with modular evolutionary change' as it has been studied by evolutionary developmental biology (evo-devo) during the last few decades. In contrast with classical evolutionary theory, evo-devo focuses on 'within-organism' developmental processes. Given the capacity of gene-selectionism to adopt an intra-organismal gene's eye view, we outline the relevance of the latter model for evo-devo. Overall, we aim for the conceptual integration between the gene's eye view on the one hand, and more organism-centred evolutionary models (both classical evolutionary theory and evo-devo) on the other.

The Physics of Open Ended Evolution

Science.gov (United States)

Adams, Alyssa M.

What makes living systems different than non-living ones? Unfortunately this question is impossible to answer, at least currently. Instead, we must face computationally tangible questions based on our current understanding of physics, computation, information, and biology. Yet we have few insights into how living systems might quantifiably differ from their non-living counterparts, as in a mathematical foundation to explain away our observations of biological evolution, emergence, innovation, and organization. The development of a theory of living systems, if at all possible, demands a mathematical understanding of how data generated by complex biological systems changes over time. In addition, this theory ought to be broad enough as to not be constrained to an Earth-based biochemistry. In this dissertation, the philosophy of studying living systems from the perspective of traditional physics is first explored as a motivating discussion for subsequent research. Traditionally, we have often thought of the physical world from a bottom-up approach: things happening on a smaller scale aggregate into things happening on a larger scale. In addition, the laws of physics are generally considered static over time. Research suggests that biological evolution may follow dynamic laws that (at least in part) change as a function of the state of the system. Of the three featured research projects, cellular automata (CA) are used as a model to study certain aspects of living systems in two of them. These aspects include self-reference, open-ended evolution, local physical universality, subjectivity, and information processing. Open-ended evolution and local physical universality are attributed to the vast amount of innovation observed throughout biological evolution. Biological systems may distinguish themselves in terms of information processing and storage, not outside the theory of computation. The final research project concretely explores real-world phenomenon by means of

The emergence and early evolution of biological carbon-fixation.

Science.gov (United States)

Braakman, Rogier; Smith, Eric

2012-01-01

The fixation of CO₂ into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of CO₂ reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a "phylometabolic" tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more

The emergence and early evolution of biological carbon-fixation.

Directory of Open Access Journals (Sweden)

Rogier Braakman

Full Text Available The fixation of CO₂ into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of CO₂ reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a "phylometabolic" tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology

Experimental evolution in budding yeast

Science.gov (United States)

Murray, Andrew

2012-02-01

I will discuss our progress in analyzing evolution in the budding yeast, Saccharomyces cerevisiae. We take two basic approaches. The first is to try and examine quantitative aspects of evolution, for example by determining how the rate of evolution depends on the mutation rate and the population size or asking whether the rate of mutation is uniform throughout the genome. The second is to try to evolve qualitatively novel, cell biologically interesting phenotypes and track the mutations that are responsible for the phenotype. Our efforts include trying to alter cell morphology, evolve multicellularity, and produce a biological oscillator.

Radiation and the evolution of life

International Nuclear Information System (INIS)

Gentner, N.E.; Myers, D.K.

1980-08-01

A general review is presented of the nature of various forms of radiation; radiant energy which reaches the earth from the sun; the role of this energy in prebiotic chemical evolution; current ideas on the origin of life; the dependence of living organisms upon radiant energy; the mechanisms responsible for the evolution of life, from the viewpoint of modern genetics and molecular biology; the biological consequences of alterations in the genetic material; and the role of ionizing radiation in production of genetic changes and in evolution. In the final analysis, the biosynthetic processes of life are driven by radiant energy from the sun. This overview is necessarily focussed on the infrared, visible and ultraviolet regions of the solar output spectrum since these particular radiations are responsible for most of the radiant energy that reaches the earth's surface. Ionizing radiation appears to have played at best a minor role in biological evolution. Small increments in the amounts of ionizing radiation are therefore unlikely to have a significant effect on life or its evolution. (auth)

Ludwig von Bertalanffy's organismic view on the theory of evolution.

Science.gov (United States)

Drack, Manfred

2015-03-01

Ludwig von Bertalanffy was a key figure in the advancement of theoretical biology. His early considerations already led him to recognize the necessity of considering the organism as a system, as an organization of parts and processes. He termed the resulting research program organismic biology, which he extended to all basic questions of biology and almost all areas of biology, hence also to the theory of evolution. This article begins by outlining the rather unknown (because often written in German) research of Bertalanffy in the field of theoretical biology. The basics of the organismic approach are then described. This is followed by Bertalanffy's considerations on the theory of evolution, in which he used methods from theoretical biology and then introduced his own, organismic, view on evolution, leading to the demand for finding laws of evolution. Finally, his view on the concept of homology is presented. © 2015 Wiley Periodicals, Inc.

Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation.

Science.gov (United States)

Martin, William F

2012-03-09

Life is a persistent, self-specified set of far from equilibrium chemical reactions. In modern microbes, core carbon and energy metabolism are what keep cells alive. In very early chemical evolution, the forerunners of carbon and energy metabolism were the processes of generating reduced carbon compounds from CO(2) and the mechanisms of harnessing energy as compounds capable of doing some chemical work. The process of serpentinization at alkaline hydrothermal vents holds promise as a model for the origin of early reducing power, because Fe(2+) in the Earth's crust reduces water to H(2) and inorganic carbon to methane. The overall geochemical process of serpentinization is similar to the biochemical process of methanogenesis, and methanogenesis is similar to acetogenesis in that both physiologies allow energy conservation from the reduction of CO(2) with electrons from H(2). Electron bifurcation is a newly recognized cytosolic process that anaerobes use generate low potential electrons, it plays an important role in some forms of methanogenesis and, via speculation, possibly in acetogenesis. Electron bifurcation likely figures into the early evolution of biological energy conservation. Copyright © 2011. Published by Elsevier B.V.

Geomagnetic polarity reversals as a mechanism for the punctuated equilibrium model of biological evolution

International Nuclear Information System (INIS)

Welsh, J.S.; Welsh, A.L.; Welsh, W.F.

2003-01-01

In contrast to what is predicted by classical Darwinian theory (phyletic gradualism), the fossil record typically displays a pattern of relatively sudden, dramatic changes as detailed by Eldregde and Gould's model of punctuated equilibrium. Evolutionary biologists have been at a loss to explain the ultimate source of the new mutations that drive evolution. One hypothesis holds that the abrupt speciation seen in the punctuated equilibrium model is secondary to an increased mutation rate resulting from periodically increased levels of ionizing radiation on the Earth's surface. Sporadic geomagnetic pole reversals, occurring every few million years on the average, are accompanied by alterations in the strength of the Earth's magnetic field and magnetosphere. This diminution may allow charged cosmic radiation to bombard Earth with less attenuation, thereby resulting in increased mutation rates. This episodic fluctuation in the magnetosphere is an attractive mechanism for the observed fossil record. Selected periods and epochs of geologic history for which data was available were reviewed for both geomagnetic pole reversal history and fossil record. Anomalies in either were scrutinized in greater depth and correlations were made. A 35 million year span (118-83 Ma) was identified during the Early/Middle Cretaceous period that was devoid of geomagnetic polarity reversals(the Cretaceous normal superchron). Examination of the fossil record (including several invertebrate and vertebrate taxons) during the Cretaceous normal superchron does not reveal any significant gap or slowing of speciation. Although increased terrestrial radiation exposure due to a diminution of the Earth's magnetosphere caused by a reversal of geomagnetic polarity is an attractive explanation for the mechanism of punctuated equilibrium, our investigation suggests that such polarity reversals cannot fully provide the driving force behind biological evolution. Further research is required to determine if

Fusion of biological membranes

Indian Academy of Sciences (India)

Home; Journals; Pramana – Journal of Physics; Volume 64; Issue 6. Fusion of biological membranes. K Katsov M Müller M Schick. Invited Talks:- Topic 11. Biologically motivated problems (protein-folding models, dynamics at the scale of the cell; biological networks, evolution models, etc.) Volume 64 Issue 6 June 2005 pp ...

First International Conference on the Evolution and Development of the Universe

CERN Document Server

EDU2008

2009-01-01

This document is the Special Issue of the First International Conference on the Evolution and Development (EDU 2008). Please refer to the preface and introduction for more details on the contributions. Keywords: acceleration, artificial cosmogenesis, artificial life, Big Bang, Big History, biological evolution, biological universe, biology, causality, classical vacuum energy, complex systems, complexity, computational universe, conscious evolution, cosmological artificial selection, cosmological natural selection, cosmology, critique, cultural evolution, dark energy, dark matter, development of the universe, development, emergence, evolution of the universe evolution, exobiology, extinction, fine-tuning, fractal space-time, fractal, information, initial conditions, intentional evolution, linear expansion of the universe, log-periodic laws, macroevolution, materialism, meduso-anthropic principle, multiple worlds, natural sciences, Nature, ontology, order, origin of the universe, particle hierarchy, philosophy,...

Physical Complexity and Cognitive Evolution

Science.gov (United States)

Jedlicka, Peter

Our intuition tells us that there is a general trend in the evolution of nature, a trend towards greater complexity. However, there are several definitions of complexity and hence it is difficult to argue for or against the validity of this intuition. Christoph Adami has recently introduced a novel measure called physical complexity that assigns low complexity to both ordered and random systems and high complexity to those in between. Physical complexity measures the amount of information that an organism stores in its genome about the environment in which it evolves. The theory of physical complexity predicts that evolution increases the amount of `knowledge' an organism accumulates about its niche. It might be fruitful to generalize Adami's concept of complexity to the entire evolution (including the evolution of man). Physical complexity fits nicely into the philosophical framework of cognitive biology which considers biological evolution as a progressing process of accumulation of knowledge (as a gradual increase of epistemic complexity). According to this paradigm, evolution is a cognitive `ratchet' that pushes the organisms unidirectionally towards higher complexity. Dynamic environment continually creates problems to be solved. To survive in the environment means to solve the problem, and the solution is an embodied knowledge. Cognitive biology (as well as the theory of physical complexity) uses the concepts of information and entropy and views the evolution from both the information-theoretical and thermodynamical perspective. Concerning humans as conscious beings, it seems necessary to postulate an emergence of a new kind of knowledge - a self-aware and self-referential knowledge. Appearence of selfreflection in evolution indicates that the human brain reached a new qualitative level in the epistemic complexity.

Culture, Urbanism and Changing Human Biology.

Science.gov (United States)

Schell, L M

2014-04-03

Anthropologists have long known that human activity driven by culture changes the environment. This is apparent in the archaeological record and through the study of the modern environment. Perhaps the largest change since the paleolithic era is the organization of human populations in cities. New environments can reshape human biology through evolution as shown by the evolution of the hominid lineage. Evolution is not the only process capable of reshaping our biology. Some changes in our human biology are adaptive and evolutionary while others are pathological. What changes in human biology may be wrought by the modern urban environment? One significant new change in the environment is the introduction of pollutants largely through urbanization. Pollutants can affect human biology in myriad ways. Evidence shows that human growth, reproduction, and cognitive functioning can be altered by some pollutants, and altered in different ways depending on the pollutant. Thus, pollutants have significance for human biologists and anthropologists generally. Further, they illustrate the bio-cultural interaction characterizing human change. Humans adapt by changing the environment, a cultural process, and then change biologically to adjust to that new environment. This ongoing, interactive process is a fundamental characteristic of human change over the millennia.

Thoughts on the cultural evolution of man. Developmental imprinting and transgenerational effect.

Science.gov (United States)

Csaba, György

2007-01-01

The biological evolution of man stopped since it has been conveyed to the objects, created by man. This paper introduces the concept of "conveyed evolution". Being part of the cultural evolution, the conveyed evolution is a continuation of the biological one. There are several similarities between the laws of biological and conveyed evolution, albeit the differences are important as well. Some laws of the conveyed evolution are described here. The conveyed evolution has man-made repair mechanisms (medicine, protection of environment) which defend man from harm. Man's fragility limits the progress of conveyed evolution. However, artificial compounds or environmental pollutants which are provoked by the conveyed evolution induce chemical (hormonal) imprinting in the developmental critical periods, which is transmitted to the progeny generations (transgenerational effect). This could cause evolutionary alterations without mutation.

Etiology of lumbar lordosis and its pathophysiology: a review of the evolution of lumbar lordosis, and the mechanics and biology of lumbar degeneration.

Science.gov (United States)

Sparrey, Carolyn J; Bailey, Jeannie F; Safaee, Michael; Clark, Aaron J; Lafage, Virginie; Schwab, Frank; Smith, Justin S; Ames, Christopher P

2014-05-01

The goal of this review is to discuss the mechanisms of postural degeneration, particularly the loss of lumbar lordosis commonly observed in the elderly in the context of evolution, mechanical, and biological studies of the human spine and to synthesize recent research findings to clinical management of postural malalignment. Lumbar lordosis is unique to the human spine and is necessary to facilitate our upright posture. However, decreased lumbar lordosis and increased thoracic kyphosis are hallmarks of an aging human spinal column. The unique upright posture and lordotic lumbar curvature of the human spine suggest that an understanding of the evolution of the human spinal column, and the unique anatomical features that support lumbar lordosis may provide insight into spine health and degeneration. Considering evolution of the skeleton in isolation from other scientific studies provides a limited picture for clinicians. The evolution and development of human lumbar lordosis highlight the interdependence of pelvic structure and lumbar lordosis. Studies of fossils of human lineage demonstrate a convergence on the degree of lumbar lordosis and the number of lumbar vertebrae in modern Homo sapiens. Evolution and spine mechanics research show that lumbar lordosis is dictated by pelvic incidence, spinal musculature, vertebral wedging, and disc health. The evolution, mechanics, and biology research all point to the importance of spinal posture and flexibility in supporting optimal health. However, surgical management of postural deformity has focused on restoring posture at the expense of flexibility. It is possible that the need for complex and costly spinal fixation can be eliminated by developing tools for early identification of patients at risk for postural deformities through patient history (genetics, mechanics, and environmental exposure) and tracking postural changes over time.

Continuous "in vitro" Evolution of a Ribozyme Ligase: A Model Experiment for the Evolution of a Biomolecule

Science.gov (United States)

Ledbetter, Michael P.; Hwang, Tony W.; Stovall, Gwendolyn M.; Ellington, Andrew D.

2013-01-01

Evolution is a defining criterion of life and is central to understanding biological systems. However, the timescale of evolutionary shifts in phenotype limits most classroom evolution experiments to simple probability simulations. "In vitro" directed evolution (IVDE) frequently serves as a model system for the study of Darwinian…

The virtue of innovation: innovation through the lenses of biological evolution

Science.gov (United States)

Kell, Douglas B.; Lurie-Luke, Elena

2015-01-01

We rehearse the processes of innovation and discovery in general terms, using as our main metaphor the biological concept of an evolutionary fitness landscape. Incremental and disruptive innovations are seen, respectively, as successful searches carried out locally or more widely. They may also be understood as reflecting evolution by mutation (incremental) versus recombination (disruptive). We also bring a platonic view, focusing on virtue and memory. We use ‘virtue’ as a measure of efforts, including the knowledge required to come up with disruptive and incremental innovations, and ‘memory’ as a measure of their lifespan, i.e. how long they are remembered. Fostering innovation, in the evolutionary metaphor, means providing the wherewithal to promote novelty, good objective functions that one is trying to optimize, and means to improve one's knowledge of, and ability to navigate, the landscape one is searching. Recombination necessarily implies multi- or inter-disciplinarity. These principles are generic to all kinds of creativity, novel ideas formation and the development of new products and technologies. PMID:25505138

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.

Evolution, epigenetics and cooperation

Indian Academy of Sciences (India)

Explanations for biological evolution in terms of changes in gene frequencies refer to outcomes rather than process. Integrating epigenetic studies with older evolutionary theories has drawn attention to the ways in which evolution occurs. Adaptation at the level of the gene is givingway to adaptation at the level of the ...

The relationship between biology teachers' understanding of the nature of science and the understanding and acceptance of the theory of evolution

Science.gov (United States)

Cofré, Hernán; Cuevas, Emilia; Becerra, Beatriz

2017-11-01

Despite the importance of the theory of evolution (TE) to scientific knowledge, a number of misconceptions continue to be found among biology teachers. In this context, the first objective of this study was to identify the impact of professional development programme (PDP) on teachers' understanding of nature of science (NOS) and evolution and on the acceptance of this theory. Its second objective was to study the relationship among these variables. Three instruments were used to quantify these variables: the Views of the Nature of Science Version D (VNOS D+), the Assessing Contextual Reasoning about Natural Selection (ACORN), and the Measure of Acceptance of Theory of Evolution (MATE). The results indicate that the PDP had a positive impact on teachers, significantly improving their understanding of the NOS and natural selection, as well as their acceptance of the TE. Furthermore, a positive correlation between the understanding of the NOS obtained by teachers in the first part of the PDP and the understanding and acceptance of evolution that these teachers showed at the end of the programme was determined. However, no relationship between an understanding of the NOS and gains in the understanding and acceptance of evolution was found.

Practices and Perspectives of College Instructors on Addressing Religious Beliefs When Teaching Evolution

Science.gov (United States)

Barnes, M. Elizabeth; Brownell, Sara E.

2016-01-01

Evolution is a core concept of biology, and yet many college biology students do not accept evolution because of their religious beliefs. However, we do not currently know how instructors perceive their role in helping students accept evolution or how they address the perceived conflict between religion and evolution when they teach evolution.…

Evolution of approaches to viral safety issues for biological products.

Science.gov (United States)

Lubiniecki, Anthony S

2011-01-01

CONFERENCE PROCEEDING Proceedings of the PDA/FDA Adventitious Viruses in Biologics: Detection and Mitigation Strategies Workshop in Bethesda, MD, USA; December 1-3, 2010 Guest Editors: Arifa Khan (Bethesda, MD), Patricia Hughes (Bethesda, MD) and Michael Wiebe (San Francisco, CA) Approaches to viral safety issues for biological products have evolved during the past 50+ years. The first cell culture products (viral vaccines) relied largely on the use of in vitro and in vivo virus screening assays that were based upon infectivity of adventitious viral agents. The use of Cohn fractionation and pasteurization by manufacturers of plasma derivatives introduced the concepts that purification and treatment with physical and chemical agents could greatly reduce the risk of viral contamination of human albumin and immunoglobulin products. But the limitations of such approaches became clear for thermolabile products that were removed early in fractionation such as antihemophilic factors, which transmitted hepatitis viruses and HIV-1 to some product recipients. These successes and limitations were taken into account by the early developers of recombinant DNA (rDNA)-derived cell culture products and by regulatory agencies, leading to the utilization of cloning technology to reduce/eliminate contamination due to human viruses and purification technologies to physically remove and inactivate adventitious and endogenous viruses, along with cell banking and cell bank characterization for adventitious and endogenous viruses, viral screening of biological raw materials, and testing of cell culture harvests, to ensure virus safety. Later development and incorporation of nanofiltration technology in the manufacturing process provided additional assurance of viral clearance for safety of biotechnology products. These measures have proven very effective at preventing iatrogenic infection of recipients of biotechnology products; however, viral contamination of production cell cultures has

Biological and genetic evolution of HIV type 1 in two siblings with different patterns of disease progression.

Science.gov (United States)

Ripamonti, Chiara; Leitner, Thomas; Laurén, Anna; Karlsson, Ingrid; Pastore, Angela; Cavarelli, Mariangela; Antonsson, Liselotte; Plebani, Anna; Fenyö, Eva Maria; Scarlatti, Gabriella

2007-12-01

To investigate the immunological and virological factors that may lead to different patterns of disease progression characteristic of HIV-1-infected children, two HIV-1-infected siblings, a slow and a fast progressor, were followed prospectively before the onset of highly active antiretroviral therapy. Viral coreceptor usage, including the use of CCR5/CXCR4 chimeric receptors, macrophage tropism, and sensitivity to the CC-chemokine RANTES, has been studied. An autologous and heterologous neutralizing antibody response has been documented using peripheral blood mononuclear cells- and GHOST(3) cell line-based assays. Viral evolution was investigated by env C2-V3 region sequence analysis. Although both siblings were infected with HIV-1 of the R5 phenotype, their viruses showed important biological differences. In the fast progressor there was a higher RANTES sensitivity of the early virus, an increased trend to change the mode of CCR5 receptor use, and a larger genetic evolution. Both children developed an autologous neutralizing antibody response starting from the second year with evidence of the continuous emergence of resistant variants. A marked viral genetic and phenotypic evolution was documented in the fast progressor sibling, which is accompanied by a high viral RANTES sensitivity and persistent neutralizing antibodies.

Structural Approaches to Sequence Evolution Molecules, Networks, Populations

CERN Document Server

Bastolla, Ugo; Roman, H. Eduardo; Vendruscolo, Michele

2007-01-01

Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.

On the thermodynamics of multilevel evolution.

Science.gov (United States)

Tessera, Marc; Hoelzer, Guy A

2013-09-01

Biodiversity is hierarchically structured both phylogenetically and functionally. Phylogenetic hierarchy is understood as a product of branching organic evolution as described by Darwin. Ecosystem biologists understand some aspects of functional hierarchy, such as food web architecture, as a product of evolutionary ecology; but functional hierarchy extends to much lower scales of organization than those studied by ecologists. We argue that the more general use of the term "evolution" employed by physicists and applied to non-living systems connects directly to the narrow biological meaning. Physical evolution is best understood as a thermodynamic phenomenon, and this perspective comfortably includes all of biological evolution. We suggest four dynamical factors that build on each other in a hierarchical fashion and set the stage for the Darwinian evolution of biological systems: (1) the entropic erosion of structure; (2) the construction of dissipative systems; (3) the reproduction of growing systems and (4) the historical memory accrued to populations of reproductive agents by the acquisition of hereditary mechanisms. A particular level of evolution can underpin the emergence of higher levels, but evolutionary processes persist at each level in the hierarchy. We also argue that particular evolutionary processes can occur at any level of the hierarchy where they are not obstructed by material constraints. This theoretical framework provides an extensive basis for understanding natural selection as a multilevel process. The extensive literature on thermodynamics in turn provides an important advantage to this perspective on the evolution of higher levels of organization, such as the evolution of altruism that can accompany the emergence of social organization. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Collective Landmarks for Deep Time: A New Tool for Evolution Education

Science.gov (United States)

Delgado, Cesar

2014-01-01

Evolution is a fundamental, organising concept in biology, yet there is widespread resistance to evolution among US students and there are rising creationist challenges in Europe. Resistance to evolution is linked to lack of understanding of the age of the Earth. An understanding of deep time is thus essential for effective biology education.…

Adaptive evolution in ecological communities.

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Martin M Turcotte

Full Text Available Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Most studies of adaptation focus on how a single environmental factor, such as increased temperature, affects evolution within a single species. The biological relevance of these experiments is limited because nature is infinitely more complex. Most species are embedded within communities containing many species that interact with one another and the physical environment. To understand the evolutionary significance of such ecological complexity, experiments must test the evolutionary impact of interactions among multiple species during adaptation. Here we highlight an experiment that manipulates species composition and tracks evolutionary responses within each species, while testing for the mechanisms by which species interact and adapt to their environment. We also discuss limitations of previous studies of adaptive evolution and emphasize how an experimental evolution approach can circumvent such shortcomings. Understanding how community composition acts as a selective force will improve our ability to predict how species adapt to natural and human-induced environmental change.

Mathematical biology

CERN Document Server

Murray, James D

1993-01-01

The book is a textbook (with many exercises) giving an in-depth account of the practical use of mathematical modelling in the biomedical sciences. The mathematical level required is generally not high and the emphasis is on what is required to solve the real biological problem. The subject matter is drawn, e.g. from population biology, reaction kinetics, biological oscillators and switches, Belousov-Zhabotinskii reaction, reaction-diffusion theory, biological wave phenomena, central pattern generators, neural models, spread of epidemics, mechanochemical theory of biological pattern formation and importance in evolution. Most of the models are based on real biological problems and the predictions and explanations offered as a direct result of mathematical analysis of the models are important aspects of the book. The aim is to provide a thorough training in practical mathematical biology and to show how exciting and novel mathematical challenges arise from a genuine interdisciplinary involvement with the biosci...

Are there laws of genome evolution?

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Eugene V Koonin

2011-08-01

Full Text Available Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.

Kamikazes and cultural evolution.

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Allen-Hermanson, Sean

2017-02-01

Is cultural evolution needed to explain altruistic selfsacrifice? Some contend that cultural traits (e.g. beliefs, behaviors, and for some "memes") replicate according to selection processes that have "floated free" from biology. One test case is the example of suicide kamikaze attacks in wartime Japan. Standard biological mechanisms-such as reciprocal altruism and kin selection-might not seem to apply here: The suicide pilots did not act on the expectation that others would reciprocate, and they were supposedly sacrificing themselves for country and emperor, not close relatives. Yet an examination of both the historical record and the demands of evolutionary theory suggest the kamikaze phenomenon does not cry out for explanation in terms of a special non-biological selection process. This weakens the case for cultural evolution, and has interesting implications for our understanding of altruistic self-sacrifice. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modeling Protein Evolution

Science.gov (United States)

Goldstein, Richard; Pollock, David

The study of biology is fundamentally different from many other scientific pursuits, such as geology or astrophysics. This difference stems from the ubiquitous questions that arise about function and purpose. These are questions concerning why biological objects operate the way they do: what is the function of a polymerase? What is the role of the immune system? No one, aside from the most dedicated anthropist or interventionist theist, would attempt to determine the purpose of the earth's mantle or the function of a binary star. Among the sciences, it is only biology in which the details of what an object does can be said to be part of the reason for its existence. This is because the process of evolution is capable of improving an object to better carry out a function; that is, it adapts an object within the constraints of mechanics and history (i.e., what has come before). Thus, the ultimate basis of these biological questions is the process of evolution; generally, the function of an enzyme, cell type, organ, system, or trait is the thing that it does that contributes to the fitness (i.e., reproductive success) of the organism of which it is a part or characteristic. Our investigations cannot escape the simple fact that all things in biology (including ourselves) are, ultimately, the result of an evolutionary process.

The theory of evolution

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Oleg Bazaluk

2015-06-01

Full Text Available The book The Theory of Evolution: from the Space Vacuum to Neural Ensembles and Moving Forward, an edition of 100 copies, was published in Russian language, in December 2014 in Kiev. Its Russian version is here: http://en.bazaluk.com/journals.html. Introduction, Chapter 10 and Conclusion published in English for the first time. Since 2004 author have been researching in the field of theory of Evolution, Big History. The book was written on the base of analysis of more than 2000 primary sources of this research topic. The volume is 90,000 words (with Reference. The book is for a wide range of professionals, from students to professors and researchers working in the fields of: philosophical anthropology, philosophy, Big History, cosmology, biology, neuroscience and etc. In the book, the author defines the evolution as continuous and nonlinear complication of the structure of matter, the types of interaction and environments; analyzes existing in modern science and philosophy approaches to the research of the process of evolution, degree of development of the factors and causes of evolution. Unifying interdisciplinary researches of evolution in cosmology, biology, neuroscience and philosophy, the author presents his vision of the model of «Evolving Matter», which allows us to consider not only the laws of transition of space vacuum in neural ensembles but also to see our Universe as a complication, heterogeneous organization. Interdisciplinary amount of information on the theory of evolution is systematized and a new method of world perception is proposed in the book.

The role of biology in planetary evolution: cyanobacterial primary production in low‐oxygen Proterozoic oceans

Science.gov (United States)

Bryant, Donald A.; Macalady, Jennifer L.

2016-01-01

Summary Understanding the role of biology in planetary evolution remains an outstanding challenge to geobiologists. Progress towards unravelling this puzzle for Earth is hindered by the scarcity of well‐preserved rocks from the Archean (4.0 to 2.5 Gyr ago) and Proterozoic (2.5 to 0.5 Gyr ago) Eons. In addition, the microscopic life that dominated Earth's biota for most of its history left a poor fossil record, consisting primarily of lithified microbial mats, rare microbial body fossils and membrane‐derived hydrocarbon molecules that are still challenging to interpret. However, it is clear from the sulfur isotope record and other geochemical proxies that the production of oxygen or oxidizing power radically changed Earth's surface and atmosphere during the Proterozoic Eon, pushing it away from the more reducing conditions prevalent during the Archean. In addition to ancient rocks, our reconstruction of Earth's redox evolution is informed by our knowledge of biogeochemical cycles catalysed by extant biota. The emergence of oxygenic photosynthesis in ancient cyanobacteria represents one of the most impressive microbial innovations in Earth's history, and oxygenic photosynthesis is the largest source of O 2 in the atmosphere today. Thus the study of microbial metabolisms and evolution provides an important link between extant biota and the clues from the geologic record. Here, we consider the physiology of cyanobacteria (the only microorganisms capable of oxygenic photosynthesis), their co‐occurrence with anoxygenic phototrophs in a variety of environments and their persistence in low‐oxygen environments, including in water columns as well as mats, throughout much of Earth's history. We examine insights gained from both the rock record and cyanobacteria presently living in early Earth analogue ecosystems and synthesize current knowledge of these ancient microbial mediators in planetary redox evolution. Our analysis supports the hypothesis that anoxygenic

The role of biology in planetary evolution: cyanobacterial primary production in low-oxygen Proterozoic oceans.

Science.gov (United States)

Hamilton, Trinity L; Bryant, Donald A; Macalady, Jennifer L

2016-02-01

Understanding the role of biology in planetary evolution remains an outstanding challenge to geobiologists. Progress towards unravelling this puzzle for Earth is hindered by the scarcity of well-preserved rocks from the Archean (4.0 to 2.5 Gyr ago) and Proterozoic (2.5 to 0.5 Gyr ago) Eons. In addition, the microscopic life that dominated Earth's biota for most of its history left a poor fossil record, consisting primarily of lithified microbial mats, rare microbial body fossils and membrane-derived hydrocarbon molecules that are still challenging to interpret. However, it is clear from the sulfur isotope record and other geochemical proxies that the production of oxygen or oxidizing power radically changed Earth's surface and atmosphere during the Proterozoic Eon, pushing it away from the more reducing conditions prevalent during the Archean. In addition to ancient rocks, our reconstruction of Earth's redox evolution is informed by our knowledge of biogeochemical cycles catalysed by extant biota. The emergence of oxygenic photosynthesis in ancient cyanobacteria represents one of the most impressive microbial innovations in Earth's history, and oxygenic photosynthesis is the largest source of O2 in the atmosphere today. Thus the study of microbial metabolisms and evolution provides an important link between extant biota and the clues from the geologic record. Here, we consider the physiology of cyanobacteria (the only microorganisms capable of oxygenic photosynthesis), their co-occurrence with anoxygenic phototrophs in a variety of environments and their persistence in low-oxygen environments, including in water columns as well as mats, throughout much of Earth's history. We examine insights gained from both the rock record and cyanobacteria presently living in early Earth analogue ecosystems and synthesize current knowledge of these ancient microbial mediators in planetary redox evolution. Our analysis supports the hypothesis that anoxygenic photosynthesis

Evolution Kills: A Web Resource for Instructors of Evolutionary Biology

Science.gov (United States)

Vondrasek, Joanna R.; Antonovics, Janis; Taylor, Douglas R.

2004-01-01

We have developed a laboratory course that demonstrates how evolution can be taught as a participatory, investigative science at the undergraduate college or advanced secondary high school level. The course emphasizes the applied importance of evolution to areas such as medicine and agriculture. Because many instructors face budgetary or other…

Language architecture and its import for evolution.

Science.gov (United States)

Chomsky, Noam

2017-10-01

Inquiry into the evolution of some biological system evidently can proceed only as far as its nature is understood. Lacking such understanding, its manifestations are likely to appear to be chaotic, highly variable, and lacking significant general properties; and, accordingly, study of its evolution cannot be seriously undertaken. These truisms hold of the study of the human faculty of language FL just as for other biological systems. As discussed below, FL appears to be a shared human capacity in essentials, with options of variation of a kind to which we return. After a long lapse, the problem of evolution of language arose in mid-twentieth century when the first efforts were made to construct accounts of FL as a biological object, internal to an individual, with particular internal languages - I-languages in current terminology - as manifestations of FL. Copyright © 2017. Published by Elsevier Ltd.

Divergent Cumulative Cultural Evolution

OpenAIRE

Marriott, Chris; Chebib, Jobran

2016-01-01

Divergent cumulative cultural evolution occurs when the cultural evolutionary trajectory diverges from the biological evolutionary trajectory. We consider the conditions under which divergent cumulative cultural evolution can occur. We hypothesize that two conditions are necessary. First that genetic and cultural information are stored separately in the agent. Second cultural information must be transferred horizontally between agents of different generations. We implement a model with these ...

Experiences and Practices of Evolution Instructors at Christian Universities That Can Inform Culturally Competent Evolution Education

Science.gov (United States)

Barnes, M. Elizabeth; Brownell, Sara E.

2018-01-01

Students' religious beliefs and religious cultures have been shown to be the main factors predicting whether they will accept evolution, yet college biology instructors teaching evolution at public institutions often have religious beliefs and cultures that are different from their religious students. This difference in religious beliefs and…

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

Evolution of density-dependent movement during experimental range expansions.

Science.gov (United States)

Fronhofer, E A; Gut, S; Altermatt, F

2017-12-01

Range expansions and biological invasions are prime examples of transient processes that are likely impacted by rapid evolutionary changes. As a spatial process, range expansions are driven by dispersal and movement behaviour. Although it is widely accepted that dispersal and movement may be context-dependent, for instance density-dependent, and best represented by reaction norms, the evolution of density-dependent movement during range expansions has received little experimental attention. We therefore tested current theory predicting the evolution of increased movement at low densities at range margins using highly replicated and controlled range expansion experiments across multiple genotypes of the protist model system Tetrahymena thermophila. Although rare, we found evolutionary changes during range expansions even in the absence of initial standing genetic variation. Range expansions led to the evolution of negatively density-dependent movement at range margins. In addition, we report the evolution of increased intrastrain competitive ability and concurrently decreased population growth rates in range cores. Our findings highlight the importance of understanding movement and dispersal as evolving reaction norms and plastic life-history traits of central relevance for range expansions, biological invasions and the dynamics of spatially structured systems in general. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Teaching Evolution: A Heuristic Study of Personal and Cultural Dissonance

Science.gov (United States)

Grimes, Larry G.

Darwinian evolution is a robustly supported scientific theory. Yet creationists continue to challenge its teaching in American public schools. Biology teachers in all 50 states are responsible for teaching science content standards that include evolution. As products of their backgrounds and affiliations teachers bring personal attitudes and beliefs to their teaching. The purpose of this study was to explore how biology teachers perceive, describe, and value their teaching of evolution. This research question was explored through a heuristic qualitative methodology. Eight veteran California high school biology teachers were queried as to their beliefs, perceptions, experiences and practices of teaching evolution. Both personal and professional documents were collected. Data was presented in the form of biographical essays that highlight teachers' backgrounds, experiences, perspectives and practices of teaching evolution. Of special interest was how they describe pressure over teaching evolution during a decade of standards and No Child Left Behind high-stakes testing mandates. Five common themes emerged. Standards have increased the overall amount of evolution that is taught. High-stakes testing has decreased the depth at which evolution is taught. Teacher belief systems strongly influence how evolution is taught. Fear of creationist challenges effect evolution teaching strategies. And lastly, concern over the potential effects of teaching evolution on student worldviews was mixed. Three categories of teacher concern over the potential impact of evolution on student worldviews were identified: Concerned, Strategist, and Carefree. In the final analysis teacher beliefs and attitudes still appeared to he the most important factor influencing how evolution is taught.

Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks

Science.gov (United States)

Fortunato, Angelo; Boddy, Amy; Mallo, Diego; Aktipis, Athena; Maley, Carlo C.; Pepper, John W.

2017-01-01

Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research. In this review, we discuss the differences and similarities between evolution among somatic cells versus evolution among organisms. We review what is known about the parameters and rate of evolution in neoplasms, as well as evidence for adaptation. We conclude that adaptation is a useful framework that accurately explains the defining characteristics of cancer. Further, convergent evolution through natural selection provides the only satisfying explanation both for how a group of diverse pathologies have enough in common to usefully share the descriptive label of “cancer” and for why this convergent condition becomes life-threatening. PMID:28148564

Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks.

Science.gov (United States)

Fortunato, Angelo; Boddy, Amy; Mallo, Diego; Aktipis, Athena; Maley, Carlo C; Pepper, John W

2017-02-01

Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research. In this review, we discuss the differences and similarities between evolution among somatic cells versus evolution among organisms. We review what is known about the parameters and rate of evolution in neoplasms, as well as evidence for adaptation. We conclude that adaptation is a useful framework that accurately explains the defining characteristics of cancer. Further, convergent evolution through natural selection provides the only satisfying explanation both for how a group of diverse pathologies have enough in common to usefully share the descriptive label of "cancer" and for why this convergent condition becomes life-threatening. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

United theory of biological evolution: Disaster-forced evolution through Supernova, radioactive ash fall-outs, genome instability, and mass extinctions

Directory of Open Access Journals (Sweden)

Toshikazu Ebisuzaki

2015-01-01

Full Text Available We present the disaster-forced biological evolution model as a general framework that includes Darwinian “phylogenic gradualism”, Eldredge-Gould's “punctuated equilibrium”, mass extinctions, and allopatric, parapatric, and sympatric speciation. It describes how reproductive isolation of organisms is established through global disasters due to supernova encounters and local disasters due to radioactive volcanic ash fall-outs by continental alkaline volcanism. Our new evolution model uniquely highlights three major factors of disaster-forced speciation: enhanced mutation rate by higher natural radiation level, smaller population size, and shrunken habitat size (i.e., isolation among the individual populations. We developed a mathematical model describing speciation of a half-isolated group from a parental group, taking into account the population size (Ne, immigration rate (m, and mutation rate (μ. The model gives a quantitative estimate of the speciation, which is consistent with the observations of speciation speed. For example, the speciation takes at least 105 generations, if mutation rate is less than 10−3 per generation per individual. This result is consistent with the previous studies, in which μ is assumed to be 10−3–10−5. On the other hand, the speciation is much faster (less than 105 generations for the case that μ is as large as 0.1 in parapatric conditions (m ＜ μ. Even a sympatric (m ～ 1 speciation can occur within 103 generations, if mutation rate is very high (μ ～ 1 mutation per individual per generation, and if Ne ＜ 20–30. Such a high mutation rate is possible during global disasters due to supernova encounters and local disasters due to radioactive ash fall-outs. They raise natural radiation level by a factor of 100–1000. Such rapid speciation events can also contribute to macro-evolution during mass extinction events, such as observed during the Cambrian explosion of biodiversity. A

New genes as drivers of phenotypic evolution

Science.gov (United States)

Chen, Sidi; Krinsky, Benjamin H.; Long, Manyuan

2014-01-01

During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution. PMID:23949544

A Call to Use Cultural Competence When Teaching Evolution to Religious College Students: Introducing Religious Cultural Competence in Evolution Education (ReCCEE)

Science.gov (United States)

Barnes, M. Elizabeth; Brownell, Sara E.

2017-01-01

Low acceptance of evolution among undergraduate students is common and is best predicted by religious beliefs. Decreasing students' perceived conflict between religion and evolution could increase their acceptance of evolution. However, college biology instructors may struggle with trying to decrease students' perceived conflict between religion…

[Is there a "biology of violence"?].

Science.gov (United States)

Karli, Pierre

2004-01-01

Human violence does not stem from any specific biological substrate. As affective processes play a pre-eminent role in the elaboration and evolution of social interactions, a "biology of violence" draws essentially upon the concepts, methods and techniques of "affective neuroscience".

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life

Directory of Open Access Journals (Sweden)

Koonin Eugene V

2007-05-01

Full Text Available Abstract Background Recent developments in cosmology radically change the conception of the universe as well as the very notions of "probable" and "possible". The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception. Hypothesis Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life.

Science.gov (United States)

Koonin, Eugene V

2007-05-31

Recent developments in cosmology radically change the conception of the universe as well as the very notions of "probable" and "possible". The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception. Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse). The plausibility of different models

Second Symposium on Chemical Evolution and the Origin of Life

International Nuclear Information System (INIS)

Devincenzi, D.L.; Dufour, P.A.

1986-05-01

Recent findings by NASA Exobiology investigators are reported. Scientific papers are presented in the following areas: cosmic evolution of biogenic compounds, prebiotic evolution (planetary and molecular), early evolution of life (biological and geochemical), evolution of advanced life, solar system exploration, and the Search for Extraterrestrial Intelligence (SETI)

Tuition vs. Intuition: Effects of Instruction on Naive Theories of Evolution

Science.gov (United States)

Shtulman, Andrew; Calabi, Prassede

2013-01-01

Recent research suggests that a major obstacle to evolution understanding is an essentialist view of the biological world. The present study investigated the effects of formal biology instruction on such misconceptions. Participants (N = 291) completed an assessment of their understanding of six aspects of evolution (variation, inheritance,…

Niche construction and the evolution of leadership

NARCIS (Netherlands)

Spisak, B.R.; O'Brien, M.; Nicholson, N.; van Vugt, M.

2015-01-01

We use the concept of niche construction - the process whereby individuals, through their activities, interactions, and choices, modify their own and each other's environments - as an example of how biological evolution and cultural evolution interacted to form an integrative foundation of modern

Biology of the sauropod dinosaurs: the evolution of gigantism.

Science.gov (United States)

Sander, P Martin; Christian, Andreas; Clauss, Marcus; Fechner, Regina; Gee, Carole T; Griebeler, Eva-Maria; Gunga, Hanns-Christian; Hummel, Jürgen; Mallison, Heinrich; Perry, Steven F; Preuschoft, Holger; Rauhut, Oliver W M; Remes, Kristian; Tütken, Thomas; Wings, Oliver; Witzel, Ulrich

2011-02-01

extensive pneumatization of the axial skeleton resulted from the evolution of an avian-style respiratory system, presumably at the base of Saurischia. An avian-style respiratory system would also have lowered the cost of breathing, reduced specific gravity, and may have been important in removing excess body heat. Another crucial innovation inherited from basal dinosaurs was a high BMR. This is required for fueling the high growth rate necessary for a multi-tonne animal to survive to reproductive maturity. The retention of the plesiomorphic oviparous mode of reproduction appears to have been critical as well, allowing much faster population recovery than in megaherbivore mammals. Sauropods produced numerous but small offspring each season while land mammals show a negative correlation of reproductive output to body size. This permitted lower population densities in sauropods than in megaherbivore mammals but larger individuals. Our work on sauropod dinosaurs thus informs us about evolutionary limits to body size in other groups of herbivorous terrestrial tetrapods. Ectothermic reptiles are strongly limited by their low BMR, remaining small. Mammals are limited by their extensive mastication and their vivipary, while ornithsichian dinosaurs were only limited by their extensive mastication, having greater average body sizes than mammals. © 2010 The Authors. Biological Reviews © 2010 Cambridge Philosophical Society.

Positioning genomics in biology education: content mapping of undergraduate biology textbooks.

Science.gov (United States)

Wernick, Naomi L B; Ndung'u, Eric; Haughton, Dominique; Ledley, Fred D

2014-12-01

Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science.

Amphioxus photoreceptors insights into the evolution of vertebrate opsins, vision and circadian rhythmicity

Czech Academy of Sciences Publication Activity Database

Pergner, Jiří; Kozmik, Zbyněk

2017-01-01

Roč. 61, č. 10-12 (2017), s. 665-681 ISSN 0214-6282 R&D Projects: GA ČR GA17-15374S; GA MŠk(CZ) LM2015062; GA MŠk LO1419 Institutional support: RVO:68378050 Keywords : chordate * opsin evolution * photoreceptor * eye evolution * phototransduction Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology Impact factor: 1.981, year: 2016

2007 Microbial Population Biology (July 22-26, 2007)

Energy Technology Data Exchange (ETDEWEB)

Anthony M. Dean

2008-04-01

Microbial Population Biology covers a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past meetings have covered topics ranging from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. We anticipate the 2007 meeting being no exception. The final form of the 2007 meeting is yet to be decided, but the following topics are likely to be included: evolutionary emergence of infectious disease and antibiotic resistance, genetic architecture and implications for the evolution of microbial populations, ageing in bacteria, biogeography, evolution of symbioses, the role of microbes in ecosystem function, and ecological genomics.

Plant biology in the future.

Science.gov (United States)

Bazzaz, F A

2001-05-08

In the beginning of modern plant biology, plant biologists followed a simple model for their science. This model included important branches of plant biology known then. Of course, plants had to be identified and classified first. Thus, there was much work on taxonomy, genetics, and physiology. Ecology and evolution were approached implicitly, rather than explicitly, through paleobotany, taxonomy, morphology, and historical geography. However, the burgeoning explosion of knowledge and great advances in molecular biology, e.g., to the extent that genes for specific traits can be added (or deleted) at will, have created a revolution in the study of plants. Genomics in agriculture has made it possible to address many important issues in crop production by the identification and manipulation of genes in crop plants. The current model of plant study differs from the previous one in that it places greater emphasis on developmental controls and on evolution by differential fitness. In a rapidly changing environment, the current model also explicitly considers the phenotypic variation among individuals on which selection operates. These are calls for the unity of science. In fact, the proponents of "Complexity Theory" think there are common algorithms describing all levels of organization, from atoms all the way to the structure of the universe, and that when these are discovered, the issue of scaling will be greatly simplified! Plant biology must seriously contribute to, among other things, meeting the nutritional needs of the human population. This challenge constitutes a key part of the backdrop against which future evolution will occur. Genetic engineering technologies are and will continue to be an important component of agriculture; however, we must consider the evolutionary implications of these new technologies. Meeting these demands requires drastic changes in the undergraduate curriculum. Students of biology should be trained in molecular, cellular, organismal

Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes.

Science.gov (United States)

Christie, Joshua R; Beekman, Madeleine

2017-03-01

Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes-specifically their organization into host cells and their uniparental (maternal) inheritance-enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller's ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes-despite their asexual mode of reproduction-can readily undergo adaptive evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Darwinism and the cultural evolution of sports.

Science.gov (United States)

De Block, Andreas; Dewitte, Siegfried

2009-01-01

This article outlines a Darwinian approach to sports that takes into account its profoundly cultural character and thereby overcomes the traditional nature-culture dichotomies in the sociology of sport. We argue that there are good reasons to view sports as culturally evolved signaling systems that serve a function similar to (biological) courtship rituals in other animals. Our approach combines the insights of evolutionary psychology, which states that biological adaptations determine the boundaries for the types of sport that are possible, and pure cultural theories, which describe the mechanism of cultural evolution without referring to sport's biological bases. Several biological and cultural factors may moderate the direct effect that signaling value has on a sport's viability or popularity. Social learning underlies many aspects of the cultural control of sports, and sports have evolved new cultural functions more-or-less unrelated to mate choice as cultural evolution itself became important in humans.

The Biology of Behaviour.

Science.gov (United States)

Broom, D. M.

1981-01-01

Discusses topics to aid in understanding animal behavior, including the value of the biological approach to psychology, functional systems, optimality and fitness, universality of environmental effects on behavior, and evolution of social behavior. (DS)

Quantum biological information theory

CERN Document Server

Djordjevic, Ivan B

2016-01-01

This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

The essential tension competition, cooperation and multilevel selection in evolution

CERN Document Server

Bahar, Sonya

2018-01-01

'The Essential Tension' explores how agents that naturally compete come to act together as a group. The author argues that the controversial concept of multilevel selection is essential to biological evolution, a proposition set to stimulate new debate. The idea of one collective unit emerging from the cooperative interactions of its constituent (and mutually competitive) parts has its roots in the ancient world. More recently, it has illuminated studies of animal behavior, and played a controversial role in evolutionary biology. In Part I, the author explores the historical development of the idea of a collectivity in biological systems, from early speculations on the sociology of human crowd behavior, through the mid-twentieth century debates over the role of group selection in evolution, to the notion of the selfish gene. Part II investigates the balance between competition and cooperation in a range of contemporary biological problems, from flocking and swarming to experimental evolution and the evolutio...

Cognitive Evolution and Religion: Cognition and Religious Evolution

Directory of Open Access Journals (Sweden)

Harvey Whitehouse

2016-03-01

Full Text Available This paper presents contemporary cognitive approaches to the evolution of religious beliefs. Arguments are put forward that different types of beliefs, or ‘modes of religiosity’, occur as a result of a number of evolutionary factors (biological, cultural, socio-political etc. At the same time, religions across the world retain a significant level of common and shared elements, also explained in evolutionary terms.

Anthropic principle in biology and radiation biology

International Nuclear Information System (INIS)

Akif'ev, A. P.; Degtyarev, S.V.

1999-01-01

It was suggested to add the anthropic principle of the Universe according to which the physical constants of fundamental particles of matter and the laws of their counteraction are those that an appearance of man and mind becomes possible and necessary, with some biological constants to the set of fundamental constants. With reparation of DNA as an example it was shown how a cell ran some parameters of Watson-Crick double helix. It was pointed that the concept of the anthropic principle of the Universe in its full body including biological constants was a key to developing of a unified theory of evolution of the Universe within the limits of scientific creationism [ru

Slowly switching between environments facilitates reverse evolution in small populations

Science.gov (United States)

Tan, Longzhi; Gore, Jeff

2011-03-01

The rate at which a physical process occurs usually changes the behavior of a system. In thermodynamics, the reversibility of a process generally increases when it occurs at an infinitely slow rate. In biological evolution, adaptations to a new environment may be reversed by evolution in the ancestral environment. Such fluctuating environments are ubiquitous in nature, although how the rate of switching affects reverse evolution is unknown. Here we use a computational approach to quantify evolutionary reversibility as a function of the rate of switching between two environments. For small population sizes, which travel on landscapes as random walkers, we find that both genotypic and phenotypic reverse evolution increase at slow switching rates. However, slow switching of environments decreases evolutionary reversibility for a greedy walker, corresponding to large populations (extensive clonal interference). We conclude that the impact of the switching rate for biological evolution is more complicated than other common physical processes, and that a quantitative approach may yield significant insight into reverse evolution.

The common extremalities in biology and physics maximum energy dissipation principle in chemistry, biology, physics and evolution

CERN Document Server

Moroz, Adam

2011-01-01

This book is the first unified systemic description of dissipative phenomena, taking place in biology, and non-dissipative (conservative) phenomena, which is more relevant to physics. Fully updated and revised, this new edition extends our understanding of nonlinear phenomena in biology and physics from the extreme / optimal perspective. The first book to provide understanding of physical phenomena from a biological perspective and biological phenomena from a physical perspective Discusses emerging fields and analysis Provides examples.

2009 MICROBIAL POPULATION BIOLOGY GORDON RESEARCH CONFERENCES JULY 19-24,2009

Energy Technology Data Exchange (ETDEWEB)

ANTHONY DEAN

2009-07-24

The 2009 Gordon Conference on Microbial Population Biology will cover a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past Conferences have covered a range of topics from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. The 2009 Conference is no exception, and will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomic approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. As in the past, this Conference provides young scientists and graduate students opportunities to present their work in poster format and exchange ideas with leading investigators from a broad spectrum of disciplines. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. The 2009 meeting will be no exception.

Tracking Alu evolution in New World primates

Directory of Open Access Journals (Sweden)

Batzer Mark A

2005-10-01

Full Text Available Abstract Background Alu elements are Short INterspersed Elements (SINEs in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu sequences for loci specific to platyrrhine (New World primates. Results Branching patterns along an Alu sequence phylogeny indicate three major classes of platyrrhine-specific Alu sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; AluTa7, AluTa10, and AluTa15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of AluSc- and AluSp-type elements. This is a novel mode of origin for new Alu subfamilies. Conclusion The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.

Branching processes in biology

CERN Document Server

Kimmel, Marek

2015-01-01

This book provides a theoretical background of branching processes and discusses their biological applications. Branching processes are a well-developed and powerful set of tools in the field of applied probability. The range of applications considered includes molecular biology, cellular biology, human evolution and medicine. The branching processes discussed include Galton-Watson, Markov, Bellman-Harris, Multitype, and General Processes. As an aid to understanding specific examples, two introductory chapters, and two glossaries are included that provide background material in mathematics and in biology. The book will be of interest to scientists who work in quantitative modeling of biological systems, particularly probabilists, mathematical biologists, biostatisticians, cell biologists, molecular biologists, and bioinformaticians. The authors are a mathematician and cell biologist who have collaborated for more than a decade in the field of branching processes in biology for this new edition. This second ex...

Evolution, epigenetics and cooperation.

Science.gov (United States)

Bateson, Patrick

2014-04-01

Explanations for biological evolution in terms of changes in gene frequencies refer to outcomes rather than process. Integrating epigenetic studies with older evolutionary theories has drawn attention to the ways in which evolution occurs. Adaptation at the level of the gene is givingway to adaptation at the level of the organism and higher-order assemblages of organisms. These ideas impact on the theories of how cooperation might have evolved. Two of the theories, i.e. that cooperating individuals are genetically related or that they cooperate for self-interested reasons, have been accepted for a long time. The idea that adaptation takes place at the level of groups is much more controversial. However, bringing together studies of development with those of evolution is taking away much of the heat in the debate about the evolution of group behaviour.

Toward the Language-Ready Brain: Biological Evolution and Primate Comparisons.

Science.gov (United States)

Arbib, Michael A

2017-02-01

The approach to language evolution suggested here focuses on three questions: How did the human brain evolve so that humans can develop, use, and acquire languages? How can the evolutionary quest be informed by studying brain, behavior, and social interaction in monkeys, apes, and humans? How can computational modeling advance these studies? I hypothesize that the brain is language ready in that the earliest humans had protolanguages but not languages (i.e., communication systems endowed with rich and open-ended lexicons and grammars supporting a compositional semantics), and that it took cultural evolution to yield societies (a cultural constructed niche) in which language-ready brains could become language-using brains. The mirror system hypothesis is a well-developed example of this approach, but I offer it here not as a closed theory but as an evolving framework for the development and analysis of conflicting subhypotheses in the hope of their eventual integration. I also stress that computational modeling helps us understand the evolving role of mirror neurons, not in and of themselves, but only in their interaction with systems "beyond the mirror." Because a theory of evolution needs a clear characterization of what it is that evolved, I also outline ideas for research in neurolinguistics to complement studies of the evolution of the language-ready brain. A clear challenge is to go beyond models of speech comprehension to include sign language and models of production, and to link language to visuomotor interaction with the physical and social world.

The Cotesia sesamiae story: insight into host-range evolution in a Hymenoptera parasitoid and implication for its use in biological control programs.

Science.gov (United States)

Kaiser, L; Dupas, S; Branca, A; Herniou, E A; Clarke, C W; Capdevielle Dulac, C; Obonyo, J; Benoist, R; Gauthier, J; Calatayud, P A; Silvain, J F; Le Ru, B P

2017-12-01

This review covers nearly 20 years of studies on the ecology, physiology and genetics of the Hymenoptera Cotesia sesamiae, an African parasitoid of Lepidoptera that reduces populations of common maize borers in East and South Africa. The first part of the review presents studies based on sampling of C. sesamiae from maize crops in Kenya. From this agrosystem including one host plant and three main host borer species, studies revealed two genetically differentiated populations of C. sesamiae species adapted to their local host community, and showed that their differentiation involved the joint evolution of virulence genes and sensory mechanisms of host acceptance, reinforced by reproductive incompatibility due to Wolbachia infection status and natural inbreeding. In the second part, we consider the larger ecosystem of wild Poales plant species hosting many Lepidoptera stem borer species that are potential hosts for C. sesamiae. The hypothesis of other host-adapted C. sesamiae populations was investigated based on a large sampling of stem borer larvae on various Poales across sub-Saharan Africa. The sampling provided information on the respective contribution of local hosts, biogeography and Wolbachia in the genetic structure of C. sesamiae populations. Molecular evolution analyses highlighted that several bracovirus genes were under positive selection, some of them being under different selection pressure in C. sesamiae populations adapted to different hosts. This suggests that C. sesamiae host races result from co-evolution acting at the local scale on different bracovirus genes. The third part considers the mechanisms driving specialization. C. sesamiae host races are more or less host-specialized. This character is crucial for efficient and environmentally-safe use of natural enemies for biological control of pests. One method to get an insight in the evolutionary stability of host-parasite associations is to characterize the phylogenetic relationships between

Thinking Evolutionarily: Evolution Education across the Life Sciences--Summary of a Convocation

Science.gov (United States)

Olson, Steve

2012-01-01

Evolution is the central unifying theme of biology. Yet today, more than a century and a half after Charles Darwin proposed the idea of evolution through natural selection, the topic is often relegated to a handful of chapters in textbooks and a few class sessions in introductory biology courses, if covered at all. In recent years, a movement has…

On the interplay between mathematics and biology: hallmarks toward a new systems biology.

Science.gov (United States)

Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

2015-03-01

This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution.

Science.gov (United States)

Alsop, Eric B; Boyd, Eric S; Raymond, Jason

2014-05-28

The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity. By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition. Clustering based on the frequency in which orthologous proteins occur among metagenomes

On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach

Science.gov (United States)

Chen, Bor-Sen; Lin, Ying-Po

2011-01-01

In the evolutionary process, the random transmission and mutation of genes provide biological diversities for natural selection. In order to preserve functional phenotypes between generations, gene networks need to evolve robustly under the influence of random perturbations. Therefore, the robustness of the phenotype, in the evolutionary process, exerts a selection force on gene networks to keep network functions. However, gene networks need to adjust, by variations in genetic content, to generate phenotypes for new challenges in the network’s evolution, ie, the evolvability. Hence, there should be some interplay between the evolvability and network robustness in evolutionary gene networks. In this study, the interplay between the evolvability and network robustness of a gene network and a biochemical network is discussed from a nonlinear stochastic system point of view. It was found that if the genetic robustness plus environmental robustness is less than the network robustness, the phenotype of the biological network is robust in evolution. The tradeoff between the genetic robustness and environmental robustness in evolution is discussed from the stochastic stability robustness and sensitivity of the nonlinear stochastic biological network, which may be relevant to the statistical tradeoff between bias and variance, the so-called bias/variance dilemma. Further, the tradeoff could be considered as an antagonistic pleiotropic action of a gene network and discussed from the systems biology perspective. PMID:22084563

New Frontiers in Language Evolution and Development.

Science.gov (United States)

Oller, D Kimbrough; Dale, Rick; Griebel, Ulrike

2016-04-01

This article introduces the Special Issue and its focus on research in language evolution with emphasis on theory as well as computational and robotic modeling. A key theme is based on the growth of evolutionary developmental biology or evo-devo. The Special Issue consists of 13 articles organized in two sections: A) Theoretical foundations and B) Modeling and simulation studies. All the papers are interdisciplinary in nature, encompassing work in biological and linguistic foundations for the study of language evolution as well as a variety of computational and robotic modeling efforts shedding light on how language may be developed and may have evolved. Copyright © 2016 Cognitive Science Society, Inc.

Evolution algebras generated by Gibbs measures

International Nuclear Information System (INIS)

Rozikov, Utkir A.; Tian, Jianjun Paul

2009-03-01

In this article we study algebraic structures of function spaces defined by graphs and state spaces equipped with Gibbs measures by associating evolution algebras. We give a constructive description of associating evolution algebras to the function spaces (cell spaces) defined by graphs and state spaces and Gibbs measure μ. For finite graphs we find some evolution subalgebras and other useful properties of the algebras. We obtain a structure theorem for evolution algebras when graphs are finite and connected. We prove that for a fixed finite graph, the function spaces have a unique algebraic structure since all evolution algebras are isomorphic to each other for whichever Gibbs measures are assigned. When graphs are infinite graphs then our construction allows a natural introduction of thermodynamics in studying of several systems of biology, physics and mathematics by theory of evolution algebras. (author)

The navigation of biological hyperspace

Science.gov (United States)

Conway Morris, Simon

2003-04-01

A recurrent argument against the reality of biological evolution is the claim that there is insufficient time for the emergence of biological complexity. Such a view is a staple of creation "scientists", but even cosmologists and biochemists have been overheard murmuring similar sentiments. Certainly the stock response, that the scientific evidence for evolution is overwhelming, must be made. However, it is also the case that whilst the efficacity of natural selection is not in dispute, it is context-free and fails to explain the specificities of life. This observation is usually greeted with a Gallic shrug: "Yes, the biosphere is very rich, but so what?" Indeed, the standard scientific response is that evolution is dogged by contingent happenstance, with the implication that a given complexity, say intelligence, is an evolutionary fluke. This, however, is inconsistent with the ubiquity of evolutionary convergence. Here I outline the argument for such convergence providing a "road-map" of possibilities that arguably has universal applications and as importantly points to a much deeper structure to life.

Cultural commons and cultural evolution

OpenAIRE

Bravo, Giangiacomo

2010-01-01

Culture evolves following a process that is akin to biological evolution, although with some significant differences. At the same time culture has often a collective good value for human groups. This paper studies culture in an evolutionary perspective, with a focus on the implications of group definition for the coexistence of different cultures. A model of cultural evolution is presented where agents interacts in an artificial environment. The belonging to a specific memetic group is a majo...

Human evolution. Evolution of early Homo: an integrated biological perspective.

Science.gov (United States)

Antón, Susan C; Potts, Richard; Aiello, Leslie C

2014-07-04

Integration of evidence over the past decade has revised understandings about the major adaptations underlying the origin and early evolution of the genus Homo. Many features associated with Homo sapiens, including our large linear bodies, elongated hind limbs, large energy-expensive brains, reduced sexual dimorphism, increased carnivory, and unique life history traits, were once thought to have evolved near the origin of the genus in response to heightened aridity and open habitats in Africa. However, recent analyses of fossil, archaeological, and environmental data indicate that such traits did not arise as a single package. Instead, some arose substantially earlier and some later than previously thought. From ~2.5 to 1.5 million years ago, three lineages of early Homo evolved in a context of habitat instability and fragmentation on seasonal, intergenerational, and evolutionary time scales. These contexts gave a selective advantage to traits, such as dietary flexibility and larger body size, that facilitated survival in shifting environments. Copyright © 2014, American Association for the Advancement of Science.

The Evolution of Darwinism.

Science.gov (United States)

Stebbins, G. Ledyard; Ayala, Francisco J.

1985-01-01

Recent developments in molecular biology and new interpretations of the fossil record are gradually altering and adding to Charles Darwin's theory, which has been the standard view of the process of evolution for 40 years. Several of these developments and interpretations are identified and discussed. (JN)

Teaching Evolution: From SMART Objectives to Threshold Experience

Science.gov (United States)

Wolf, Alexander; Akkaraju, Shylaja

2014-01-01

Despite the centrality of evolution to the study of biology, the pedagogical methods employed to teach the subject are often instructor-centered and rarely embedded in every topic throughout the curriculum. In addition, students' prior beliefs about evolution are often dismissed rather than incorporated into the classroom. In this article we…

Has Human Evolution Stopped?

Directory of Open Access Journals (Sweden)

Alan R. Templeton

2010-07-01

Full Text Available It has been argued that human evolution has stopped because humans now adapt to their environment via cultural evolution and not biological evolution. However, all organisms adapt to their environment, and humans are no exception. Culture defines much of the human environment, so cultural evolution has actually led to adaptive evolution in humans. Examples are given to illustrate the rapid pace of adaptive evolution in response to cultural innovations. These adaptive responses have important implications for infectious diseases, Mendelian genetic diseases, and systemic diseases in current human populations. Moreover, evolution proceeds by mechanisms other than natural selection. The recent growth in human population size has greatly increased the reservoir of mutational variants in the human gene pool, thereby enhancing the potential for human evolution. The increase in human population size coupled with our increased capacity to move across the globe has induced a rapid and ongoing evolutionary shift in how genetic variation is distributed within and among local human populations. In particular, genetic differences between human populations are rapidly diminishing and individual heterozygosity is increasing, with beneficial health effects. Finally, even when cultural evolution eliminates selection on a trait, the trait can still evolve due to natural selection on other traits. Our traits are not isolated, independent units, but rather are integrated into a functional whole, so selection on one trait can cause evolution to occur on another trait, sometimes with mildly maladaptive consequences.

Using the biological literature a practical guide

CERN Document Server

Schmidt, Diane

2014-01-01

IntroductionSearching the Biological LiteratureGeneral SourcesAssociationsBibliographiesClassification, Nomenclature, and SystematicsDictionaries and EncyclopediasDirectoriesField GuidesSeriesFull-Text SourcesGeneral WorksGuides for young ScientistsGuides to the LiteratureHandbooksHistoriesMathematics and StatisticsMethods and TechniquesTextbooks and TreatisesWriting GuidesPeriodicalsReviews of the LiteratureAbstracts and IndexesBiochemistry and BiophysicsMolecular and Cellular BiologyGenetics, Biotechnology, and Developmental BiologyMicrobiology and ImmunologyEcology, Evolution, and Animal BehaviorPlant BiologyAnatomy and PhysiologyEntomologyZoologyIndex.

Derivation of the extrinsic values of biological diversity from its intrinsic value and of both from the first principles of evolution.

Science.gov (United States)

White, Peter S

2013-12-01

Conservation ethics have been based on 2 philosophical value systems: extrinsic value (defined broadly to include all values that derive from something external to the thing valued) and intrinsic value. Valuing biological diversity on the basis of an extrinsic value system is problematic because measurement is often difficult; extrinsic value changes as spatial or temporal scales change; extrinsic value differs on the basis of external factors; some species have trivial or negative extrinsic values; and extrinsic value varies across human cultures and societies and with such factors as socioeconomic conditions, individual experiences, and educational backgrounds. Valuing biological diversity on the basis of an intrinsic value system also poses challenges because intrinsic value can be seen as a disguised form of human extrinsic value; intrinsic value is initially ambiguous as to which objects or characteristics of biological diversity are to being valued; all aspects of biological diversity (e.g., species and ecosystems) are transitory; species and ecosystems are not static concrete entities; and intrinsic value of one species is often in conflict with the intrinsic value of other species. Extrinsic and intrinsic value systems share a common origin, such that extrinsic values are always derived from intrinsic value and life mutely expresses both intrinsic and extrinsic values-these are derived from and are products of biological evolution. Probing the values that underlie conservation helps the community clearly articulate its aims. Derivación de los Valores Extrínsecos de la Biodiversidad a Partir de sus Valores Intrínsecos y de Ambos a Partir de los Primeros Principios de la Evolución. © 2013 Society for Conservation Biology.

Evolution, Fruit Flies and Gerontology

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 11. Evolution, Fruit Flies and Gerontology Evolutionary Biology Helps Unravel the Mysteries of Ageing. Amitabh Joshi. General Article Volume 1 Issue 11 November 1996 pp 51-63 ...

Biology of the sauropod dinosaurs: the evolution of gigantism

Science.gov (United States)

Sander, P Martin; Christian, Andreas; Clauss, Marcus; Fechner, Regina; Gee, Carole T; Griebeler, Eva-Maria; Gunga, Hanns-Christian; Hummel, Jürgen; Mallison, Heinrich; Perry, Steven F; Preuschoft, Holger; Rauhut, Oliver W M; Remes, Kristian; Tütken, Thomas; Wings, Oliver; Witzel, Ulrich

2011-01-01

The herbivorous sauropod dinosaurs of the Jurassic and Cretaceous periods were the largest terrestrial animals ever, surpassing the largest herbivorous mammals by an order of magnitude in body mass. Several evolutionary lineages among Sauropoda produced giants with body masses in excess of 50 metric tonnes by conservative estimates. With body mass increase driven by the selective advantages of large body size, animal lineages will increase in body size until they reach the limit determined by the interplay of bauplan, biology, and resource availability. There is no evidence, however, that resource availability and global physicochemical parameters were different enough in the Mesozoic to have led to sauropod gigantism. We review the biology of sauropod dinosaurs in detail and posit that sauropod gigantism was made possible by a specific combination of plesiomorphic characters (phylogenetic heritage) and evolutionary innovations at different levels which triggered a remarkable evolutionary cascade. Of these key innovations, the most important probably was the very long neck, the most conspicuous feature of the sauropod bauplan. Compared to other herbivores, the long neck allowed more efficient food uptake than in other large herbivores by covering a much larger feeding envelope and making food accessible that was out of the reach of other herbivores. Sauropods thus must have been able to take up more energy from their environment than other herbivores. The long neck, in turn, could only evolve because of the small head and the extensive pneumatization of the sauropod axial skeleton, lightening the neck. The small head was possible because food was ingested without mastication. Both mastication and a gastric mill would have limited food uptake rate. Scaling relationships between gastrointestinal tract size and basal metabolic rate (BMR) suggest that sauropods compensated for the lack of particle reduction with long retention times, even at high uptake rates. The

Evolution of ageing since Darwin

Indian Academy of Sciences (India)

2008-12-23

Dec 23, 2008 ... causes of senescence in terms of evolution by natural selec- tion. He rejected the historical ... ism's longevity was somehow determined by its physiolog- ..... Gavrilov L. A. and Gavrilova N. S. 1991 The biology of life span: a.

Raman spectroscopy as a tool for ecology and evolution.

Science.gov (United States)

Germond, Arno; Kumar, Vipin; Ichimura, Taro; Moreau, Jerome; Furusawa, Chikara; Fujita, Hideaki; Watanabe, Tomonobu M

2017-06-01

Scientists are always on the lookout for new modalities of information which could reveal new biological features that are useful for deciphering the complexity of biological systems. Here, we introduce Raman spectroscopy as a prime candidate for ecology and evolution. To encourage the integration of this microscopy technique in the field of ecology and evolution, it is crucial to discuss first how Raman spectroscopy fits within the conceptual, technical and pragmatic considerations of ecology and evolution. In this paper, we show that the spectral information holds reliable indicators of intra- and interspecies variations, which can be related to the environment, selective pressures and fitness. Moreover, we show how the technical and pragmatic aspects of this modality (non-destructive, non-labelling, speed, relative low cost, etc.) enable it to be combined with more conventional methodologies. With this paper, we hope to open new avenues of research and extend the scope of available methodologies used in ecology and evolution. © 2017 The Authors.

Between a Pod and a Hard Test: The Deep Evolution of Amoebae

Czech Academy of Sciences Publication Activity Database

Kang, S.; Tice, A. K.; Spiegel, F. W.; Silberman, J. D.; Pánek, T.; Čepička, I.; Kostka, Martin; Kosakyan, A.; Alcantara, D. M. C.; Roger, A. J.; Shadwick, L.; Smirnov, A.; Kudryavtsev, A.; Lahr, D. J. G.; Brown, M. W.

2017-01-01

Roč. 34, č. 9 (2017), s. 2258-2270 ISSN 0737-4038 Institutional support: RVO:60077344 Keywords : phylogenomics * transcriptomes * Amoebozoa * reductive evolution * phylotranscriptomics Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology Impact factor: 6.202, year: 2016

Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity.

Science.gov (United States)

Speijer, Dave

2011-05-01

Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes. Copyright © 2011 WILEY Periodicals, Inc.

Axiological and epistemological contributions to teaching the theory of evolution Darwin

Directory of Open Access Journals (Sweden)

Lucken Bueno Lucas

2011-10-01

Full Text Available From the essential role of theme “biological evolution” in scientific formation of students and the diversity of issues identified in the literature for teaching of the same, we developed a qualitative study through contributions of Didactics of Science and Critical Meaningful Learning, characterized by a review of theoretical and methodological on the treatise subject, a historical-epistemological synthesis of Darwinism and its axiological analysis, the elaboration of a didactic sequence for teaching evolution and your appreciation of biology teachers, and a discursive textual analysis of that assessment. Based on this study, therefore, we discuss the possible contributions to the teaching of biology, of proposals that articulate and introduce axiological contributions, historical and philosophical in teaching of biological evolution.

The Effect of Contextual Material on Evolution in the Jordanian Secondary-School Curriculum on Students' Acceptance of the Theory of Evolution

Science.gov (United States)

De Baz, Theodora; El-Weher, Mahmoud

2012-01-01

The purpose of this study was to detect the extent to which contextual material of a unit on "The origin and evolution of living organisms" included in the high-school biology curriculum in Jordan affected students' acceptance of the theory of evolution. The participants of this study consisted of 107 tenth-grade students randomly drawn…

Chance, purpose, and progress in evolution and christianity.

Science.gov (United States)

Mix, Lucas J; Masel, Joanna

2014-08-01

Evolutionary biology has a complex relationship with ideas of chance, purpose, and progress. Probability plays a subtle role; strikingly, founding figures in statistics were motivated by evolutionary questions. The findings of evolutionary biology have been used both in support of narratives of progress, and in their deconstruction. Likewise, professional biologists bring to their scientific work a set of preconceptions about chance and progress, grounded in their philosophical, religious, and/or political views. From the religious side, questions of purpose are ever-present. We explore this interplay in five broad categories: chance, progress, intelligence, eugenics, and the evolution of religious practices, each the subject of a semester long symposium. The intellectual influence of evolutionary biology has had a broad societal impact in these areas. Based on our experience, we draw attention to a number of relevant facts that, while accepted by experts in their respective fields, may be unfamiliar outside them. We list common areas of miscommunication, including specific examples and discussing causes: sometimes semantics and sometimes more substantive knowledge barriers. We also make recommendations for those attempting similar dialogue. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Evolution and non-equilibrium physics

DEFF Research Database (Denmark)

Becker, Nikolaj; Sibani, Paolo

2014-01-01

We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of the Tangled Nature Model (TNM) of biological evolution...

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.

Modeling evolution and immune system by cellular automata

International Nuclear Information System (INIS)

Bezzi, M.

2001-01-01

In this review the behavior of two different biological systems is investigated using cellular automata. Starting from this spatially extended approach it is also tried, in some cases, to reduce the complexity of the system introducing mean-field approximation, and solving (or trying to solve) these simplified systems. It is discussed the biological meaning of the results, the comparison with experimental data (if available) and the different features between spatially extended and mean-field versions. The biological systems considered in this review are the following: Darwinian evolution in simple ecosystems and immune system response. In the first section the main features of molecular evolution are introduced, giving a short survey of genetics for physicists and discussing some models for prebiotic systems and simple ecosystems. It is also introduced a cellular automaton model for studying a set of evolving individuals in a general fitness landscape, considering also the effects of co-evolution. In particular the process of species formation (speciation) is described in sect. 5. The second part deals with immune system modeling. The biological features of immune response are discussed, as well as it is introduced the concept of shape space and of idiotypic network. More detailed reviews which deal with immune system models (mainly focused on idiotypic network models) can be found. Other themes here discussed: the applications of CA to immune system modeling, two complex cellular automata for humoral and cellular immune response. Finally, it is discussed the biological data and the general conclusions are drawn in the last section

Evolution to Autonomy

Directory of Open Access Journals (Sweden)

Horace Lockwood Fairlamb

2007-08-01

Full Text Available Since both modern moral theory and evolutionary theory arose in the shadow of Newtonian and Humean conceptions of nature, debates about evolutionary ethics have typically been vexed by deeper problems with the nature of evolution itself as well as meta-ethical questions about the link between facts and values. Humean skepticism and mechanistic selectionism have recently coincided in postmodern attacks on essentialism,on meta-narratives of progress, on models of human nature, and on moral collectivism. Against this most recent wave of skepticism, however, contemporary reconstructions of evolution in light of complex systems science suggest useful ways of reinterpreting both evolutionary causation, the biology of human nature, and their implications for ethics.

Validation of an Instrument for Assessing Conceptual Change with Respect to the Theory of Evolution by Secondary Biology Students

Science.gov (United States)

Goff, Kevin David

This pilot study evaluated the validity of a new quantitative, closed-response instrument for assessing student conceptual change regarding the theory of evolution. The instrument has two distinguishing design features. First, it is designed not only to gauge student mastery of the scientific model of evolution, but also to elicit a trio of deeply intuitive tendencies that are known to compromise many students' understanding: the projection of intentional agency, teleological directionality, and immutable essences onto biological phenomena. Second, in addition to a section of conventional multiple choice questions, the instrument contains a series of items where students may simultaneously endorse both scientifically normative propositions and intuitively appealing yet unscientific propositions, without having to choose between them. These features allow for the hypothesized possibility that the three intuitions are partly innate, themselves products of cognitive evolution in our hominin ancestors, and thus may continue to inform students' thinking even after instruction and conceptual change. The test was piloted with 340 high school students from diverse schools and communities. Confirmatory factor analysis and other statistical methods provided evidence that the instrument already has strong potential for validly distinguishing students who hold a correct scientific understanding from those who do not, but that revision and retesting are needed to render it valid for gauging students' adherence to intuitive misconceptions. Ultimately the instrument holds promise as a tool for classroom intervention studies by conceptual change researchers, for diagnostic testing and data gathering by instructional leaders, and for provoking classroom dialogue and debate by science teachers.

Evolutionary Medicine and Future of Humanity: Will Evolution Have the Final Word?

Directory of Open Access Journals (Sweden)

Maciej Henneberg

2013-06-01

Full Text Available Evolutionary medicine in its classical form assumes that since cultural evolution is faster than biological evolution, ailments of modern people are a result of mismatch between adaptations to the past environments and current situations. A core principle is that we, humans, having evolved for millions of years in a specific natural environment (environment of evolutionary adaptation EEA are biologically adapted to this past environment and the ancient lifestyle. This adaptation to the past produces major mismatch of our bodies with the present, highly anthropic and thus “artificial” living conditions. This article provides two areas of possible future evolution, diet and physical activity levels which have been dramatically altered in industrialised societies. Consequently, micro-evolution is an on-going process.

Extended genomes: symbiosis and evolution

OpenAIRE

Hurst, Gregory D. D.

2017-01-01

Many aspects of an individual's biology derive from its interaction with symbiotic microbes, which further define many aspects of the ecology and evolution of the host species. The centrality of microbes in the function of individual organisms has given rise to the concept of the holobiont?that an individual's biology is best understood as a composite of the ?host organism? and symbionts within. This concept has been further elaborated to posit the holobiont as a unit of selection. In this re...

Teaching Tree-Thinking to Undergraduate Biology Students.

Science.gov (United States)

Meisel, Richard P

2010-07-27

Evolution is the unifying principle of all biology, and understanding how evolutionary relationships are represented is critical for a complete understanding of evolution. Phylogenetic trees are the most conventional tool for displaying evolutionary relationships, and "tree-thinking" has been coined as a term to describe the ability to conceptualize evolutionary relationships. Students often lack tree-thinking skills, and developing those skills should be a priority of biology curricula. Many common student misconceptions have been described, and a successful instructor needs a suite of tools for correcting those misconceptions. I review the literature on teaching tree-thinking to undergraduate students and suggest how this material can be presented within an inquiry-based framework.

Design in nature how the constructal law governs evolution in biology, physics, technology, and social organization

CERN Document Server

Bejan, Adrian

2013-01-01

In this groundbreaking book, Adrian Bejan takes the recurring patterns in nature—trees, tributaries, air passages, neural networks, and lightning bolts—and reveals how a single principle of physics, the constructal law, accounts for the evolution of these and many other designs in our world. Everything—from biological life to inanimate systems—generates shape and structure and evolves in a sequence of ever-improving designs in order to facilitate flow. River basins, cardiovascular systems, and bolts of lightning are very efficient flow systems to move a current—of water, blood, or electricity. Likewise, the more complex architecture of animals evolve to cover greater distance per unit of useful energy, or increase their flow across the land. Such designs also appear in human organizations, like the hierarchical “flowcharts” or reporting structures in corporations and political bodies. All are governed by the same principle, known as the constructal law, and configure and reconfigure themselves...

Molecular biology of Homo sapiens: Abstracts of papers presented at the 51st Cold Spring Harbor symposium on quantitative biology

International Nuclear Information System (INIS)

Watson, J.D.; Siniscalco, M.

1986-01-01

This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Genetic Diagnosis, Human Evolution, Drugs Made Off Human Genes, Receptors, and Gene Therapy. (DT)

Plant vs. Animal, Which is the Most Prefer Understanding of Evolution?

Directory of Open Access Journals (Sweden)

Hana Gardenia Mahbubah

2017-12-01

Full Text Available Evolution is one of the main subjects of biology taught in science colleges. Unfortunately, students seem less attention to this subject. In the subject of evolution, the lesson commonly uses the animal as a model to improve the students understanding. The purpose of this study is to compare the ability of tree thinking students who use animals and plants as a model in the evolution lesson. Tree thinking refers to an approach to evolution that emphasizes reading and interpreting phylogenetic tree. This study involved 20 undergraduate students enrolled in the evolution course for biology majors at Universitas Pendidikan Indonesia (UPI. The tree thinking ability of students was measured using Tree Thinking Concept Inventory (TTCI of Naegle with a little modification. In this test, we analyzed student preferences using animal or plant models using phylogenetic tree diagrams. Results showed that students’ TTCI score was higher when using animal models (65.42% than plant models (55%. These results suggested that students remain to prefer animal models compare to plant models to study evolution. Nevertheless, the use of plants as models can be an alternative to learning evolution in the future.

Adaptation hypothesis of biological efficiency of ionizing radiation

International Nuclear Information System (INIS)

Kudritskij, Yu.K.; Georgievskij, A.B.; Karpov, V.I.

1992-01-01

Adaptation hypothesis of biological efficiency of ionizing radiation is based on acknowledgement of invariance of fundamental laws and principles of biology related to unity of biota and media, evolution and adaptation for radiobiology. The basic arguments for adaptation hypothesis validity, its correspondence to the requirements imposed on scientific hypothes are presented

Some nonlinear challenges in biology

International Nuclear Information System (INIS)

Mosconi, Francesco; Julou, Thomas; Desprat, Nicolas; Sinha, Deepak Kumar; Allemand, Jean-François; Croquette, Vincent; Bensimon, David

2008-01-01

Driven by a deluge of data, biology is undergoing a transition to a more quantitative science. Making sense of the data, building new models, asking the right questions and designing smart experiments to answer them are becoming ever more relevant. In this endeavour, nonlinear approaches can play a fundamental role. The biochemical reactions that underlie life are very often nonlinear. The functional features exhibited by biological systems at all levels (from the activity of an enzyme to the organization of a colony of ants, via the development of an organism or a functional module like the one responsible for chemotaxis in bacteria) are dynamically robust. They are often unaffected by order of magnitude variations in the dynamical parameters, in the number or concentrations of actors (molecules, cells, organisms) or external inputs (food, temperature, pH, etc). This type of structural robustness is also a common feature of nonlinear systems, exemplified by the fundamental role played by dynamical fixed points and attractors and by the use of generic equations (logistic map, Fisher–Kolmogorov equation, the Stefan problem, etc.) in the study of a plethora of nonlinear phenomena. However, biological systems differ from these examples in two important ways: the intrinsic stochasticity arising from the often very small number of actors and the role played by evolution. On an evolutionary time scale, nothing in biology is frozen. The systems observed today have evolved from solutions adopted in the past and they will have to adapt in response to future conditions. The evolvability of biological system uniquely characterizes them and is central to biology. As the great biologist T Dobzhansky once wrote: 'nothing in biology makes sense except in the light of evolution'. (open problem)

Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications.

Science.gov (United States)

Barthlott, W; Mail, M; Neinhuis, C

2016-08-06

A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing.This article is part of the themed issue 'Bioinspired hierarchically structured surfaces for green science'. © 2016 The Author(s).

Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications

Science.gov (United States)

Mail, M.; Neinhuis, C.

2016-01-01

A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing. This article is part of the themed issue ‘Bioinspired hierarchically structured surfaces for green science’. PMID:27354736

Teaching Evolution to Students with Compromised Backgrounds & Lack of Confidence about Evolution--Is It Possible?

Science.gov (United States)

Schauer, Alexandria; Cotner, Sehoya; Moore, Randy

2014-01-01

Students regard evolutionary theory differently than science in general. Students' reported confidence in their ability to understand science in general (e.g., posing scientific questions, interpreting tables and graphs, and understanding the content of their biology course) significantly outweighed their confidence in understanding evolution. We…

Extinction Events Can Accelerate Evolution

DEFF Research Database (Denmark)

Lehman, Joel; Miikkulainen, Risto

2015-01-01

Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate...... evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending...... computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific...

Six Classroom Exercises to Teach Natural Selection to Undergraduate Biology Students

Science.gov (United States)

Kalinowski, Steven T.; Leonard, Mary J.; Andrews, Tessa M.; Litt, Andrea R.

2013-01-01

Students in introductory biology courses frequently have misconceptions regarding natural selection. In this paper, we describe six activities that biology instructors can use to teach undergraduate students in introductory biology courses how natural selection causes evolution. These activities begin with a lesson introducing students to natural…

Evolution of Karyotypes in Chameleons

Czech Academy of Sciences Publication Activity Database

Rovatsos, M.; Altmanová, M.; Johnson Pokorná, Martina; Velenský, P.; Baca, A. S.; Kratochvíl, L.

2017-01-01

Roč. 8, č. 12 (2017), č. článku 382. ISSN 2073-4425 Institutional support: RVO:67985904 Keywords : karyotype evolution * ITS * rDNA Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 3.600, year: 2016

Getting to Darwin: Obstacles to Accepting Evolution by Natural Selection

Science.gov (United States)

Thagard, Paul; Findlay, Scott

2010-01-01

Darwin's theory of evolution by natural selection is central to modern biology, but is resisted by many people. This paper discusses the major psychological obstacles to accepting Darwin's theory. Cognitive obstacles to adopting evolution by natural selection include conceptual difficulties, methodological issues, and coherence problems that…

Teaching Evolution: A Heuristic Study of Personal and Cultural Dissonance

Science.gov (United States)

Grimes, Larry G.

2012-01-01

Darwinian evolution is a robustly supported scientific theory. Yet creationists continue to challenge its teaching in American public schools. Biology teachers in all 50 states are responsible for teaching science content standards that include evolution. As products of their backgrounds and affiliations teachers bring personal attitudes and…

Molecular biology: Self-sustaining chemistry

Directory of Open Access Journals (Sweden)

Wrede Paul

2007-10-01

Full Text Available Abstract Molecular biology is an established interdisciplinary field within biology that deals fundamentally with the function of any nucleic acid in the cellular context. The molecular biology section in Chemistry Central Journal focusses on the genetically determined chemistry and biochemistry occuring in the cell. How can thousands of chemical reactions interact smoothly to maintain the life of cells, even in a variable environment? How is this self-sustaining system achieved? These are questions that should be answered in the light of molecular biology and evolution, but with the application of biophysical, physico-chemical, analytical and preparative technologies. As the Section Editor for the molecular biology section in Chemistry Central Journal, I hope to receive manuscripts that present new approaches aimed at better answering and shedding light upon these fascinating questions related to the chemistry of livings cells.

Art as A Playground for Evolution

DEFF Research Database (Denmark)

Beloff, Laura

2016-01-01

Art works which engage with the topic of human enhancement and evolution have begun appearing parallel to increased awareness about anthropogenic changes to our environment and acceleration of the speed of technological developments that impact us and our biological environment. The article...... and related topics is proposed as play activity for adults, which simultaneously experiments directly with ideas concerning evolution and human development. The author proposes that these kinds of experimental art projects support our mental adaptation to evolutionary changes....

Mechanisms of adaptive evolution. Darwinism and Lamarckism restated.

Science.gov (United States)

Aboitiz, F

1992-07-01

This article discusses the conceptual basis of the different mechanisms of adaptive evolution. It is argued that only two such mechanisms may conceivably exist, Lamarckism and Darwinism. Darwinism is the fundamental process generating the diversity of species. Some aspects of the gene-centered approach to Darwinism are questioned, since they do not account for the generation of biological diversity. Diversity in biological design must be explained in relation to the diversity of interactions of organisms (or other higher-level units) with their environment. This aspect is usually overlooked in gene-centered views of evolution. A variant of the gene-selectionist approach has been proposed to account for the spread of cultural traits in human societies. Alternatively, I argue that social evolution is rather driven by what I call pseudo-Lamarckian inheritance. Finally, I argue that Lamarckian and pseudo-Lamarckian inheritance are just special cases of faithful replication which are found in the development of some higher-order units, such as multicellular organisms and human societies.

Monod and the spirit of molecular biology.

Science.gov (United States)

Morange, Michel

2015-06-01

The founders of molecular biology shared views on the place of biology within science, as well as on the relations of molecular biology to Darwinism. Jacques Monod was no exception, but the study of his writings is particularly interesting because he expressed his point of view very clearly and pushed the implications of some of his choices further than most of his contemporaries. The spirit of molecular biology is no longer the same as in the 1960s but, interestingly, Monod anticipated some recent evolutions of this discipline. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Molecular biology of Homo sapiens: Abstracts of papers presented at the 51st Cold Spring Harbor symposium on quantitative biology

Energy Technology Data Exchange (ETDEWEB)

Watson, J.D.; Siniscalco, M.

1986-01-01

This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Genetic Diagnosis, Human Evolution, Drugs Made Off Human Genes, Receptors, and Gene Therapy. (DT)

Quantum evolution life in the multiverse

CERN Document Server

McFadden, Johnjoe

2000-01-01

Quantum Evolution presents a revolutionary new scientific theory by asking: is there a force of will behind evolution? In his astonishing first book, Johnjoe McFadden shows that there is. 'McFadden's bold hypothesis that quantum physics plays a key role in the origin and evolution of life looks increasingly plausible. The weird behaviour of matter and information at the quantum level could be just what is needed to explain life's astonishing properties. If these ideas are right, they will transform our understanding of the relationship between physics and biology.' PAUL DAVIES In this brilliant debut, Johnjoe McFadden puts forward a theory of quantum evolution. He shows how living organisms have the ability to will themselves into action. Indeed, such an ability may be life's most fundamental attribute. This has radical implications. Evolution may not be random at all, as recent evolutionary theories have taught: rather, cells may, in certain circumstances, be able to choose to mutate particular genes that pr...

Diversification and enrichment of clinical biomaterials inspired by Darwinian evolution.

Science.gov (United States)

Green, D W; Watson, G S; Watson, J A; Lee, D-J; Lee, J-M; Jung, H-S

2016-09-15

Regenerative medicine and biomaterials design are driven by biomimicry. There is the essential requirement to emulate human cell, tissue, organ and physiological complexity to ensure long-lasting clinical success. Biomimicry projects for biomaterials innovation can be re-invigorated with evolutionary insights and perspectives, since Darwinian evolution is the original dynamic process for biological organisation and complexity. Many existing human inspired regenerative biomaterials (defined as a nature generated, nature derived and nature mimicking structure, produced within a biological system, which can deputise for, or replace human tissues for which it closely matches) are without important elements of biological complexity such as, hierarchy and autonomous actions. It is possible to engineer these essential elements into clinical biomaterials via bioinspired implementation of concepts, processes and mechanisms played out during Darwinian evolution; mechanisms such as, directed, computational, accelerated evolutions and artificial selection contrived in the laboratory. These dynamos for innovation can be used during biomaterials fabrication, but also to choose optimal designs in the regeneration process. Further evolutionary information can help at the design stage; gleaned from the historical evolution of material adaptations compared across phylogenies to changes in their environment and habitats. Taken together, harnessing evolutionary mechanisms and evolutionary pathways, leading to ideal adaptations, will eventually provide a new class of Darwinian and evolutionary biomaterials. This will provide bioengineers with a more diversified and more efficient innovation tool for biomaterial design, synthesis and function than currently achieved with synthetic materials chemistry programmes and rational based materials design approach, which require reasoned logic. It will also inject further creativity, diversity and richness into the biomedical technologies that

The effect of parity on morphological evolution among phrynosomatid lizards.

Science.gov (United States)

Oufiero, C E; Gartner, G E A

2014-11-01

The shift from egg laying to live-bearing is one of the most well-studied transitions in evolutionary biology. Few studies, however, have assessed the effect of this transition on morphological evolution. Here, we evaluated the effect of reproductive mode on the morphological evolution of 10 traits, among 108 species of phrynosomatid lizards. We assess whether the requirement for passing shelled eggs through the pelvic girdle has led to morphological constraints in oviparous species and whether long gestation times in viviparous species have led to constraints in locomotor morphology. We fit models to the data that vary both in their tempo (strength and rate of selection) and mode of evolution (Brownian or Ornstein-Uhlenbeck) and estimates of trait optima. We found that most traits are best fit by a generalized multipeak OU model, suggesting differing trait optima for viviparous vs. oviparous species. Additionally, rates (σ(2) ) of both pelvic girdle and forelimb trait evolution varied with parity; viviparous species had higher rates. Hindlimb traits, however, exhibited no difference in σ(2) between parity modes. In a functional context, our results suggest that the passage of shelled eggs constrains the morphology of the pelvic girdle, but we found no evidence of morphological constraint of the locomotor apparatus in viviparous species. Our results are consistent with recent lineage diversification analyses, leading to the conclusion that transitions to viviparity increase both lineage and morphological diversification. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Chemistry and biology by new multiple choice

International Nuclear Information System (INIS)

Seo, Hyeong Seok; Kim, Seong Hwan

2003-02-01

This book is divided into two parts, the first part is about chemistry, which deals with science of material, atom structure and periodic law, chemical combination and power between molecule, state of material and solution, chemical reaction and an organic compound. The second part give description of biology with molecule and cell, energy in cells and chemical synthesis, molecular biology and heredity, function on animal, function on plant and evolution and ecology. This book has explanation of chemistry and biology with new multiple choice.

Towards an alternative evolution model.

Science.gov (United States)

van Waesberghe, H

1982-01-01

Lamarck and Darwin agreed on the inconstancy of species and on the exclusive gradualism of evolution (nature does not jump). Darwinism, revived as neo-Darwinism, was almost generally accepted from about 1930 till 1960. In the sixties the evolutionary importance of selection has been called in question by the neutralists. The traditional conception of the gene is disarranged by recent molecular-biological findings. Owing to the increasing confusion about the concept of genotype, this concept is reconsidered. The idea of the genotype as a cluster of genes is replaced by a cybernetical interpretation of the genotype. As nature does jump, exclusive gradualism is dismissed. Saltatory evolution is a natural phenomenon, provided by a sudden collapse of the thresholds which resist against evolution. The fossil record and the taxonomic system call for a macromutational interpretation. As Lamarck and Darwin overlooked the resistance of evolutionary thresholds, an alternative evolution model is needed, the first to be constructed on a palaeontological and taxonomic basis.

Biological trade and markets.

Science.gov (United States)

Hammerstein, Peter; Noë, Ronald

2016-02-05

Cooperation between organisms can often be understood, like trade between merchants, as a mutually beneficial exchange of services, resources or other 'commodities'. Mutual benefits alone, however, are not sufficient to explain the evolution of trade-based cooperation. First, organisms may reject a particular trade if another partner offers a better deal. Second, while human trade often entails binding contracts, non-human trade requires unwritten 'terms of contract' that 'self-stabilize' trade and prevent cheating even if all traders strive to maximize fitness. Whenever trading partners can be chosen, market-like situations arise in nature that biologists studying cooperation need to account for. The mere possibility of exerting partner choice stabilizes many forms of otherwise cheatable trade, induces competition, facilitates the evolution of specialization and often leads to intricate forms of cooperation. We discuss selected examples to illustrate these general points and review basic conceptual approaches that are important in the theory of biological trade and markets. Comparing these approaches with theory in economics, it turns out that conventional models-often called 'Walrasian' markets-are of limited relevance to biology. In contrast, early approaches to trade and markets, as found in the works of Ricardo and Cournot, contain elements of thought that have inspired useful models in biology. For example, the concept of comparative advantage has biological applications in trade, signalling and ecological competition. We also see convergence between post-Walrasian economics and biological markets. For example, both economists and biologists are studying 'principal-agent' problems with principals offering jobs to agents without being sure that the agents will do a proper job. Finally, we show that mating markets have many peculiarities not shared with conventional economic markets. Ideas from economics are useful for biologists studying cooperation but need

Biological radiolesions and repair

International Nuclear Information System (INIS)

Laskowski, W.

1981-01-01

In 7 chapters, the book answers the following questions: 1) What reactions are induced in biological matter by absorption of radiation energy. 2) In what parts of the cell do the radiation-induced reactions with detectable biological effects occur. 3) In which way are these cell components changed by different qualities of radiation. 4) What are the cell mechanisms by which radiation-induced changes can be repaired. 5) What is the importance of these repair processes for man, his life and evolution. At the end of each chapter, there is a bibliography of relevant publications in this field. (orig./MG) [de

The biology of human sexuality: evolution, ecology and physiology

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PW Bateman

2006-09-01

Full Text Available Many evolutionary biologists argue that human sexual behaviour can be studied in exactly the same way as that of other species. Many sociologists argue that social influences effectively obscure, and are more important than, a reductionist biological approach to human sexual behaviour. Here,we authors attempt to provide a broad introduction to human sexual behaviour from a biological standpoint and to indicate where the ambiguous areas are. We outline the evolutionary selective pressures that are likely to have influenced human behaviour and mate choice in the past and in the present; ecological features that influence such things as degree of parental care and polygamy; and the associated physiology of human sexuality. Then they end with a discussion of �abnormal� sexuality.

Evolution of floral symmetry Peter K Endress, Current Opinion in ...

Indian Academy of Sciences (India)

First page Back Continue Last page Graphics. Evolution of floral symmetry Peter K Endress, Current Opinion in Plant Biology 2001, 4:86–91. Polysymmetric (more than one plane of symmetry) to monosymmetric in angiosperm (flowering plants) evolution; the other way in Antirrhinaceae. Left and right handed helicity. Bees ...

Heme pathway evolution in kinetoplastid protists

Czech Academy of Sciences Publication Activity Database

Cenci, U.; Moog, D.; Curtis, B.A.; Tanifuji, G.; Eme, L.; Lukeš, Julius; Archibald, J.M.

2016-01-01

Roč. 16, MAY 18 (2016), č. článku 109. ISSN 1471-2148 Institutional support: RVO:60077344 Keywords : heme * kinetoplastea * Paramoeba pemaquidensis * Perkinsela * evolution * endosymbiosis * Prokinetoplastina * lateral gene transfer Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.221, year: 2016

The quest for a new modelling framework in mathematical biology. Comment on "On the interplay between mathematics and biology: Hallmarks towards a new systems biology" by N. Bellomo et al.

Science.gov (United States)

Eftimie, Raluca

2015-03-01

One of the main unsolved problems of modern physics is finding a "theory of everything" - a theory that can explain, with the help of mathematics, all physical aspects of the universe. While the laws of physics could explain some aspects of the biology of living systems (e.g., the phenomenological interpretation of movement of cells and animals), there are other aspects specific to biology that cannot be captured by physics models. For example, it is generally accepted that the evolution of a cell-based system is influenced by the activation state of cells (e.g., only activated and functional immune cells can fight diseases); on the other hand, the evolution of an animal-based system can be influenced by the psychological state (e.g., distress) of animals. Therefore, the last 10-20 years have seen also a quest for a "theory of everything"-approach extended to biology, with researchers trying to propose mathematical modelling frameworks that can explain various biological phenomena ranging from ecology to developmental biology and medicine [1,2,6]. The basic idea behind this approach can be found in a few reviews on ecology and cell biology [6,7,9-11], where researchers suggested that due to the parallel between the micro-scale dynamics and the emerging macro-scale phenomena in both cell biology and in ecology, many mathematical methods used for ecological processes could be adapted to cancer modelling [7,9] or to modelling in immunology [11]. However, this approach generally involved the use of different models to describe different biological aspects (e.g., models for cell and animal movement, models for competition between cells or animals, etc.).

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Science.gov (United States)

Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

2014-06-01

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

Genome increase as a clock for the origin and evolution of life

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Sharov Alexei A

2006-06-01

Full Text Available Abstract Background The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. Several positive feedback mechanisms including gene cooperation and duplication with subsequent specialization may result in the exponential growth of biological complexity in macro-evolution. Results I propose a hypothesis that biological complexity increased exponentially during evolution. Regression of the logarithm of functional non-redundant genome size versus time of origin in major groups of organisms showed a 7.8-fold increase per 1 billion years, and hence the increase of complexity can be viewed as a clock of macro-evolution. A strong version of the exponential hypothesis is that the rate of complexity increase in early (pre-prokaryotic evolution of life was at most the same (or even slower than observed in the evolution of prokaryotes and eukaryotes. Conclusion The increase of functional non-redundant genome size in macro-evolution was consistent with the exponential hypothesis. If the strong exponential hypothesis is true, then the origin of life should be dated 10 billion years ago. Thus, the possibility of panspermia as a source of life on earth should be discussed on equal basis with alternative hypotheses of de-novo life origin. Panspermia may be proven if bacteria similar to terrestrial ones are found on other planets or satellites in the solar system. Reviewers This article was reviewed by Eugene V. Koonin, Chris Adami and Arcady Mushegian.

The use of information theory in evolutionary biology.

Science.gov (United States)

Adami, Christoph

2012-05-01

Information is a key concept in evolutionary biology. Information stored in a biological organism's genome is used to generate the organism and to maintain and control it. Information is also that which evolves. When a population adapts to a local environment, information about this environment is fixed in a representative genome. However, when an environment changes, information can be lost. At the same time, information is processed by animal brains to survive in complex environments, and the capacity for information processing also evolves. Here, I review applications of information theory to the evolution of proteins and to the evolution of information processing in simulated agents that adapt to perform a complex task. © 2012 New York Academy of Sciences.

UV SURFACE ENVIRONMENT OF EARTH-LIKE PLANETS ORBITING FGKM STARS THROUGH GEOLOGICAL EVOLUTION

Energy Technology Data Exchange (ETDEWEB)

Rugheimer, S.; Sasselov, D. [Harvard Smithsonian Center for Astrophysics, 60 Garden st., 02138 MA Cambridge (United States); Segura, A. [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, México (Mexico); Kaltenegger, L., E-mail: srugheimer@cfa.harvard.edu [Carl Sagan Institute, Cornell University, Ithaca, NY 14853 (United States)

2015-06-10

The UV environment of a host star affects the photochemistry in the atmosphere, and ultimately the surface UV environment for terrestrial planets and therefore the conditions for the origin and evolution of life. We model the surface UV radiation environment for Earth-sized planets orbiting FGKM stars in the circumstellar Habitable Zone for Earth through its geological evolution. We explore four different types of atmospheres corresponding to an early-Earth atmosphere at 3.9 Gyr ago and three atmospheres covering the rise of oxygen to present-day levels at 2.0 Gyr ago, 0.8 Gyr ago, and modern Earth. In addition to calculating the UV flux on the surface of the planet, we model the biologically effective irradiance, using DNA damage as a proxy for biological damage. We find that a pre-biotic Earth (3.9 Gyr ago) orbiting an F0V star receives 6 times the biologically effective radiation as around the early Sun and 3520 times the modern Earth–Sun levels. A pre-biotic Earth orbiting GJ 581 (M3.5 V) receives 300 times less biologically effective radiation, about 2 times modern Earth–Sun levels. The UV fluxes calculated here provide a grid of model UV environments during the evolution of an Earth-like planet orbiting a range of stars. These models can be used as inputs into photo-biological experiments and for pre-biotic chemistry and early life evolution experiments.

UV SURFACE ENVIRONMENT OF EARTH-LIKE PLANETS ORBITING FGKM STARS THROUGH GEOLOGICAL EVOLUTION

International Nuclear Information System (INIS)

Rugheimer, S.; Sasselov, D.; Segura, A.; Kaltenegger, L.

2015-01-01

The UV environment of a host star affects the photochemistry in the atmosphere, and ultimately the surface UV environment for terrestrial planets and therefore the conditions for the origin and evolution of life. We model the surface UV radiation environment for Earth-sized planets orbiting FGKM stars in the circumstellar Habitable Zone for Earth through its geological evolution. We explore four different types of atmospheres corresponding to an early-Earth atmosphere at 3.9 Gyr ago and three atmospheres covering the rise of oxygen to present-day levels at 2.0 Gyr ago, 0.8 Gyr ago, and modern Earth. In addition to calculating the UV flux on the surface of the planet, we model the biologically effective irradiance, using DNA damage as a proxy for biological damage. We find that a pre-biotic Earth (3.9 Gyr ago) orbiting an F0V star receives 6 times the biologically effective radiation as around the early Sun and 3520 times the modern Earth–Sun levels. A pre-biotic Earth orbiting GJ 581 (M3.5 V) receives 300 times less biologically effective radiation, about 2 times modern Earth–Sun levels. The UV fluxes calculated here provide a grid of model UV environments during the evolution of an Earth-like planet orbiting a range of stars. These models can be used as inputs into photo-biological experiments and for pre-biotic chemistry and early life evolution experiments

Human development I: Twenty Fundamental Problems of Biology, Medicine, and Neuro-Psychology Related to Biological Information

Directory of Open Access Journals (Sweden)

Tyge Dahl Hermansen

2006-01-01

Full Text Available In a new series of papers, we address a number of unsolved problems in biology today. First of all, the unsolved enigma concerning how the differentiation from a single zygote to an adult individual happens has been object for severe research for decades. By uncovering a new holistic biological paradigm that introduces an energetic-informational interpretation of reality as a new way to experience biology, these papers will try to solve the problems connected with the events of biological ontogenesis involving a fractal hierarchy, from a single cell to the function of the human brain. The problems discussed are interpreted within the frames of a universe of roomy fractal structures containing energetic patterns that are able to deliver biological information. We think biological organization is guided by energetic changes on the level of quantum mechanics, interacting with the intention that again guides the energetic conformation of the fractal structures to gain disorders or healthiness. Furthermore, we introduce two new concepts: “metamorphous top down” evolution and “adult human metamorphosis”. The first is a new evolutionary theory involving metamorphosis as a main concept of evolution. The last is tightly linked to the evolutionary principle and explains how human self-recovery is governed. Other subjects of special interest that we shall look deeper into are the immunological self-nonself discrimination, the structure and function of the human brain, the etiology and salutogenesis of mental and somatic diseases, and the structure of the consciousness of a human being. We shall criticize Szentagothai’s model for the modulated structure of the human cerebral cortex and Jerne’s theory of the immunological regulatory anti-idiotypic network.

A system for studying evolution of life-like virtual organisms

Directory of Open Access Journals (Sweden)

Baranova Natalya N

2006-08-01

Full Text Available Abstract Background Fitness landscapes, the dependences of fitness on the genotype, are of critical importance for the evolution of living beings. Unfortunately, fitness landscapes that are relevant to the evolution of complex biological functions are very poorly known. As a result, the existing theory of evolution is mostly based on postulated fitness landscapes, which diminishes its usefulness. Attempts to deduce fitness landscapes from models of actual biological processes led, so far, to only limited success. Results We present a model system for studying the evolution of biological function, which makes it possible to attribute fitness to genotypes in a natural way. The system mimics a very simple cell and takes into account the basic properties of gene regulation and enzyme kinetics. A virtual cell contains only two small molecules, an organic nutrient A and an energy carrier X, and proteins of five types – two transcription factors, two enzymes, and a membrane transporter. The metabolism of the cell consists of importing A from the environment and utilizing it in order to produce X and an unspecified end product. The genome may carry an arbitrary number of genes, each one encoding a protein of one of the five types. Both major mutations that affect whole genes and minor mutations that affect individual characteristics of genes are possible. Fitness is determined by the ability of the cell to maintain homeostasis when its environment changes. The system has been implemented as a computer program, and several numerical experiments have been performed on it. Evolution of the virtual cells usually involves a rapid initial increase of fitness, which eventually slows down, until a fitness plateau is reached. The origin of a wide variety of genetic networks is routinely observed in independent experiments performed under the same conditions. These networks can have different, including very high, levels of complexity and often include large

The metaphysics of evolution.

Science.gov (United States)

Dupré, John

2017-10-06

This paper briefly describes process metaphysics, and argues that it is better suited for describing life than the more standard thing, or substance, metaphysics. It then explores the implications of process metaphysics for conceptualizing evolution. After explaining what it is for an organism to be a process, the paper takes up the Hull/Ghiselin thesis of species as individuals and explores the conditions under which a species or lineage could constitute an individual process. It is argued that only sexual species satisfy these conditions, and that within sexual species the degree of organization varies. This, in turn, has important implications for species' evolvability. One important moral is that evolution will work differently in different biological domains.

Evolution: Don't Debate, Educate.

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Bybee, Rodger W.

2000-01-01

Discusses controversy over the teaching of biological evolution and other scientific ideas such as Big Bang theory. Recommends that teachers avoid debating creationists, help students develop a greater understanding and appreciation for science as a way of explaining the natural world, and emphasize inquiry and the nature of science. (Contains 19…

Stochastic many-body problems in ecology, evolution, neuroscience, and systems biology

Science.gov (United States)

Butler, Thomas C.

Using the tools of many-body theory, I analyze problems in four different areas of biology dominated by strong fluctuations: The evolutionary history of the genetic code, spatiotemporal pattern formation in ecology, spatiotemporal pattern formation in neuroscience and the robustness of a model circadian rhythm circuit in systems biology. In the first two research chapters, I demonstrate that the genetic code is extremely optimal (in the sense that it manages the effects of point mutations or mistranslations efficiently), more than an order of magnitude beyond what was previously thought. I further show that the structure of the genetic code implies that early proteins were probably only loosely defined. Both the nature of early proteins and the extreme optimality of the genetic code are interpreted in light of recent theory [1] as evidence that the evolution of the genetic code was driven by evolutionary dynamics that were dominated by horizontal gene transfer. I then explore the optimality of a proposed precursor to the genetic code. The results show that the precursor code has only limited optimality, which is interpreted as evidence that the precursor emerged prior to translation, or else never existed. In the next part of the dissertation, I introduce a many-body formalism for reaction-diffusion systems described at the mesoscopic scale with master equations. I first apply this formalism to spatially-extended predator-prey ecosystems, resulting in the prediction that many-body correlations and fluctuations drive population cycles in time, called quasicycles. Most of these results were previously known, but were derived using the system size expansion [2, 3]. I next apply the analytical techniques developed in the study of quasi-cycles to a simple model of Turing patterns in a predator-prey ecosystem. This analysis shows that fluctuations drive the formation of a new kind of spatiotemporal pattern formation that I name "quasi-patterns." These quasi

Teaching Molecular Biology with Microcomputers.

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Reiss, Rebecca; Jameson, David

1984-01-01

Describes a series of computer programs that use simulation and gaming techniques to present the basic principles of the central dogma of molecular genetics, mutation, and the genetic code. A history of discoveries in molecular biology is presented and the evolution of these computer assisted instructional programs is described. (MBR)

Form and Function in the Evolution of Grammar.

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Newmeyer, Frederick J

2017-03-01

This article focuses on claims about the origin and evolution of language from the point of view of the formalist-functionalist debate in linguistics. In linguistics, an account of a grammatical phenomenon is considered "formal" if it accords center stage to the structural properties of that phenomenon, and "functional" if it appeals to the language user's communicative needs or to domain-general human capacities. The gulf between formalism and functionalism has been bridged in language evolution research, in that some leading formalists, Ray Jackendoff for one, appeal to functional mechanisms such as natural selection. In Jackendoff's view, the biological evolution of language has proceeded in stages, each stage improving communicative efficiency. This article calls into question that idea, pointing to the fact that well-understood purely historical processes suffice to explain the emergence of many grammatical properties. However, one central aspect of formalist linguistic theorizing-the idea of the autonomy of syntax-poses a challenge to the idea, central to most functionalist approaches, that the nature of grammar is a product of purely historical (as opposed to biological) evolution. The article concludes with a discussion of the origins of the autonomy of syntax, speculating that it may well have arisen over evolutionary (as opposed to historical) time. Copyright © 2016 Cognitive Science Society, Inc.

Biological design in science classrooms

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Scott, Eugenie C.; Matzke, Nicholas J.

2007-01-01

Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront “intelligent design” (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older “creation science” movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education. PMID:17494747

Evolution of parasitism in kinetoplastid flagellates

Czech Academy of Sciences Publication Activity Database

Lukeš, Julius; Skalický, Tomáš; Týč, Jiří; Votýpka, Jan; Yurchenko, Vyacheslav

2014-01-01

Roč. 195, č. 2 (2014), s. 115-122 ISSN 0166-6851 R&D Projects: GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : Evolution * Phylogeny * Vectors * Diversity * Parasitism * Trypanosome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.787, year: 2014

"Reinventing Life": Introductory Biology for a Rapidly Evolving World

Science.gov (United States)

Coker, Jeffrey Scott

2009-01-01

Evolutionary concepts are essential for a scientific understanding of most issues surrounding modern medicine, agriculture, biotechnology, and the environment. If the mantra for biology education in the 20th century was, "Nothing in biology makes sense except in the light of evolution," the mantra for the 21st century must be, "Nothing in biology…

Origin and evolution of life on terrestrial planets.

Science.gov (United States)

Brack, A; Horneck, G; Cockell, C S; Bérces, A; Belisheva, N K; Eiroa, Carlos; Henning, Thomas; Herbst, Tom; Kaltenegger, Lisa; Léger, Alain; Liseau, Réne; Lammer, Helmut; Selsis, Franck; Beichman, Charles; Danchi, William; Fridlund, Malcolm; Lunine, Jonathan; Paresce, Francesco; Penny, Alan; Quirrenbach, Andreas; Röttgering, Huub; Schneider, Jean; Stam, Daphne; Tinetti, Giovanna; White, Glenn J

2010-01-01

The ultimate goal of terrestrial planet-finding missions is not only to discover terrestrial exoplanets inside the habitable zone (HZ) of their host stars but also to address the major question as to whether life may have evolved on a habitable Earth-like exoplanet outside our Solar System. We note that the chemical evolution that finally led to the origin of life on Earth must be studied if we hope to understand the principles of how life might evolve on other terrestrial planets in the Universe. This is not just an anthropocentric point of view: the basic ingredients of terrestrial life, that is, reduced carbon-based molecules and liquid H(2)O, have very specific properties. We discuss the origin of life from the chemical evolution of its precursors to the earliest life-forms and the biological implications of the stellar radiation and energetic particle environments. Likewise, the study of the biological evolution that has generated the various life-forms on Earth provides clues toward the understanding of the interconnectedness of life with its environment.

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.

High School Biology Teachers' Knowledge Structure, Acceptance and Teaching of Evolution.

Science.gov (United States)

Rutledge, Michael L.; Mitchell, Melissa A.

2002-01-01

Determines teachers' conceptions of evolutionary theory using the technique of concept mapping. Discusses the methodology, the survey items, and concept map features. Makes specific recommendations for the teaching of evolution. (Contains 32 references.) (DDR)

Science Ideals and Science Careers in a University Biology Department

Science.gov (United States)

Long, David E.

2014-01-01

In an ethnographic study set within a biology department of a public university in the United States, incongruity between the ideals and practice of science education are investigated. Against the background of religious conservative students' complaints about evolution in the curriculum, biology faculty describe their political intents for…

Integrative assessment of Evolutionary theory acceptance and knowledge levels of Biology undergraduate students from a Brazilian university

Science.gov (United States)

Tavares, Gustavo Medina; Bobrowski, Vera Lucia

2018-03-01

The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students' perceptions towards evolution, and studies can help to reveal those factors. We used a conceptual questionnaire, the Measure of Acceptance of the Theory of Evolution (MATE) instrument, and a Knowledge test to assess (1) the level of acceptance and understanding of 23 undergraduate Biology students nearing the end of their course, (2) other factors that could affect these levels, including course structure, and (3) the most difficult topics regarding evolutionary biology. The results of this study showed that the students, on average, had a 'Very High Acceptance' (89.91) and a 'Very Low Knowledge' (59.42%) of Evolutionary theory, and also indicated a moderate positive correlation between the two (r = 0.66, p = .001). The most difficult topics were related to the definition of evolution and dating techniques. We believe that the present study provides evidence for policymakers to reformulate current school and university curricula in order to improve the teachers' acceptance and understanding of evolution and other biological concepts, consequently, helping students reduce their misconceptions related to evolutionary biology.

Case studies in teaching evolution: The intersection of dilemmas in practice

Science.gov (United States)

Fisher, Rachel

Despite recent science education reform documents citing evolution as a core concept to be taught in grades K-12, research shows problems with how it is currently taught. Evolution is often avoided, teachers minimize its importance within biology, infuse misconceptions, and/or interject non-scientific ideologies into lessons. My research focused on how teachers in two geographically and culturally distinct school districts in the southwestern U.S. negotiate dilemmas during an evolution unit. One school district was rural and had a large population of Mormon students, while the other district was urban, with a large majority Mexican/Mexican-American students. Using a case study approach, I observed three biology teachers during their evolution lessons, interviewed them throughout the unit, co-planned lessons with them, and collected artifacts from this unit, including anonymous student work. I also included data from four genetics lessons for each teacher to determine if the issues that arose during the evolution unit were a result of the general practice of the teacher, or if they were unique to evolution. Findings showed teachers' backgrounds and comfort levels with evolution, in addition to their perceptions of community context, affected how they negotiated pedagogical, conceptual, political, and cultural dilemmas. This study's findings will inform in-service teachers' future practice and professional development tools to aid with their teaching---this may include methods to negotiate some of the political (e.g. state standards) or cultural (e.g. religious resistance) issues inherent to teaching evolution.

Differences in the Concept of Fitness Between Artificial Evolution and Natural Selection

OpenAIRE

Adami, Christoph; Bryson, David M.; Ofria, Charles; Pennock, Robert T.; Lichocki, Pawel; Keller, Laurent; Floreano, Dario

2012-01-01

Evolutionary algorithms were proposed to automatically find solutions to computational problems, much like evolution discovers new adaptive traits. Lately, they have been used to address challenging questions about the evolution of modularity, the genetic code, communication, division of labor and cooperation. Evolutionary algorithms are increasingly popular in biological studies, because they give precise control over the experimental conditions and allow the study of evolution at unpreceden...

Culture shapes the evolution of cognition.

Science.gov (United States)

Thompson, Bill; Kirby, Simon; Smith, Kenny

2016-04-19

A central debate in cognitive science concerns the nativist hypothesis, the proposal that universal features of behavior reflect a biologically determined cognitive substrate: For example, linguistic nativism proposes a domain-specific faculty of language that strongly constrains which languages can be learned. An evolutionary stance appears to provide support for linguistic nativism, because coordinated constraints on variation may facilitate communication and therefore be adaptive. However, language, like many other human behaviors, is underpinned by social learning and cultural transmission alongside biological evolution. We set out two models of these interactions, which show how culture can facilitate rapid biological adaptation yet rule out strong nativization. The amplifying effects of culture can allow weak cognitive biases to have significant population-level consequences, radically increasing the evolvability of weak, defeasible inductive biases; however, the emergence of a strong cultural universal does not imply, nor lead to, nor require, strong innate constraints. From this we must conclude, on evolutionary grounds, that the strong nativist hypothesis for language is false. More generally, because such reciprocal interactions between cultural and biological evolution are not limited to language, nativist explanations for many behaviors should be reconsidered: Evolutionary reasoning shows how we can have cognitively driven behavioral universals and yet extreme plasticity at the level of the individual-if, and only if, we account for the human capacity to transmit knowledge culturally. Wherever culture is involved, weak cognitive biases rather than strong innate constraints should be the default assumption.

Pragmatic turn in biology: From biological molecules to genetic content operators.

Science.gov (United States)

Witzany, Guenther

2014-08-26

Erwin Schrödinger's question "What is life?" received the answer for decades of "physics + chemistry". The concepts of Alain Turing and John von Neumann introduced a third term: "information". This led to the understanding of nucleic acid sequences as a natural code. Manfred Eigen adapted the concept of Hammings "sequence space". Similar to Hilbert space, in which every ontological entity could be defined by an unequivocal point in a mathematical axiomatic system, in the abstract "sequence space" concept each point represents a unique syntactic structure and the value of their separation represents their dissimilarity. In this concept molecular features of the genetic code evolve by means of self-organisation of matter. Biological selection determines the fittest types among varieties of replication errors of quasi-species. The quasi-species concept dominated evolution theory for many decades. In contrast to this, recent empirical data on the evolution of DNA and its forerunners, the RNA-world and viruses indicate cooperative agent-based interactions. Group behaviour of quasi-species consortia constitute de novo and arrange available genetic content for adaptational purposes within real-life contexts that determine epigenetic markings. This review focuses on some fundamental changes in biology, discarding its traditional status as a subdiscipline of physics and chemistry.

Evolution of natural agents: preservation, advance, and emergence of functional information

OpenAIRE

Sharov, Alexei A.

2016-01-01

Biological evolution is often viewed narrowly as a change of morphology or allele frequency in a sequence of generations. Here I pursue an alternative informational concept of evolution, as preservation, advance, and emergence of functional information in natural agents. Functional information is a network of signs (e.g., memory, transient messengers, and external signs) that are used by agents to preserve and regulate their functions. Functional information is preserved in evolution via comp...

A Topical Trajectory on Survival: An Analysis of Link-Making in a Sequence of Lessons on Evolution

Science.gov (United States)

Rocksén, Miranda; Olander, Clas

2017-01-01

This study explores the concept of link-making in relation to communicative strategies applied in the teaching and studying of biological evolution. The analysis focused on video recordings of 11 lessons on biological evolution conducted in a Swedish 9th grade class of students aged 15 years. It reveals how the teacher and students connected…

Correlated evolution of thermal niches and functional physiology in tropical freshwater fishes.

Science.gov (United States)

Culumber, Zachary W; Tobler, Michael

2018-05-01

The role of ecology in phenotypic and species diversification is widely documented. Nonetheless, numerous nonadaptive processes can shape realized niches and phenotypic variation in natural populations, complicating inferences about adaptive evolution at macroevolutionary scales. We tested for evolved differences in thermal tolerances and their association with the realized thermal niche (including metrics describing diurnal and seasonal patterns of temperature extremes and variability) across a genus of tropical freshwater fishes reared in a standardized environment. There was limited evolution along the thermal niche axis associated with variation in maximum temperature and in upper thermal limits. In contrast, there was considerable diversification along the first major axis of the thermal niche associated with minimum temperatures and in lower thermal limits. Across our adaptive landscape analyses, 70% of species exhibited evidence of divergence in thermal niches. Most importantly, the first two major axes of thermal niche variation were significantly correlated with variation in lower thermal limits. Our results indicate adaptation to divergent thermal niches and adaptive evolution of related functional traits, and highlight the importance of divergence in lower thermal limits for the evolution of tropical biodiversity. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Darwinism Extended - A survey of how the idea of cultural evolution evolved

NARCIS (Netherlands)

Buskes, C.J.J.

2013-01-01

In the past 150 years there have been many attempts to draw parallels between cultural and biological evolution. Most of these attempts were flawed due to lack of knowledge and false ideas about evolution. In recent decades these shortcomings have been cleared away, thus triggering a renewed

Darwinism Extended - A Survey of How the Idea of Cultural Evolution Evolved

NARCIS (Netherlands)

Buskes, C.J.J.

2013-01-01

In the past 150 years there have been many attempts to draw parallels between cultural and biological evolution. Most of these attempts were flawed due to lack of knowledge and false ideas about evolution. In recent decades these shortcomings have been cleared away, thus triggering a renewed

Patterns and Processes of Vertebrate Evolution

Science.gov (United States)

Carroll, Robert Lynn

1997-04-01

This new text provides an integrated view of the forces that influence the patterns and rates of vertebrate evolution from the level of living populations and species to those that resulted in the origin of the major vertebrate groups. The evolutionary roles of behavior, development, continental drift, and mass extinctions are compared with the importance of variation and natural selection that were emphasized by Darwin. It is extensively illustrated, showing major transitions between fish and amphibians, dinosaurs and birds, and land mammals to whales. No book since Simpson's Major Features of Evolution has attempted such a broad study of the patterns and forces of evolutionary change. Undergraduate students taking a general or advanced course on evolution, and graduate students and professionals in evolutionary biology and paleontology will find the book of great interest.

Structural biological composites: An overview

Science.gov (United States)

Meyers, Marc A.; Lin, Albert Y. M.; Seki, Yasuaki; Chen, Po-Yu; Kad, Bimal K.; Bodde, Sara

2006-07-01

Biological materials are complex composites that are hierarchically structured and multifunctional. Their mechanical properties are often outstanding, considering the weak constituents from which they are assembled. They are for the most part composed of brittle (often, mineral) and ductile (organic) components. These complex structures, which have risen from millions of years of evolution, are inspiring materials scientists in the design of novel materials. This paper discusses the overall design principles in biological structural composites and illustrates them for five examples; sea spicules, the abalone shell, the conch shell, the toucan and hornbill beaks, and the sheep crab exoskeleton.

The Bible and evolution: Opinions amongst southern African clergy and theologians from the Reformed church tradition

Directory of Open Access Journals (Sweden)

Peet J. van Dyk

2013-02-01

Full Text Available The main objectives of the present study were to determine the opinions of southern African clergy and theologians (from the Reformed church tradition about evolution and faith and to assess their degree of knowledge regarding the biological theory of evolution. A total of 1720 structured electronic questionnaires were sent out via email to all clergy belonging to the �Nederduitse Gereformeerde� and �Hervormde� churches, of which 89 were received back. The SPSS 20 statistical program was used to conduct descriptive and inferential statistical analyses of these data. Most participants were positive about the theory of biological evolution, but expressed the belief that evolution should be seen as a process guided by God. However, most participants failed to appreciate the fact that this view was contrary to the non-teleological nature of the biological theory of evolution and failed to distinguish between what should be accepted in faith and what can be demonstrated or �proved� (e.g. as is common in intelligent design circles. Many participants were not clear about the finer aspects of evolutionary theory and therefore often believed common misconceptions about it. In conclusion, one could say that participants were positive about evolution and, at least nominally, agreed with non-fundamentalist views of the Bible.

Distinctively human motivation and another view on human evolution

OpenAIRE

Prudkov, Pavel N.

2006-01-01

Human evolution is a multidisciplinary problem, one of its aspects is the origin and development of distinctively human psychological features. Cognitive properties (language, symbolic thinking) are considered as such features and numerous authors hypothesize its evolution. We suggest that the most important human characteristic is connected with motivation rather than cognition; this is the ability to construct and maintain long-term goal-directed processes having no biological basis. Once...

Early Microbial Evolution: The Age of Anaerobes.

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Martin, William F; Sousa, Filipa L

2015-12-18

In this article, the term "early microbial evolution" refers to the phase of biological history from the emergence of life to the diversification of the first microbial lineages. In the modern era (since we knew about archaea), three debates have emerged on the subject that deserve discussion: (1) thermophilic origins versus mesophilic origins, (2) autotrophic origins versus heterotrophic origins, and (3) how do eukaryotes figure into early evolution. Here, we revisit those debates from the standpoint of newer data. We also consider the perhaps more pressing issue that molecular phylogenies need to recover anaerobic lineages at the base of prokaryotic trees, because O2 is a product of biological evolution; hence, the first microbes had to be anaerobes. If molecular phylogenies do not recover anaerobes basal, something is wrong. Among the anaerobes, hydrogen-dependent autotrophs--acetogens and methanogens--look like good candidates for the ancestral state of physiology in the bacteria and archaea, respectively. New trees tend to indicate that eukaryote cytosolic ribosomes branch within their archaeal homologs, not as sisters to them and, furthermore tend to root archaea within the methanogens. These are major changes in the tree of life, and open up new avenues of thought. Geochemical methane synthesis occurs as a spontaneous, abiotic exergonic reaction at hydrothermal vents. The overall similarity between that reaction and biological methanogenesis fits well with the concept of a methanogenic root for archaea and an autotrophic origin of microbial physiology. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

50 Years of JBE: The Evolution of Biology as a School Subject

Science.gov (United States)

Jenkins, Edgar

2016-01-01

When the "Journal of Biological Education" was first published in 1967, biology was still very much the Cinderella of the three school sciences in many countries. Most selective secondary school biology courses readily betrayed their origins as an unconvincing coalition of botany and zoology. In the non-selective secondary modern…

Computational Modeling of Biological Systems From Molecules to Pathways

CERN Document Server

2012-01-01

Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

Belief versus acceptance: why do people not believe in evolution?

Science.gov (United States)

Williams, James D

2009-11-01

Despite being an established and accepted scientific theory for 150 years, repeated public polls show that evolution is not believed by large numbers of people. This essay examines why people do not accept evolution and argues that its poor representation in some science textbooks allows misconceptions, established and reinforced in early childhood, to take hold. There is also a lack of up-to-date examples of evidence for evolution in school textbooks. Poor understanding by science graduates and teachers of the nature of science and incorrect definitions by them of key terminology, serve only to undermine efforts to improve public understanding of evolution. This paper has several recommendations, including the introduction of evolution to primary age children and a call to bring evolution back as the central tenet of biology.

Big cat, small cat: reconstructing body size evolution in living and extinct Felidae.

Science.gov (United States)

Cuff, A R; Randau, M; Head, J; Hutchinson, J R; Pierce, S E; Goswami, A

2015-08-01

The evolution of body mass is a fundamental topic in evolutionary biology, because it is closely linked to manifold life history and ecological traits and is readily estimable for many extinct taxa. In this study, we examine patterns of body mass evolution in Felidae (Placentalia, Carnivora) to assess the effects of phylogeny, mode of evolution, and the relationship between body mass and prey choice in this charismatic mammalian clade. Our data set includes 39 extant and 26 extinct taxa, with published body mass data supplemented by estimates based on condylobasal length. These data were run through 'SURFACE' and 'bayou' to test for patterns of body mass evolution and convergence between taxa. Body masses of felids are significantly different among prey choice groupings (small, mixed and large). We find that body mass evolution in cats is strongly influenced by phylogeny, but different patterns emerged depending on inclusion of extinct taxa and assumptions about branch lengths. A single Ornstein-Uhlenbeck optimum best explains the distribution of body masses when first-occurrence data were used for the fossil taxa. However, when mean occurrence dates or last known occurrence dates were used, two selective optima for felid body mass were recovered in most analyses: a small optimum around 5 kg and a large one around 100 kg. Across living and extinct cats, we infer repeated evolutionary convergences towards both of these optima, but, likely due to biased extinction of large taxa, our results shift to supporting a Brownian motion model when only extant taxa are included in analyses. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Biologic relativity: Who is the observer and what is observed?

Science.gov (United States)

Torday, John S; Miller, William B

2016-05-01

When quantum physics and biological phenomena are analogously explored, it emerges that biologic causation must also be understood independently of its overt appearance. This is similar to the manner in which Bohm characterized the explicate versus the implicate order as overlapping frames of ambiguity. Placed in this context, the variables affecting epigenetic inheritance can be properly assessed as a key mechanistic principle of evolution that significantly alters our understanding of homeostasis, pleiotropy, and heterochrony, and the purposes of sexual reproduction. Each of these become differing manifestations of a new biological relativity in which biologic space-time becomes its own frame. In such relativistic cellular contexts, it is proper to question exactly who has observer status, and who and what are being observed. Consideration within this frame reduces biology to cellular information sharing through cell-cell communication to resolve ambiguities at every scope and scale. In consequence, it becomes implicit that eukaryotic evolution derives from the unicellular state, remaining consistently adherent to it in a continuous evolutionary arc based upon elemental, non-stochastic physiologic first principles. Furthermore, the entire cell including its cytoskeletal apparatus and membranes that participate in the resolution of biological uncertainties must be considered as having equivalent primacy with genomes in evolutionary terms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Boosting Students' Attitudes & Knowledge about Evolution Sets Them up for College Success

Science.gov (United States)

Carter, B. Elijah; Infanti, Lynn M.; Wiles, Jason R.

2015-01-01

Students who enter college with a solid grounding in, and positive attitudes toward, evolutionary science are better prepared for and achieve at higher levels in university-level biology courses. We found highly significant, positive relationships between student knowledge of evolution and attitudes toward evolution, as well as between…

Evolution of critical day length for diapause induction enables range expansion of Diorhabda carinulata, a biological control agent against tamarisk (Tamarix spp.).

Science.gov (United States)

Bean, Dan W; Dalin, Peter; Dudley, Tom L

2012-07-01

In classical weed biological control, small collections of arthropods are made from one or a few sites in the native range of the target plant and are introduced to suppress the plant where it has become invasive, often across a wide geographic range. Ecological mismatches in the new range are likely, and success using the biocontrol agent may depend on postrelease evolution of beneficial life history traits. In this study, we measure the evolution of critical day length for diapause induction (day length at which 50% of the population enters dormancy), in a beetle (Diorhabda carinulata) introduced into North America from China to control an exotic shrub, Tamarix spp. Beetle populations were sampled from four sites in North America 7 years after introduction, and critical day length was shown to have declined, forming a cline over a latitudinal gradient At one field site, decreased critical day length was correlated with 16 additional days of reproductive activity, resulting in a closer match between beetle life history and the phenology of Tamarix. These findings indicate an enhanced efficacy and an increasingly wider range for D. carinulata in Tamarix control.

Programmed evolution for optimization of orthogonal metabolic output in bacteria.

Directory of Open Access Journals (Sweden)

Todd T Eckdahl

Full Text Available Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields - evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem. As analog computers, bacteria process known and unknown inputs and direct the output of their biochemical hardware. Second, the system employs the evolution of bacteria toward an optimal metabolic solution by imposing fitness defined by metabolic output. The current study is a proof-of-concept for Programmed Evolution applied to the optimization of a metabolic pathway for the conversion of caffeine to theophylline in E. coli. Introduced genotype variations included strength of the promoter and ribosome binding site, plasmid copy number, and chaperone proteins. We constructed 24 strains using all combinations of the genetic variables. We used a theophylline riboswitch and a tetracycline resistance gene to link theophylline production to fitness. After subjecting the mixed population to selection, we measured a change in the distribution of genotypes in the population and an increased conversion of caffeine to theophylline among the most fit strains, demonstrating Programmed Evolution. Programmed Evolution inverts the standard paradigm in metabolic engineering by harnessing evolution instead of fighting it. Our modular system enables researchers to program bacteria and use evolution to determine the combination of genetic control elements that optimizes catabolic or anabolic output and to maintain it in a population of cells. Programmed Evolution could be used for applications in

Programmed Evolution for Optimization of Orthogonal Metabolic Output in Bacteria

Science.gov (United States)

Eckdahl, Todd T.; Campbell, A. Malcolm; Heyer, Laurie J.; Poet, Jeffrey L.; Blauch, David N.; Snyder, Nicole L.; Atchley, Dustin T.; Baker, Erich J.; Brown, Micah; Brunner, Elizabeth C.; Callen, Sean A.; Campbell, Jesse S.; Carr, Caleb J.; Carr, David R.; Chadinha, Spencer A.; Chester, Grace I.; Chester, Josh; Clarkson, Ben R.; Cochran, Kelly E.; Doherty, Shannon E.; Doyle, Catherine; Dwyer, Sarah; Edlin, Linnea M.; Evans, Rebecca A.; Fluharty, Taylor; Frederick, Janna; Galeota-Sprung, Jonah; Gammon, Betsy L.; Grieshaber, Brandon; Gronniger, Jessica; Gutteridge, Katelyn; Henningsen, Joel; Isom, Bradley; Itell, Hannah L.; Keffeler, Erica C.; Lantz, Andrew J.; Lim, Jonathan N.; McGuire, Erin P.; Moore, Alexander K.; Morton, Jerrad; Nakano, Meredith; Pearson, Sara A.; Perkins, Virginia; Parrish, Phoebe; Pierson, Claire E.; Polpityaarachchige, Sachith; Quaney, Michael J.; Slattery, Abagael; Smith, Kathryn E.; Spell, Jackson; Spencer, Morgan; Taye, Telavive; Trueblood, Kamay; Vrana, Caroline J.; Whitesides, E. Tucker

2015-01-01

Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields – evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem. As analog computers, bacteria process known and unknown inputs and direct the output of their biochemical hardware. Second, the system employs the evolution of bacteria toward an optimal metabolic solution by imposing fitness defined by metabolic output. The current study is a proof-of-concept for Programmed Evolution applied to the optimization of a metabolic pathway for the conversion of caffeine to theophylline in E. coli. Introduced genotype variations included strength of the promoter and ribosome binding site, plasmid copy number, and chaperone proteins. We constructed 24 strains using all combinations of the genetic variables. We used a theophylline riboswitch and a tetracycline resistance gene to link theophylline production to fitness. After subjecting the mixed population to selection, we measured a change in the distribution of genotypes in the population and an increased conversion of caffeine to theophylline among the most fit strains, demonstrating Programmed Evolution. Programmed Evolution inverts the standard paradigm in metabolic engineering by harnessing evolution instead of fighting it. Our modular system enables researchers to program bacteria and use evolution to determine the combination of genetic control elements that optimizes catabolic or anabolic output and to maintain it in a population of cells. Programmed Evolution could be used for applications in energy

The biological evolution of guilt, shame and anxiety: A new theory of negative legacy emotions.

Science.gov (United States)

Breggin, Peter R

2015-07-01

Human beings are the most social and the most violent creatures on Earth. The combination of cooperation and aggression enabled us to dominate our ecosystem. However, the existence of violent impulses would have made it difficult or impossible for humans to live in close-knit families and clans without destroying each other. Nature's answer was the development of guilt, shame and anxiety-internal emotional inhibitions or restraints specifically against aggressive self-assertion within the family and other close relationships. The theory of negative legacy emotions proposes the first unitary concept for the biopsychosocial function of guilt, shame and anxiety, and seeks their origin in biological evolution and natural selection. Natural selection favored individuals with built-in emotional restraints that reduced conflicts within their family and tribal unit, optimizing their capacity to survive and reproduce within the protection of their small, intimate societies, while maintaining their capacity for violence against outsiders. Unfortunately, these negative legacy emotions are rudimentary and often ineffective in their psychosocial and developmental function. As a result, they produce many unintended untoward effects, including the frequent breakdown of restraints in the family and the uninhibited unleashing of violence against outsiders. Copyright © 2015 Elsevier Ltd. All rights reserved.

Teaching and Learning Evolution: Testing the Principles of a Constructivist Approach through Action Research

Science.gov (United States)

Oliver, Mary

2011-01-01

A tenth grade class in an international school studied evolution for four weeks as part of the study of Biology. A diagnostic test was used to determine the main misconceptions students have as they come to the study of evolution. This was followed by a series of explorations of different conceptual models to account for evolution, structured…

Experimental evolution of protozoan traits in response to interspecific competition.

Science.gov (United States)

terHorst, C P

2011-01-01

Decades of experiments have demonstrated the ecological effect of competition, but experimental evidence for competitive effects on trait evolution is rare. I measured the evolution of six protozoan traits in response to competitors from the inquiline community of pitcher plants. Replicate populations of Colpoda, a ciliated protozoan, were allowed to evolve in response to intra- and interspecific competition for 20 days (approximately 100 generations), before traits were measured in two common garden environments. Populations that evolved with interspecific competition had smaller cell sizes, produced fewer cysts and had higher population growth rates relative to populations grown in monoculture. The presence of interspecific competitors led to differential lineage sorting, most likely by increasing the strength of selection. These results are the first to demonstrate protozoan evolution in response to competition and may have implications for species coexistence in this system. © 2010 The Author. Journal of Evolutionary Biology © 2010 European Society For Evolutionary Biology.

Cultural evolution as a nonstationary stochastic process

DEFF Research Database (Denmark)

Nicholson, Arwen; Sibani, Paolo

2016-01-01

We present an individual based model of cultural evolution, where interacting agents are coded by binary strings standing for strategies for action, blueprints for products or attitudes and beliefs. The model is patterned on an established model of biological evolution, the Tangled Nature Model...... (TNM), where a “tangle” of interactions between agents determines their reproductive success. In addition, our agents also have the ability to copy part of each other's strategy, a feature inspired by the Axelrod model of cultural diversity. Unlike the latter, but similarly to the TNM, the model...

Impact of constitutional copy number variants on biological pathway evolution.

Science.gov (United States)

Poptsova, Maria; Banerjee, Samprit; Gokcumen, Omer; Rubin, Mark A; Demichelis, Francesca

2013-01-23

Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations. To trace potential evolutionary changes of well-described biological pathways, we jointly queried the genomes and the transcriptomes of a collection of individuals with Caucasian, Asian or Yoruban descent combining high-resolution array and sequencing data. We implemented an enrichment analysis of pathways accounting for CNVs and genes sizes and detected significant enrichment not only in signal transduction and extracellular biological processes, but also in metabolism pathways. Upon the estimation of CNV population differentiation (CNVs with different polymorphism frequencies across populations), we evaluated that 22% of the pathways contain at least one gene that is proximal to a CNV (CNV-gene pair) that shows significant population differentiation. The majority of these CNV-gene pairs belong to signal transduction pathways and 6% of the CNV-gene pairs show statistical association between the copy number states and the transcript levels. The analysis suggested possible examples of positive selection within individual populations including NF-kB, MAPK signaling pathways, and Alu/L1 retrotransposition factors. Altogether, our results suggest that constitutional CNVs may modulate subtle pathway changes through specific pathway enzymes, which may become fixed in some populations.

Morphology and behaviour: functional links in development and evolution

Science.gov (United States)

Bertossa, Rinaldo C.

2011-01-01

Development and evolution of animal behaviour and morphology are frequently addressed independently, as reflected in the dichotomy of disciplines dedicated to their study distinguishing object of study (morphology versus behaviour) and perspective (ultimate versus proximate). Although traits are known to develop and evolve semi-independently, they are matched together in development and evolution to produce a unique functional phenotype. Here I highlight similarities shared by both traits, such as the decisive role played by the environment for their ontogeny. Considering the widespread developmental and functional entanglement between both traits, many cases of adaptive evolution are better understood when proximate and ultimate explanations are integrated. A field integrating these perspectives is evolutionary developmental biology (evo-devo), which studies the developmental basis of phenotypic diversity. Ultimate aspects in evo-devo studies—which have mostly focused on morphological traits—could become more apparent when behaviour, ‘the integrator of form and function’, is integrated into the same framework of analysis. Integrating a trait such as behaviour at a different level in the biological hierarchy will help to better understand not only how behavioural diversity is produced, but also how levels are connected to produce functional phenotypes and how these evolve. A possible framework to accommodate and compare form and function at different levels of the biological hierarchy is outlined. At the end, some methodological issues are discussed. PMID:21690124

A first attempt to bring computational biology into advanced high school biology classrooms.

Science.gov (United States)

Gallagher, Suzanne Renick; Coon, William; Donley, Kristin; Scott, Abby; Goldberg, Debra S

2011-10-01

Computer science has become ubiquitous in many areas of biological research, yet most high school and even college students are unaware of this. As a result, many college biology majors graduate without adequate computational skills for contemporary fields of biology. The absence of a computational element in secondary school biology classrooms is of growing concern to the computational biology community and biology teachers who would like to acquaint their students with updated approaches in the discipline. We present a first attempt to correct this absence by introducing a computational biology element to teach genetic evolution into advanced biology classes in two local high schools. Our primary goal was to show students how computation is used in biology and why a basic understanding of computation is necessary for research in many fields of biology. This curriculum is intended to be taught by a computational biologist who has worked with a high school advanced biology teacher to adapt the unit for his/her classroom, but a motivated high school teacher comfortable with mathematics and computing may be able to teach this alone. In this paper, we present our curriculum, which takes into consideration the constraints of the required curriculum, and discuss our experiences teaching it. We describe the successes and challenges we encountered while bringing this unit to high school students, discuss how we addressed these challenges, and make suggestions for future versions of this curriculum.We believe that our curriculum can be a valuable seed for further development of computational activities aimed at high school biology students. Further, our experiences may be of value to others teaching computational biology at this level. Our curriculum can be obtained at http://ecsite.cs.colorado.edu/?page_id=149#biology or by contacting the authors.

The Experimental Detection of an Emotional Response to the Idea of Evolution

Science.gov (United States)

Bland, Mark W.; Morrison, Elizabeth

2015-01-01

Evolution is widely regarded as biology's unifying theme, yet rates of rejection of evolutionary science remain high. Anecdotal evidence suggests that cognitive dissonance leading to an emotional response is a barrier to learning about and accepting evolution. We explored the hypothesis that students whose worldviews may be inconsistent with the…

Synthetic biology: a challenge to mechanical explanations in biology?

Science.gov (United States)

Morange, Michel

2012-01-01

In their plans to modify organisms, synthetic biologists have contrasted engineering and tinkering. By drawing this contrast between their endeavors and what has happened during the evolution of organisms by natural selection, they underline the novelty of their projects and justify their ambitions. Synthetic biologists are at odds with a long tradition that has considered organisms as "perfect machines." This tradition had already been questioned by Stephen Jay Gould in the 1970s and received a major blow with the comparison made by François Jacob between organisms and the results of "bricolage" (tinkering). These contrasts between engineering and tinkering, synthetic biology and evolution, have no raison d'être. Machines built by humans are increasingly inspired by observations made on organisms. This is not a simple reversal of the previous trend-the mechanical conception of organisms-in which the characteristics of the latter were explained by comparison with human-built machines. Relations between organisms and machines have always been complex and ambiguous.

New Gene Evolution: Little Did We Know

Science.gov (United States)

Long, Manyuan; VanKuren, Nicholas W.; Chen, Sidi; Vibranovski, Maria D.

2014-01-01

Genes are perpetually added to and deleted from genomes during evolution. Thus, it is important to understand how new genes are formed and evolve as critical components of the genetic systems determining the biological diversity of life. Two decades of effort have shed light on the process of new gene origination, and have contributed to an emerging comprehensive picture of how new genes are added to genomes, ranging from the mechanisms that generate new gene structures to the presence of new genes in different organisms to the rates and patterns of new gene origination and the roles of new genes in phenotypic evolution. We review each of these aspects of new gene evolution, summarizing the main evidence for the origination and importance of new genes in evolution. We highlight findings showing that new genes rapidly change existing genetic systems that govern various molecular, cellular and phenotypic functions. PMID:24050177

A view of evolution by a Christian biologist

OpenAIRE

Elizabeth Jordaan; G. C. Loots

1984-01-01

This paper, which originated as an address to a gathering of Dutch Reformed Ministers in Potchefstroom, deals with the response of a Christian to concepts of evolution. The paper looks at the concept of “the beginning”, the origin of life , genetics, mutation and natural selection, the origin of diversity or speciation, man as a biological species, the missing link (in which attention is given to various theories), and finally theories of human evolution. These include the neoteny theory, the...

Reflexions sur L'Evolution de L'Enseignement de la Biologie en Afrique.

Science.gov (United States)

Sasson, A.

1980-01-01

Reviews the main stages of the evolution of biology teaching in Africa. Discusses the UNESCO pilot project, the teaching aids produced for English- and French-speaking countries of Africa, and the "Teacher's Guide on the Biology of Human Populations" and projects needs for further assistance. (CS)

Genome Evolution in the Genus Sorghum (Poaceae)

OpenAIRE

PRICE, H. JAMES; DILLON, SALLY L.; HODNETT, GEORGE; ROONEY, WILLIAM L.; ROSS, LARRY; JOHNSTON, J. SPENCER

2005-01-01

• Background and Aims The roles of variation in DNA content in plant evolution and adaptation remain a major biological enigma. Chromosome number and 2C DNA content were determined for 21 of the 25 species of the genus Sorghum and analysed from a phylogenetic perspective.

The Informatics (R) Evolution in Biology: The Case of Genomics

International Nuclear Information System (INIS)

Michan Aguirre, Layla; Alvarez, Eduardo; Montoya Perez, Laura Elizabeth

2011-01-01

Biology has been revolutionized by the introduction of new disciplines, such is the case of genomics that introduced in the 80s has turned unlikely to modern science, the discipline refers to the study not only of genes but their roles, relations among themselves and with the environment. Arises, with the consolidation of the human genome project and introduces us to a period of transition in which specific genetic knowledge becomes critical. Differs from other approaches in the type of information provided, the prospects for technical and intellectual improvements in the collection and use of data from the whole genome, (Murray, 2000). This work aims to investigate the recent biology, in particular, to show the history of genomics, through literature search and bibliometric analysis.

Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles.

Science.gov (United States)

Griffith, Oliver W; Blackburn, Daniel G; Brandley, Matthew C; Van Dyke, James U; Whittington, Camilla M; Thompson, Michael B

2015-09-01

To understand evolutionary transformations it is necessary to identify the character states of extinct ancestors. Ancestral character state reconstruction is inherently difficult because it requires an accurate phylogeny, character state data, and a statistical model of transition rates and is fundamentally constrained by missing data such as extinct taxa. We argue that model based ancestral character state reconstruction should be used to generate hypotheses but should not be considered an analytical endpoint. Using the evolution of viviparity and reversals to oviparity in squamates as a case study, we show how anatomical, physiological, and ecological data can be used to evaluate hypotheses about evolutionary transitions. The evolution of squamate viviparity requires changes to the timing of reproductive events and the successive loss of features responsible for building an eggshell. A reversal to oviparity requires that those lost traits re-evolve. We argue that the re-evolution of oviparity is inherently more difficult than the reverse. We outline how the inviability of intermediate phenotypes might present physiological barriers to reversals from viviparity to oviparity. Finally, we show that ecological data supports an oviparous ancestral state for squamates and multiple transitions to viviparity. In summary, we conclude that the first squamates were oviparous, that frequent transitions to viviparity have occurred, and that reversals to oviparity in viviparous lineages either have not occurred or are exceedingly rare. As this evidence supports conclusions that differ from previous ancestral state reconstructions, our paper highlights the importance of incorporating biological evidence to evaluate model-generated hypotheses. © 2015 Wiley Periodicals, Inc.

Sociodemographic aspect of society evolution

Directory of Open Access Journals (Sweden)

Raisa Viktorovna Nifanova

2013-12-01

Full Text Available In the article, the authors have classified theories of human aging, having emphasized the theory of «cellular death» on the basis of generalization of an extensive theoretical and empirical material of domestic and foreign researchers. The main theories of specific duration of human life, the biological and social and economic criteria and health factors of causes of death and longevity are briefly presented. The achievements of the genetics of a human body aging are discussed. In the article, the author stopped on a problem of the human genofond stability and obvious delay of its biological evolution in the historical development. Despite a deep socialization of humanity, people remains in captivity of biological life, obey all the laws of the biological organization including those that keep it and provide it to following generations. The biological factors influencing reproduction of the population, unlike social factors, are more stable in time. Various socioeconomic and physiographic conditions interacted for a long time with biological factors, determine a certain life expectancy. In the modern conditions for forward development of society, the special value gets a question of the human potential realization — gold fund of of manufacture, science, culture. With a «century of biology» which starts with the development of molecular biology, genetics, biological cybernetics, the science has new opportunities for effective adaptation of human to new conditions

Evolution of regulatory networks towards adaptability and stability in a changing environment

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Lee, Deok-Sun

2014-11-01

Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing environment and stability against dynamical perturbations. We find that sparse and heterogeneous connectivity patterns emerge, which show qualitative agreement with real transcriptional regulatory networks and metabolic networks. The characteristic scaling behavior of stability reflects the balance between robustness and flexibility. The scaling of fluctuation in the perturbation spread shows a dynamic crossover, which is analyzed by investigating separately the stochasticity of internal dynamics and the network structure differences depending on the evolution pathways. Our study delineates how the ambivalent pressure of evolution shapes biological networks, which can be helpful for studying general complex systems interacting with environments.

Phylogenomic Insights into Animal Evolution.

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Telford, Maximilian J; Budd, Graham E; Philippe, Hervé

2015-10-05

Animals make up only a small fraction of the eukaryotic tree of life, yet, from our vantage point as members of the animal kingdom, the evolution of the bewildering diversity of animal forms is endlessly fascinating. In the century following the publication of Darwin's Origin of Species, hypotheses regarding the evolution of the major branches of the animal kingdom - their relationships to each other and the evolution of their body plans - was based on a consideration of the morphological and developmental characteristics of the different animal groups. This morphology-based approach had many successes but important aspects of the evolutionary tree remained disputed. In the past three decades, molecular data, most obviously primary sequences of DNA and proteins, have provided an estimate of animal phylogeny largely independent of the morphological evolution we would ultimately like to understand. The molecular tree that has evolved over the past three decades has drastically altered our view of animal phylogeny and many aspects of the tree are no longer contentious. The focus of molecular studies on relationships between animal groups means, however, that the discipline has become somewhat divorced from the underlying biology and from the morphological characteristics whose evolution we aim to understand. Here, we consider what we currently know of animal phylogeny; what aspects we are still uncertain about and what our improved understanding of animal phylogeny can tell us about the evolution of the great diversity of animal life. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evolution viewed from physics, physiology and medicine.

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Noble, Denis

2017-10-06

Stochasticity is harnessed by organisms to generate functionality. Randomness does not, therefore, necessarily imply lack of function or 'blind chance' at higher levels. In this respect, biology must resemble physics in generating order from disorder. This fact is contrary to Schrödinger's idea of biology generating phenotypic order from molecular- level order, which inspired the central dogma of molecular biology. The order originates at higher levels, which constrain the components at lower levels. We now know that this includes the genome, which is controlled by patterns of transcription factors and various epigenetic and reorganization mechanisms. These processes can occur in response to environmental stress, so that the genome becomes 'a highly sensitive organ of the cell' (McClintock). Organisms have evolved to be able to cope with many variations at the molecular level. Organisms also make use of physical processes in evolution and development when it is possible to arrive at functional development without the necessity to store all information in DNA sequences. This view of development and evolution differs radically from that of neo-Darwinism with its emphasis on blind chance as the origin of variation. Blind chance is necessary, but the origin of functional variation is not at the molecular level. These observations derive from and reinforce the principle of biological relativity, which holds that there is no privileged level of causation. They also have important implications for medical science.

The evolution of lethal intergroup violence

OpenAIRE

Kelly, Raymond C.

2005-01-01

Recent findings and analyses in evolutionary biology, archaeology, and ethnology provide a favorable conjuncture for examining the evolution of lethal intergroup violence among hominids during the 2.9-million-year Paleolithic time span. Here, I seek to identify and investigate the main turning points in this evolutionary trajectory and to delineate the periodization that follows from this inquiry.

The evolution of lethal intergroup violence.

Science.gov (United States)

Kelly, Raymond C

2005-10-25

Recent findings and analyses in evolutionary biology, archaeology, and ethnology provide a favorable conjuncture for examining the evolution of lethal intergroup violence among hominids during the 2.9-million-year Paleolithic time span. Here, I seek to identify and investigate the main turning points in this evolutionary trajectory and to delineate the periodization that follows from this inquiry.

Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes

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Christie, Joshua R.; Beekman, Madeleine

2017-01-01

Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes—specifically their organization into host cells and their uniparental (maternal) inheritance—enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller’s ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes—despite their asexual mode of reproduction—can readily undergo adaptive evolution. PMID:28025277

Two bridges between biology and learning

Directory of Open Access Journals (Sweden)

Jorun Nyléhn

2016-04-01

Full Text Available Human biology, in terms of organization of our brains and our evolutionary past, constrains and enables learning. Two examples where neurobiology and evolution influences learning are given and discussed in relation to education: mirror neurons and adaptive memory. Mirror neurons serves imitation and understanding of other peoples intentions. Adaptive memory implies that our memory is an adaptation influenced by our evolutionary past, enabling us to solve problems in the present and in the future. Additionally, the aim is to contribute to bridges between natural and social sciences in an attempt to achieve an improved understanding of learning. The relevance of perspectives on learning founded in biology are discussed, and the article argues for including biological perspectives in discussions of education and learning processes.

Curious parallels and curious connections--phylogenetic thinking in biology and historical linguistics.

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Atkinson, Quentin D; Gray, Russell D

2005-08-01

In The Descent of Man (1871), Darwin observed "curious parallels" between the processes of biological and linguistic evolution. These parallels mean that evolutionary biologists and historical linguists seek answers to similar questions and face similar problems. As a result, the theory and methodology of the two disciplines have evolved in remarkably similar ways. In addition to Darwin's curious parallels of process, there are a number of equally curious parallels and connections between the development of methods in biology and historical linguistics. Here we briefly review the parallels between biological and linguistic evolution and contrast the historical development of phylogenetic methods in the two disciplines. We then look at a number of recent studies that have applied phylogenetic methods to language data and outline some current problems shared by the two fields.

Sex-determination systems and their evolution: Mammals

International Nuclear Information System (INIS)

Colorado Garzon, Fredy A; Matta Camacho, Nubia E; Sanchez, Antonio

2012-01-01

Sex-determination methods are very diverse as they have become an enduring research field, understanding the causes of gonadal development and elucidating the main factors involved in sex-determination of offspring required relating information from far-ranging areas such as cytology, embryology, morphology, molecular biology and even ecology and evolution. This article presents an overview of sex-determination in placental mammals, encompassing several levels of biological organization. The importance of the underlying molecular tools in the context of sex-determination assays and their implications in conservation genetics is also discussed.

How does a high school biology teacher interact with his 10th grade students?: Examining science talk in evolution and human genetics instruction from a sociolinguistics perspective

Science.gov (United States)

Avsar Erumit, Banu

This qualitative study employed a case study design (Creswell, 2014) with a high school biology teacher to examine a) the types of discourse patterns that a high school teacher was using in evolution and human genetics units, b) the purposes and cognitive features of the teacher's questions, their impact on students' subsequent responses, and the types of teacher follow ups occurred in these two units, and c) the factors that I thought might be somehow influencing the teaching and learning of these two topics in this classroom. The findings showed that lecture and recitation were the two most frequently used discourse types in the two units. Guided discussion and guided small group work in which students' ideas and questions were more welcomed than in lecture and recitation, were used only in the evolution unit, which was also unit in which the teacher used hands-on activities. In the human genetics unit, he only used worksheet-based activities, which he called paper and pencil labs. Teacher questions were posed mainly to assess the correctness of students' factual knowledge, remind them of previously covered information, and check with students to clarify the meaning of their utterances or their progress on a task. The two primary types of cognitive processes associated with students' responses were recall information and evaluate teacher's questions, mostly with a short response. The most frequently heard voice in the classroom was teacher's. Whole class interactions did not feature equal participation as some much more engaged students dominated. The results of the teacher questionnaires. teacher interviews, teacher debriefings, and lesson observations showed that Evan had an informed understanding of NOS, a high level of acceptance of evolution, and adequate understanding of evolution. The factors that seemed to negatively influence his teaching and students' engagement in that classroom included but not limited to the teacher's lack of experience in teaching

Earth's earliest biosphere: Its origin and evolution

International Nuclear Information System (INIS)

Schopf, J.W.

1983-01-01

Some of the subjects discussed are related to the early biogeologic history, the nature of the earth prior to the oldest known rock record, the early earth and the Archean rock record, the prebiotic organic syntheses and the origin of life, Precambrian organic geochemistry, the biochemical evolution of anaerobic energy conversion, the isotopic inferences of ancient biochemistries, Archean stromatolites providing evidence of the earth's earliest benthos, Archean microfossils, the geologic evolution of the Archean-Early Proterozoic earth, and the environmental evolution of the Archean-Early Proterozoic earth. Other topics examined are concerned with geochemical evidence bearing on the origin of aerobiosis, biological and biochemical effects of the development of an aerobic environment, Early Proterozoic microfossils, the evolution of earth's earliest ecosystems, and geographic and geologic data for processed rock samples. Attention is given to a processing procedure for abiotic samples and calculation of model atmospheric compositions, and procedures of organic geochemical analysis

Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics.

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List, Johann-Mattis; Pathmanathan, Jananan Sylvestre; Lopez, Philippe; Bapteste, Eric

2016-08-20

For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields. We compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir's drift). Apart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to

Conceptual Ecology of the Evolution Acceptance among Greek Education Students: Knowledge, Religious Practices and Social Influences

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Athanasiou, Kyriacos; Papadopoulou, Penelope

2012-01-01

In this study, we explored some of the factors related to the acceptance of evolution theory among Greek university students training to be teachers in early childhood education, using conceptual ecology for biological evolution as a theoretical framework. We examined the acceptance of evolution theory and we also looked into the relationship…

Reproductive biology of an odacine labrid, Odax pullus

KAUST Repository

Laman Trip, Elizabeth; Clements, Kendall D.; Raubenheimer, David; Choat, John Howard

2011-01-01

-specific, i.e. associated with the phylogeny of labrid sexual development, and is not constrained by environmental effects on the evolution of sex change in temperate regions. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society

The Jukes-Cantor Model of Molecular Evolution

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Erickson, Keith

2010-01-01

The material in this module introduces students to some of the mathematical tools used to examine molecular evolution. This topic is standard fare in many mathematical biology or bioinformatics classes, but could also be suitable for classes in linear algebra or probability. While coursework in matrix algebra, Markov processes, Monte Carlo…

Mirror Neurons and the Evolution of Language

Science.gov (United States)

Corballis, Michael C.

2010-01-01

The mirror system provided a natural platform for the subsequent evolution of language. In nonhuman primates, the system provides for the understanding of biological action, and possibly for imitation, both prerequisites for language. I argue that language evolved from manual gestures, initially as a system of pantomime, but with gestures…

[Classification of organisms and structuralism in biology].

Science.gov (United States)

Vasil'eva, L I

2001-01-01

Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.

Evolution of complexity in RNA-like replicator systems

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Hogeweg Paulien

2008-03-01

Full Text Available Abstract Background The evolution of complexity is among the most important questions in biology. The evolution of complexity is often observed as the increase of genetic information or that of the organizational complexity of a system. It is well recognized that the formation of biological organization – be it of molecules or ecosystems – is ultimately instructed by the genetic information, whereas it is also true that the genetic information is functional only in the context of the organization. Therefore, to obtain a more complete picture of the evolution of complexity, we must study the evolution of both information and organization. Results Here we investigate the evolution of complexity in a simulated RNA-like replicator system. The simplicity of the system allows us to explicitly model the genotype-phenotype-interaction mapping of individual replicators, whereby we avoid preconceiving the functionality of genotypes (information or the ecological organization of replicators in the model. In particular, the model assumes that interactions among replicators – to replicate or to be replicated – depend on their secondary structures and base-pair matching. The results showed that a population of replicators, originally consisting of one genotype, evolves to form a complex ecosystem of up to four species. During this diversification, the species evolve through acquiring unique genotypes with distinct ecological functionality. The analysis of this diversification reveals that parasitic replicators, which have been thought to destabilize the replicator's diversity, actually promote the evolution of diversity through generating a novel "niche" for catalytic replicators. This also makes the current replicator system extremely stable upon the evolution of parasites. The results also show that the stability of the system crucially depends on the spatial pattern formation of replicators. Finally, the evolutionary dynamics is shown to

Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2015

Science.gov (United States)

2015-12-01

yield stability. Transgenic approach plays an important role in crop improvement. Currently, transgenes are randomly inserted into maize genome...Improve Microbial Biofuel Production - Mary Dunlop, University of Vermont 2:30-3:00 PM Targeted Integration of Genes into the Maize Genome Facilitated...highlights gaps in the present understanding of M13 biology. Understanding the subtleties of regulation will be important for maximally ex- ploiting the

Bioattractors: dynamical systems theory and the evolution of regulatory processes

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Jaeger, Johannes; Monk, Nick

2014-01-01

In this paper, we illustrate how dynamical systems theory can provide a unifying conceptual framework for evolution of biological regulatory systems. Our argument is that the genotype–phenotype map can be characterized by the phase portrait of the underlying regulatory process. The features of this portrait – such as attractors with associated basins and their bifurcations – define the regulatory and evolutionary potential of a system. We show how the geometric analysis of phase space connects Waddington's epigenetic landscape to recent computational approaches for the study of robustness and evolvability in network evolution. We discuss how the geometry of phase space determines the probability of possible phenotypic transitions. Finally, we demonstrate how the active, self-organizing role of the environment in phenotypic evolution can be understood in terms of dynamical systems concepts. This approach yields mechanistic explanations that go beyond insights based on the simulation of evolving regulatory networks alone. Its predictions can now be tested by studying specific, experimentally tractable regulatory systems using the tools of modern systems biology. A systematic exploration of such systems will enable us to understand better the nature and origin of the phenotypic variability, which provides the substrate for evolution by natural selection. PMID:24882812

The evolution of siderophore production as a competitive trait.

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Niehus, Rene; Picot, Aurore; Oliveira, Nuno M; Mitri, Sara; Foster, Kevin R

2017-06-01

Microbes have the potential to be highly cooperative organisms. The archetype of microbial cooperation is often considered to be the secretion of siderophores, molecules scavenging iron, where cooperation is threatened by "cheater" genotypes that use siderophores without making them. Here, we show that this view neglects a key piece of biology: siderophores are imported by specific receptors that constrain their use by competing strains. We study the effect of this specificity in an ecoevolutionary model, in which we vary siderophore sharing among strains, and compare fully shared siderophores with private siderophores. We show that privatizing siderophores fundamentally alters their evolution. Rather than a canonical cooperative good, siderophores become a competitive trait used to pillage iron from other strains. We also study the physiological regulation of siderophores using in silico long-term evolution. Although shared siderophores evolve to be downregulated in the presence of a competitor, as expected for a cooperative trait, privatized siderophores evolve to be upregulated. We evaluate these predictions using published experimental work, which suggests that some siderophores are upregulated in response to competition akin to competitive traits like antibiotics. Although siderophores can act as a cooperative good for single genotypes, we argue that their role in competition is fundamental to understanding their biology. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Power Laws, Scale-Free Networks and Genome Biology

CERN Document Server

Koonin, Eugene V; Karev, Georgy P

2006-01-01

Power Laws, Scale-free Networks and Genome Biology deals with crucial aspects of the theoretical foundations of systems biology, namely power law distributions and scale-free networks which have emerged as the hallmarks of biological organization in the post-genomic era. The chapters in the book not only describe the interesting mathematical properties of biological networks but moves beyond phenomenology, toward models of evolution capable of explaining the emergence of these features. The collection of chapters, contributed by both physicists and biologists, strives to address the problems in this field in a rigorous but not excessively mathematical manner and to represent different viewpoints, which is crucial in this emerging discipline. Each chapter includes, in addition to technical descriptions of properties of biological networks and evolutionary models, a more general and accessible introduction to the respective problems. Most chapters emphasize the potential of theoretical systems biology for disco...

"McLean v. Arkansas" (1982) and Beyond: Implications for Biology Professors

Science.gov (United States)

Bland, Mark W.; Moore, Randy

2011-01-01

To assess current trends of evolution instruction in high schools of the mid-South, we invited Arkansas high school biology teachers from across the state to respond to a survey designed to address this issue. We also asked students enrolled in a freshman-level, nonmajors biology course at a midsize public Arkansas university to recall their…

Origin and evolution of SINEs in eukaryotic genomes.

Science.gov (United States)

Kramerov, D A; Vassetzky, N S

2011-12-01

Short interspersed elements (SINEs) are one of the two most prolific mobile genomic elements in most of the higher eukaryotes. Although their biology is still not thoroughly understood, unusual life cycle of these simple elements amplified as genomic parasites makes their evolution unique in many ways. In contrast to most genetic elements including other transposons, SINEs emerged de novo many times in evolution from available molecules (for example, tRNA). The involvement of reverse transcription in their amplification cycle, huge number of genomic copies and modular structure allow variation mechanisms in SINEs uncommon or rare in other genetic elements (module exchange between SINE families, dimerization, and so on.). Overall, SINE evolution includes their emergence, progressive optimization and counteraction to the cell's defense against mobile genetic elements.

A view of evolution by a Christian biologist

Directory of Open Access Journals (Sweden)

Elizabeth Jordaan

1984-03-01

Full Text Available This paper, which originated as an address to a gathering of Dutch Reformed Ministers in Potchefstroom, deals with the response of a Christian to concepts of evolution. The paper looks at the concept of “the beginning”, the origin of life , genetics, mutation and natural selection, the origin of diversity or speciation, man as a biological species, the missing link (in which attention is given to various theories, and finally theories of human evolution. These include the neoteny theory, the savannah theory and the aquatic theory. Following a discussion of the various aspects of these theories, the authors go on to a discussion of the evolution of intelligence and culture, and reach the conclusion that “for a Christian, evolution may help him to understand more about God and his love and his work, and also then to have more security in the belief in God”.

The Biological Significance of Evolution in Autoimmune Phenomena

Directory of Open Access Journals (Sweden)

Carlos A. Cañas

2012-01-01

Full Text Available It is an inherent part of living to be in constant modification, which are due to answers resulting from environmental changes. The different systems make adaptations based on natural selection. With respect to the immune system of mammals, these changes have a lot to do with the interactions that occur continuously with other living species, especially microorganisms. The immune system is primarily designed to defend from germs and this response triggers inflammatory reactions which must be regulated in order not to generate damage to healthy tissue. The regulatory processes were added over time to prevent such damage. Through evolution the species have stored “an immunological experience,” which provides information that is important for developing effective responses in the future. The human species, which is at a high level of evolutionary immunological accumulation, have multiple immune defense strategies which, in turn, are highly regulated. Imbalances in these can result in autoimmunity.

Evolution of circadian rhythms: from bacteria to human.

Science.gov (United States)

Bhadra, Utpal; Thakkar, Nirav; Das, Paromita; Pal Bhadra, Manika

2017-07-01

The human body persists in its rhythm as per its initial time zone, and transition always occur according to solar movements around the earth over 24 h. While traveling across different latitudes and longitudes, at the pace exceeding the earth's movement, the changes in the external cues exceed the level of toleration of the body's biological clock. This poses an alteration in our physiological activities of sleep-wake pattern, mental alertness, organ movement, and eating habits, causing them to temporarily lose the track of time. This is further re-synchronized with the physiological cues of the destination over time. The mechanism of resetting of the clocks with varying time zones and cues occur in organisms from bacteria to humans. It is the result of the evolution of different pathways and molecular mechanisms over the time. There has been evolution of numerous comprehensive mechanisms using various research tools to get a deeper insight into the rapid turnover of molecular mechanisms in various species. This review reports insights into the evolution of the circadian mechanism and its evolutionary shift which is vital and plays a major role in assisting different organisms to adapt in different zones and controls their internal biological clocks with changing external cues. Copyright © 2017 Elsevier B.V. All rights reserved.

Directed evolution: selecting today's biocatalysts : selecting today's biocatalysts

NARCIS (Netherlands)

Otten, Linda; Quax, Wim

2005-01-01

Directed evolution has become a full-grown tool in molecular biology nowadays. The methods that are involved in creating a mutant library are extensive and can be divided into several categories according to their basic ideas. Furthermore, both screening and selection can be used to target the

New travelling wave solutions for nonlinear stochastic evolution

Indian Academy of Sciences (India)

The nonlinear stochastic evolution equations have a wide range of applications in physics, chemistry, biology, economics and finance from various points of view. In this paper, the (′/)-expansion method is implemented for obtaining new travelling wave solutions of the nonlinear (2 + 1)-dimensional stochastic ...

Understanding Cancer Genome and Its Evolution by Next Generation Sequencing

DEFF Research Database (Denmark)

Hou, Yong

Cancer will cause 13 million deaths by the year of 2030, ranking the second leading cause of death worldwide. Previous studies indicate that most of the cancers originate from cells that acquired somatic mutations and evolved as Darwin Theory. Ten biological insights of cancer have been summarized...... recently. Cutting-age technologies like next generation sequencing (NGS) enable exploring cancer genome and evolution much more efficiently. However, integrated cancer genome sequencing studies showed great inter-/intra-tumoral heterogeneity (ITH) and complex evolution patterns beyond the cancer biological...... knowledge we previously know. There is very limited knowledge of East Asia lung cancer genome except enrichment of EGFR mutations and lack of KRAS mutations. We carried out integrated genomic, transcriptomic and methylomic analysis of 335 primary Chinese lung adenocarcinomas (LUAD) and 35 corresponding...

Without it no music: Cognition, biology, and evolution of musicality

NARCIS (Netherlands)

Honing, H.; ten Cate, C.; Peretz, I.; Trehub, S.E.

2015-01-01

Musicality can be defined as a natural, spontaneously developing trait based on and constrained by biology and cognition. Music, by contrast, can be defined as a social and cultural construct based on that very musicality. One critical challenge is to delineate the constituent elements of

Interaction-based evolution: how natural selection and nonrandom mutation work together

Science.gov (United States)

2013-01-01

Background The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. Presentation of the hypothesis Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation—while not Lamarckian, or “directed” to increase fitness—is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination’s fitness. Testing and implications of the hypothesis This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional

Distinguishing between "function" and "effect" in genome biology.

Science.gov (United States)

Doolittle, W Ford; Brunet, Tyler D P; Linquist, Stefan; Gregory, T Ryan

2014-05-09

Much confusion in genome biology results from conflation of possible meanings of the word "function." We suggest that, in this connection, attention should be paid to evolutionary biologists and philosophers who have previously dealt with this problem. We need only decide that although all genomic structures have effects, only some of them should be said to have functions. Although it will very often be difficult or impossible to establish function (strictly defined), it should not automatically be assumed. We enjoin genomicists in particular to pay greater attention to parsing biological effects. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolution of oil droplets in a chemorobotic platform

Science.gov (United States)

Gutierrez, Juan Manuel Parrilla; Hinkley, Trevor; Taylor, James Ward; Yanev, Kliment; Cronin, Leroy

2014-12-01

Evolution, once the preserve of biology, has been widely emulated in software, while physically embodied systems that can evolve have been limited to electronic and robotic devices and have never been artificially implemented in populations of physically interacting chemical entities. Herein we present a liquid-handling robot built with the aim of investigating the properties of oil droplets as a function of composition via an automated evolutionary process. The robot makes the droplets by mixing four different compounds in different ratios and placing them in a Petri dish after which they are recorded using a camera and the behaviour of the droplets analysed using image recognition software to give a fitness value. In separate experiments, the fitness function discriminates based on movement, division and vibration over 21 cycles, giving successive fitness increases. Analysis and theoretical modelling of the data yields fitness landscapes analogous to the genotype-phenotype correlations found in biological evolution.

Stable States of Biological Organisms

Science.gov (United States)

Yukalov, V. I.; Sornette, D.; Yukalova, E. P.; Henry, J.-Y.; Cobb, J. P.

2009-04-01

A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole. The organism is modeled by a five-dimensional dynamical system. The organism homeostasis is described by the evolution equations for five interacting components: healthy cells, ill cells, innate immune cells, specific immune cells, and pathogens. The stability analysis demonstrates that, in a wide domain of the parameter space, the system exhibits robust structural stability. There always exist four stable stationary solutions characterizing four qualitatively differing states of the organism: alive state, boundary state, critical state, and dead state.

Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2014

Energy Technology Data Exchange (ETDEWEB)

Voigt, Christopher [Massachusetts Institute of Technology

2014-07-01

SEED2014 focused on advances in the science and technology emerging from the field of synthetic biology. We broadly define this as technologies that accelerate the process of genetic engineering. It highlighted new tool development, as well as the application of these tools to diverse problems in biotechnology, including therapeutics, industrial chemicals and fuels, natural products, and agriculture. Systems spanned from in vitro experiments and viruses, through diverse bacteria, to eukaryotes (yeast, mammalian cells, plants).

Evolution and Engineering in Escherichia coli

DEFF Research Database (Denmark)

Wendel, Sofie

Synthetic biology (synbio) is a chance for our societies to advance from oil-­‐‑dependent to bio-­‐‑based production, with the help of microbes. The two pillars of synbio are fundamental biological knowledge and applied engineering. In the present thesis, these two aspects of synbio are explored......, and their connections described. First,the different definitions and features of synbio are covered, after which two individual research projects are reported.Evolution is the basis for all life on Earth, and we are constantly learning more about its mechanisms. This thesis describes important elements of evolutionary...... projects presented also illustrate how every synbio venture contains features of fundamental as well as applied science. With fundamental studies inspiring new engineering efforts, and application development enabling further study of basic biology, it is clear how synbio is created in the overlap between...

Nature vs Nurture: Effects of Learning on Evolution

Science.gov (United States)

Nagrani, Nagina

In the field of Evolutionary Robotics, the design, development and application of artificial neural networks as controllers have derived their inspiration from biology. Biologists and artificial intelligence researchers are trying to understand the effects of neural network learning during the lifetime of the individuals on evolution of these individuals by qualitative and quantitative analyses. The conclusion of these analyses can help develop optimized artificial neural networks to perform any given task. The purpose of this thesis is to study the effects of learning on evolution. This has been done by applying Temporal Difference Reinforcement Learning methods to the evolution of Artificial Neural Tissue controller. The controller has been assigned the task to collect resources in a designated area in a simulated environment. The performance of the individuals is measured by the amount of resources collected. A comparison has been made between the results obtained by incorporating learning in evolution and evolution alone. The effects of learning parameters: learning rate, training period, discount rate, and policy on evolution have also been studied. It was observed that learning delays the performance of the evolving individuals over the generations. However, the non zero learning rate throughout the evolution process signifies natural selection preferring individuals possessing plasticity.

Biology, genome organization and evolution of parvoviruses in marine shrimp

Science.gov (United States)

A number of parvoviruses are now know to infect marine shrimp, and these viruses alone or in combination with other viruses have the potential to cause major losses in shrimp aquaculture globally. This review provides a comprehensive overview of the biology, genome organization, gene expression, and...

Resources for Teaching About Evolution from the U.S. Geological Survey

Science.gov (United States)

Gordon, L. C.

2001-12-01

As a scientific research agency, the U.S. Geological Survey (USGS) is in an ideal position to provide scientific information and resources to educators. The USGS is not a curriculum developer, nor an expert in pedagogy, yet the USGS does have a wealth of scientific information on subjects such as fossils, geologic time, biological resources and plate tectonics that naturally come in to play in the teaching of evolution. Among USGS resources are the general interest pamphlets Geologic Time, Dinosaurs: Facts And Fiction, Our Changing Continent, and Fossils Rocks, and Time, and its accompanying poster, Fossils Through Time. In addition to printed versions, the pamphlets are available at no cost on the Internet at http://pubs.usgs.gov/gip/. The popular booklet, This Dynamic Earth: The Story of Plate Tectonics, available at http://pubs.usgs.gov/publications/text/dynamic.html, touches on evolution-related subjects such as Alfred Wegener's use of fossils to develop his theory of continental drift, "polar" dinosaur fossils found in Australia, marine fossils in the rocks of the Himalayas, and the use of fossil ages to determine rates of plate motions. Paleontological research at the USGS is highlighted on the Internet at http://geology.er.usgs.gov/paleo/. The web site includes links to technical publications, profiles of scientists, a geologic time scale, a glossary, information on important fossil groups, and a list of non-USGS references on fossils: all very useful to educators. A wealth of biological information and data can be found in the National Biological Information Infrastructure (NBII), a multi-agency collaborative program led by the USGS. In addition to data on the Nation's biological resources, the NBII web site http://www.nbii.gov/ includes a section on systematics and scientific names (helpful for illustrating the evolutionary relationships among living organisms), and links to non-USGS curriculum materials. A fact sheet, Unveiling the NBII as a Teaching

Synthetic biology analysed tools for discussion and evaluation

CERN Document Server

2016-01-01

Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It provides a biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution. Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic bi...

On the possible role of robustness in the evolution of infectious diseases

Science.gov (United States)

Ogbunugafor, C. Brandon; Pease, James B.; Turner, Paul E.

2010-06-01

Robustness describes the capacity for a biological system to remain canalized despite perturbation. Genetic robustness affords maintenance of phenotype despite mutational input, necessarily involving the role of epistasis. Environmental robustness is phenotypic constancy in the face of environmental variation, where epistasis may be uninvolved. Here we discuss genetic and environmental robustness, from the standpoint of infectious disease evolution, and suggest that robustness may be a unifying principle for understanding how different disease agents evolve. We focus especially on viruses with RNA genomes due to their importance in the evolution of emerging diseases and as model systems to test robustness theory. We present new data on adaptive constraints for a model RNA virus challenged to evolve in response to UV radiation. We also draw attention to other infectious disease systems where robustness theory may prove useful for bridging evolutionary biology and biomedicine, especially the evolution of antibiotic resistance in bacteria, immune evasion by influenza, and malaria parasite infections.

SEAS: A simulated evolution approach for analog circuit synthesis

NARCIS (Netherlands)

Ning, Zhen-Qiu; Ning, Zhen-Qiu; Mouthaan, A.J.; Wallinga, Hans

1991-01-01

The authors present a simulated evolution approach for analog circuit synthesis based on an analogy with the natural selection process in biological environments and on the iterative improvements in solving engineering problems. A prototype framework based on this idea, called SEAS, has been

Getting to Darwin: Obstacles to Accepting Evolution by Natural Selection

Science.gov (United States)

Thagard, Paul; Findlay, Scott

2010-06-01

Darwin’s theory of evolution by natural selection is central to modern biology, but is resisted by many people. This paper discusses the major psychological obstacles to accepting Darwin’s theory. Cognitive obstacles to adopting evolution by natural selection include conceptual difficulties, methodological issues, and coherence problems that derive from the intuitiveness of alternative theories. The main emotional obstacles to accepting evolution are its apparent conflict with valued beliefs about God, souls, and morality. We draw on the philosophy of science and on a psychological theory of cognitive and emotional belief revision to make suggestions about what can be done to improve acceptance of Darwinian ideas.

Genetic, epigenetic and exogenetic information in development and evolution.

Science.gov (United States)

Griffiths, Paul E

2017-10-06

The idea that development is the expression of information accumulated during evolution and that heredity is the transmission of this information is surprisingly hard to cash out in strict, scientific terms. This paper seeks to do so using the sense of information introduced by Francis Crick in his sequence hypothesis and central dogma of molecular biology. It focuses on Crick's idea of precise determination. This is analysed using an information-theoretic measure of causal specificity. This allows us to reconstruct some of Crick's claims about information in transcription and translation. Crick's approach to information has natural extensions to non-coding regions of DNA, to epigenetic marks, and to the genetic or environmental upstream causes of those epigenetic marks. Epigenetic information cannot be reduced to genetic information. The existence of biological information in epigenetic and exogenetic factors is relevant to evolution as well as to development.

Cyanobacterial evolution during the Precambrian

Science.gov (United States)

Schirrmeister, Bettina E.; Sanchez-Baracaldo, Patricia; Wacey, David

2016-07-01

Life on Earth has existed for at least 3.5 billion years. Yet, relatively little is known of its evolution during the first two billion years, due to the scarceness and generally poor preservation of fossilized biological material. Cyanobacteria, formerly known as blue green algae were among the first crown Eubacteria to evolve and for more than 2.5 billion years they have strongly influenced Earth's biosphere. Being the only organism where oxygenic photosynthesis has originated, they have oxygenated Earth's atmosphere and hydrosphere, triggered the evolution of plants -being ancestral to chloroplasts- and enabled the evolution of complex life based on aerobic respiration. Having such a strong impact on early life, one might expect that the evolutionary success of this group may also have triggered further biosphere changes during early Earth history. However, very little is known about the early evolution of this phylum and ongoing debates about cyanobacterial fossils, biomarkers and molecular clock analyses highlight the difficulties in this field of research. Although phylogenomic analyses have provided promising glimpses into the early evolution of cyanobacteria, estimated divergence ages are often very uncertain, because of vague and insufficient tree-calibrations. Results of molecular clock analyses are intrinsically tied to these prior calibration points, hence improving calibrations will enable more precise divergence time estimations. Here we provide a review of previously described Precambrian microfossils, biomarkers and geochemical markers that inform upon the early evolution of cyanobacteria. Future research in micropalaeontology will require novel analyses and imaging techniques to improve taxonomic affiliation of many Precambrian microfossils. Consequently, a better understanding of early cyanobacterial evolution will not only allow for a more specific calibration of cyanobacterial and eubacterial phylogenies, but also provide new dates for the tree

Pax genes in eye development and evolution

Czech Academy of Sciences Publication Activity Database

Kozmik, Zbyněk

2005-01-01

Roč. 15, č. 4 (2005), s. 430-438 ISSN 0959-437X R&D Projects: GA MŠk(CZ) 1M0520; GA ČR(CZ) GA204/04/1358 Institutional research plan: CEZ:AV0Z5052915 Keywords : paxpax * eye development * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.361, year: 2005

Systems biology solutions for biochemical production challenges

DEFF Research Database (Denmark)

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

2017-01-01

There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...... characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity...... compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains...

Molecular phylogeny and evolution of mosquito parasitic Microsporidia (Microsporidia: Amblyosporidae)

Czech Academy of Sciences Publication Activity Database

Vossbrinck, C. R.; Andreadis, T.; Vávra, Jiří; Becnel, J. J.

2004-01-01

Roč. 51, č. 1 (2004), s. 88-95 ISSN 1066-5234 Institutional research plan: CEZ:AV0Z6022909 Keywords : Microsporidia * molecular phylogeny * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.403, year: 2004

Solar Radiation as Driving Force In Early Evolution

Science.gov (United States)

Rothschild, Lynn J.; Peterson, David L. (Technical Monitor)

2002-01-01

Ultraviolet radiation (UVR) has provided an evolutionary challenge to life on Earth in that it is both an agent of mutation and as well as a selective force. Today surface fluxes of UVR vary diurnally, seasonally, etc. Still, the UVR flux was probably substantially higher during the early phases of evolution, suggesting that its role in evolution was even more prominent during this time. In this presentation, the creative role of UVR in evolution is discussed, specifically in connection with the role that UVR may have played in the evolution of early microbial ecosystems. The presentation will include discussions of the direct influence of UVR on such processes as photosynthesis and genetic damage, as well as the indirect influence of UVR as mediated through the production of reactive oxygen species. These biological effects of UVR will be viewed against the backdrop of the physical nature of the early Earth, surely a very different place then than now.

Directed evolution of enzymes using microfluidic chips

Science.gov (United States)

Pilát, Zdeněk.; Ježek, Jan; Šmatlo, Filip; Kaůka, Jan; Zemánek, Pavel

2016-12-01

Enzymes are highly versatile and ubiquitous biological catalysts. They can greatly accelerate large variety of reactions, while ensuring appropriate catalytic activity and high selectivity. These properties make enzymes attractive biocatalysts for a wide range of industrial and biomedical applications. Over the last two decades, directed evolution of enzymes has transformed the field of protein engineering. We have devised microfluidic systems for directed evolution of haloalkane dehalogenases in emulsion droplets. In such a device, individual bacterial cells producing mutated variants of the same enzyme are encapsulated in microdroplets and supplied with a substrate. The conversion of a substrate by the enzyme produced by a single bacterium changes the pH in the droplet which is signalized by pH dependent fluorescence probe. The droplets with the highest enzymatic activity can be separated directly on the chip by dielectrophoresis and the resultant cell lineage can be used for enzyme production or for further rounds of directed evolution. This platform is applicable for fast screening of large libraries in directed evolution experiments requiring mutagenesis at multiple sites of a protein structure.

Analyzing Change in Students' Gene-to-Evolution Models in College-Level Introductory Biology

Science.gov (United States)

Dauer, Joseph T.; Momsen, Jennifer L.; Speth, Elena Bray; Makohon-Moore, Sasha C.; Long, Tammy M.

2013-01-01

Research in contemporary biology has become increasingly complex and organized around understanding biological processes in the context of systems. To better reflect the ways of thinking required for learning about systems, we developed and implemented a pedagogical approach using box-and-arrow models (similar to concept maps) as a foundational…

Male-limited evolution suggests no extant intralocus sexual conflict ...

Indian Academy of Sciences (India)

Male-limited evolution suggests no extant intralocus sexual conflict over the sexually dimorphic cuticular hydrocarbons of Drosophila melanogaster ... Spain; Indian Institute of Science Education and Research, Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli PO 140 306, India; Department of Biology and Centre for ...

Synergistic Synthetic Biology: Units in Concert

Science.gov (United States)

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications. PMID:25022769

Synergistic Synthetic Biology: Units in Concert

International Nuclear Information System (INIS)

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

Modeling of biological intelligence for SCM system optimization.

Science.gov (United States)

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

Directory of Open Access Journals (Sweden)

Shengyong Chen

2012-01-01

Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

Science.gov (United States)

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

Evolution of specialization and ecological character displacement: metabolic plasticity matters.

NARCIS (Netherlands)

Egas, C.J.M.; Reydon, Th.A.C.; Hemerik, L.

2005-01-01

An important question in evolutionary biology, especially with respect to herbivorous arthropods, is the evolution of specialization. In a previous paper, the combined evolutionary dynamics of specialization and ecological character displacement was studied, focusing on the role of herbivore

The role of Pax genes in eye evolution

Czech Academy of Sciences Publication Activity Database

Kozmik, Zbyněk

2008-01-01

Roč. 75, 2-4 (2008), s. 335-339 ISSN 0361-9230 R&D Projects: GA AV ČR IAA500520604; GA MŠk(CZ) 1M0520 Institutional research plan: CEZ:AV0Z50520514 Keywords : eye * Pax * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.281, year: 2008

Can fisheries-induced evolution shift reference points for fisheries management?

DEFF Research Database (Denmark)

Heino, Mikko; Baulier, Loїc; Boukal, David S.

2013-01-01

Biological reference points are important tools for fisheries management. Reference points are not static, but may change when a population's environment or the population itself changes. Fisheries-induced evolution is one mechanism that can alter population characteristics, leading to “shifting...

Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa?

Czech Academy of Sciences Publication Activity Database

Flegontov, Pavel; Gray, M.W.; Burger, G.; Lukeš, Julius

2011-01-01

Roč. 57, č. 4 (2011), 225-232 ISSN 0172-8083 Institutional research plan: CEZ:AV0Z60220518 Keywords : Euglena * Diplonema * Mitochondrial genome * RNA editing * Constructive neutral evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.556, year: 2011

Karyotype evolution in harvestmen of the suborder Cyphophthalmi (Opiliones)

Czech Academy of Sciences Publication Activity Database

Svojanovská, H.; Nguyen, Petr; Hiřman, M.; Tuf, I. H.; Wahab, R. A.; Haddad, C. R.; Šťáhlavský, F.

2016-01-01

Roč. 148, 2-3 (2016), s. 227-236 ISSN 1424-8581 R&D Projects: GA ČR(CZ) GP14-35819P Institutional support: RVO:60077344 Keywords : 18S rDNA * FISH * karyotype evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.354, year: 2016

New thinking: the evolution of human cognition.

Science.gov (United States)

Heyes, Cecilia

2012-08-05

Humans are animals that specialize in thinking and knowing, and our extraordinary cognitive abilities have transformed every aspect of our lives. In contrast to our chimpanzee cousins and Stone Age ancestors, we are complex political, economic, scientific and artistic creatures, living in a vast range of habitats, many of which are our own creation. Research on the evolution of human cognition asks what types of thinking make us such peculiar animals, and how they have been generated by evolutionary processes. New research in this field looks deeper into the evolutionary history of human cognition, and adopts a more multi-disciplinary approach than earlier 'Evolutionary Psychology'. It is informed by comparisons between humans and a range of primate and non-primate species, and integrates findings from anthropology, archaeology, economics, evolutionary biology, neuroscience, philosophy and psychology. Using these methods, recent research reveals profound commonalities, as well striking differences, between human and non-human minds, and suggests that the evolution of human cognition has been much more gradual and incremental than previously assumed. It accords crucial roles to cultural evolution, techno-social co-evolution and gene-culture co-evolution. These have produced domain-general developmental processes with extraordinary power-power that makes human cognition, and human lives, unique.

Adult sex ratio variation: implications for breeding system evolution.

Science.gov (United States)

Székely, T; Weissing, F J; Komdeur, J

2014-08-01

Adult sex ratio (ASR) exhibits immense variation in nature, although neither the causes nor the implications of this variation are fully understood. According to theory, the ASR is expected to influence sex roles and breeding systems, as the rarer sex in the population has more potential partners to mate with than the more common sex. Changes in mate choice, mating systems and parental care suggest that the ASR does influence breeding behaviour, although there is a need for more tests, especially experimental ones. In the context of breeding system evolution, the focus is currently on operational sex ratios (OSRs). We argue that the ASR plays a role of similar importance and urge researchers to study the ASR and the OSR side by side. Finally, we plead for a dynamic view of breeding system evolution with feedbacks between mating, parenting, OSR and ASR on both ecological and evolutionary time scales. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates

Czech Academy of Sciences Publication Activity Database

Lukeš, Julius; Leander, B. S.; Keeling, P. J.

2009-01-01

Roč. 106, č. 1 (2009), s. 9963-9970 ISSN 0027-8424 R&D Projects: GA ČR GA204/09/1667; GA MŠk LC07032; GA MŠk 2B06129 Institutional research plan: CEZ:AV0Z60220518 Keywords : comparative genomics * convergent evolution * dinoflagellates * Euglenozoa * mitochondria * molecular evolution * plastids * RNA editing * RNA editing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.432, year: 2009

Prospects for the study of evolution in the deep biosphere.

Science.gov (United States)

Biddle, Jennifer F; Sylvan, Jason B; Brazelton, William J; Tully, Benjamin J; Edwards, Katrina J; Moyer, Craig L; Heidelberg, John F; Nelson, William C

2011-01-01

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org).

Degeneracy: a link between evolvability, robustness and complexity in biological systems

Directory of Open Access Journals (Sweden)

Whitacre James M

2010-02-01

Full Text Available Abstract A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability and evidence of an intimate relationship between robustness and complexity in biology. This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability.

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.

Cellular potts models multiscale extensions and biological applications

CERN Document Server

Scianna, Marco

2013-01-01

A flexible, cell-level, and lattice-based technique, the cellular Potts model accurately describes the phenomenological mechanisms involved in many biological processes. Cellular Potts Models: Multiscale Extensions and Biological Applications gives an interdisciplinary, accessible treatment of these models, from the original methodologies to the latest developments. The book first explains the biophysical bases, main merits, and limitations of the cellular Potts model. It then proposes several innovative extensions, focusing on ways to integrate and interface the basic cellular Potts model at the mesoscopic scale with approaches that accurately model microscopic dynamics. These extensions are designed to create a nested and hybrid environment, where the evolution of a biological system is realistically driven by the constant interplay and flux of information between the different levels of description. Through several biological examples, the authors demonstrate a qualitative and quantitative agreement with t...

Proteomics Improves the New Understanding of Honeybee Biology.

Science.gov (United States)

Hora, Zewdu Ararso; Altaye, Solomon Zewdu; Wubie, Abebe Jemberie; Li, Jianke

2018-04-11

The honeybee is one of the most valuable insect pollinators, playing a key role in pollinating wild vegetation and agricultural crops, with significant contribution to the world's food production. Although honeybees have long been studied as model for social evolution, honeybee biology at the molecular level remained poorly understood until the year 2006. With the availability of the honeybee genome sequence and technological advancements in protein separation, mass spectrometry, and bioinformatics, aspects of honeybee biology such as developmental biology, physiology, behavior, neurobiology, and immunology have been explored to new depths at molecular and biochemical levels. This Review comprehensively summarizes the recent progress in honeybee biology using proteomics to study developmental physiology, task transition, and physiological changes in some of the organs, tissues, and cells based on achievements from the authors' laboratory in this field. The research advances of honeybee proteomics provide new insights for understanding of honeybee biology and future research directions.

Adaptive laboratory evolution – principles and applications for biotechnology

Science.gov (United States)

2013-01-01

Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. Although regularly performed for more than 25 years, the advent of transcript and cheap next-generation sequencing technologies has resulted in many recent studies, which successfully applied this technique in order to engineer microbial cells for biotechnological applications. Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations. However, recent studies show how some of the limitations may be overcome in order to successfully incorporate adaptive laboratory evolution in microbial cell factory design. Over the last two decades important insights into nutrient and stress metabolism of relevant model species were acquired, whereas some other aspects such as niche-specific differences of non-conventional cell factories are not completely understood. Altogether the current status and its future perspectives highlight the importance and potential of adaptive laboratory evolution as approach in biotechnological engineering. PMID:23815749

The evolution of "Life": A Metadarwinian integrative approach.

Science.gov (United States)

De Loof, Arnold

2017-01-01

It is undeniably very logical to first formulate an unambiguous definition of "Life" before engaging in defining the parameters instrumental to Life's evolution. Because nearly everybody assumes, erroneously in my opinion, that catching Life's essence in a single sentence is impossible, this way of thinking remained largely unexplored in evolutionary theory. Upon analyzing what exactly happens at the transition from "still alive" to "just dead," the following definition emerged. What we call "Life" (L) is an activity . It is nothing other than the total sum (∑) of all communication acts (C) executed, at moment t, by entities organized as sender-receiver compartments: L = ∑C Such "living" entities are self-electrifying and talking ( = communicating) aggregates of fossil stardust operating in an environment heavily polluted by toxic calcium. Communication is a multifaceted, complex process that is seldom well explained in introductory textbooks of biology. Communication is instrumental to adaptation because, at the cellular level, any act of communication is in fact a problem-solving act. It can be logically deduced that not Natural Selection itself but communication/problem-solving activity preceding selection is the universal driving force of evolution. This is against what textbooks usually claim, although doubt on the status of Natural Selection as driving force has been around for long. Finally, adopting the sender-receiver with its 2 memory systems (genetic and cognitive, both with their own rules) and 2 types of progeny ("physical children" and "pupils") as the universal unit of architecture and function of all living entities, also enables the seamless integration of cultural and organic evolution, another long-standing tough problem in evolutionary theory. Paraphrasing Theodosius Dobzhansky, the very essence of biology is: "Nothing in biology and evolutionary theory makes sense except in the light of the ability of living matter to communicate, and by

Cesare Lombroso: an anthropologist between evolution and degeneration.

Science.gov (United States)

Mazzarello, Paolo

2011-01-01

Cesare Lombroso (1835-1909) was a prominent Italian medical doctor and intellectual in the second half of the nineteenth century. He became world famous for his theory that criminality, madness and genius were all sides of the same psychobiological condition: an expression of degeneration, a sort of regression along the phylogenetic scale, and an arrest at an early stage of evolution. Degeneration affected criminals especially, in particular the "born delinquent" whose development had stopped at an early stage, making them the most "atavistic" types of human being. Lombroso also advocated the theory that genius was closely linked with madness. A man of genius was a degenerate, an example of retrograde evolution in whom madness was a form of "biological compensation" for excessive intellectual development. To confirm this theory, in August 1897, Lombroso, while attending the Twelfth International Medical Congress in Moscow, decided to meet the great Russian writer Lev Tolstoy in order to directly verify, in him, his theory of degeneration in the genius. Lombroso's anthropological ideas fuelled a heated debate on the biological determinism of human behaviour.

Synthetic biology platform technologies for antimicrobial applications.

Science.gov (United States)

Braff, Dana; Shis, David; Collins, James J

2016-10-01

The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels. Copyright © 2016 Elsevier B.V. All rights reserved.

EPISTEMOLOGY IN THE CONTEXT OF THE MODERN BIOLOGICAL EVOLUTIONAL PARADIGM

Directory of Open Access Journals (Sweden)

О. S. Tokovenko

2014-12-01

Full Text Available The purpose of the work is finding the reasonability of using bio-evolutionary paradigm for researching ratio morphic cognitive activity. Methodology. Methodological grounds consist of the original principles and conceptual apparatus of evolutionary epistemology. Scientific novelty. The article identifies opportunities for using of biological and evolutionary paradigm to study the peculiarities of ratiomorphic cognitive backgrounds and their influence on the formation and development of human knowledge. Conclusions. The article concludes that together with the idea of hyper cycles (feedback loop with mutual transmission of information in cognitive process the concept of ratiomorphic cognitive backgrounds, as well as attempts to examine cognitive processes based on the scientific criteria (empirical verification, explanatory power and ability to predict should be certainly considered as a positive contribution to the development of evolutionary epistemology into modern epistemological research. However, it is also indicated the fact of narrowing the heuristic possibilities of this epistemological direction because of excessive metaphor of bio-evolutionary paradigm. Further development of evolutionary epistemological research is considered in shifting the emphasis from biological and evolutionary towards cultural and evolutionary paradigm.

A second inheritance system: the extension of biology through culture.

Science.gov (United States)

Whiten, Andrew

2017-10-06

By the mid-twentieth century (thus following the 'Modern Synthesis' in evolutionary biology), the behavioural sciences offered only the sketchy beginnings of a scientific literature documenting evidence for cultural inheritance in animals-the transmission of traditional behaviours via learning from others (social learning). By contrast, recent decades have seen a massive growth in the documentation of such cultural phenomena, driven by long-term field studies and complementary laboratory experiments. Here, I review the burgeoning scope of discoveries in this field, which increasingly suggest that this 'second inheritance system', built on the shoulders of the primary genetic inheritance system, occurs widely among vertebrates and possibly in invertebrates too. Its novel characteristics suggest significant implications for our understanding of evolutionary biology. I assess the extent to which this second system extends the scope of evolution, both by echoing principal properties of the primary, organic evolutionary system, and going beyond it in significant ways. This is well established in human cultural evolution; here, I address animal cultures more generally. The further major, and related, question concerns the extent to which the consequences of widespread animal cultural transmission interact with the primary, genetically based inheritance systems, shaping organic evolution.

The Criticism of Atheistic Evolution

Directory of Open Access Journals (Sweden)

Farah Ramin

2010-03-01

Full Text Available With regard to close relation between evolution theory and religious knowledge, and its prodigious influence on arising new schools in philosophy this paper firstly considers the outcome of Darwin’s theologian theory in brief secondly it talks about recent controversies such as: ambiguity of Fitness concept, tautology and the usage of probability calculation in this theory,opposition of the second law of thermodynamics (Entropy, biological information in DNA, irreducible complexity, Fine-tuning of decisive nature constant and Anthropic Principle .

Uncovering the underlying physical mechanisms of biological systems via quantification of landscape and flux

International Nuclear Information System (INIS)

Xu Li; Chu Xiakun; Yan Zhiqiang; Zheng Xiliang; Zhang Kun; Zhang Feng; Yan Han; Wu Wei; Wang Jin

2016-01-01

In this review, we explore the physical mechanisms of biological processes such as protein folding and recognition, ligand binding, and systems biology, including cell cycle, stem cell, cancer, evolution, ecology, and neural networks. Our approach is based on the landscape and flux theory for nonequilibrium dynamical systems. This theory provides a unifying principle and foundation for investigating the underlying mechanisms and physical quantification of biological systems. (topical review)

The molecular biology and evolution of feline immunodeficiency viruses of cougars

Science.gov (United States)

Poss, Mary; Ross, Howard; Rodrigo, Allen; Terwee, Julie; VandeWoude, Sue; Biek, Roman

2008-01-01

Feline immunodeficiency virus (FIV) is a lentivirus that has been identified in many members of the family Felidae but domestic cats are the only FIV host in which infection results in disease. We studied FIVpco infection of cougars (Puma concolor) as a model for asymptomatic lentivirus infections to understand the mechanisms of host-virus coexistence. Several natural cougar populations were evaluated to determine if there are any consequences of FIVpco infection on cougar fecundity, survival, or susceptibility to other infections. We have sequenced full length viral genomes and conducted a detailed analysis of viral molecular evolution on these sequences and on genome fragments of serially sampled animals to determine the evolutionary forces experienced by this virus in cougars. In addition, we have evaluated the molecular genetics of FIVpco in a new host, domestic cats, to determine the evolutionary consequences to a host-adapted virus associated with cross-species infection. Our results indicate that there are no significant differences in survival, fecundity or susceptibility to other infections between FIVpco-infected and uninfected cougars. The molecular evolution of FIVpco is characterized by a slower evolutionary rate and an absence of positive selection, but also by proviral and plasma viral loads comparable to those of epidemic lentiviruses such as HIV-1 or FIVfca. Evolutionary and recombination rates and selection profiles change significantly when FIVpco replicates in a new host. PMID:18295904

[Mobile genetic elements in plant sex evolution].

Science.gov (United States)

Gerashchenkov, G A; Rozhnova, N A

2010-11-01

The most significant theories of the appearance and maintenance of sex are presented. However, in the overwhelming majority of existing theories, the problem of sex, which is the central problem of evolutionary biology, is considered primarily through the prism of reproductive features of living organisms, whereas the issue of molecular driving forces of sexual reproduction id restricted to the possible role of mobile genetic elements (MGEs) in the appearance of sexual reproduction. The structural and functional significance of MGEs in the genomic organization of plants is illustrated. It is shown that MGEs could act as important molecular drivers of sex evolution in plants. The involvement of MGEs in the formation of sex chromosomes and possible participation in seeds-without-sex reproduction (apomixis) is discussed. Thus, the hypothesis on the active MGE participation in sex evolution is in good agreement with the modern views on pathways and directions of sex evolution in plants.

Systems Biology Investigations of Pseudomonas aeruginosa Evolution in Association with Human Airway Infections

DEFF Research Database (Denmark)

Pedersen, Søren Damkiær

Most knowledge about evolutionary adaptation has been gained from experimental evolution studies, in which organisms have been allowed to evolve under simple, well-defined conditions in the laboratory. While these studies have provided novel insight into the fundamental processes of evolutionary....... aeruginosa DK2 clone lineage during 200,000 generations of evolution in the CF airways from its entrance in the clinic in the 1970’ies until the end of 2010. Genetic analysis showed that the DK2 lineage between 1973 and 2007 accumulated mutations in a near-linear manner with an overall genomic signature...... included fixation of mutations in the rpoD gene encoding the principle sigma factor σ70. The findings presented in this thesis provide insight into the genetic mechanisms and evolutionary processes that shape the adaptation of bacteria colonizing complex natural environments. Increased knowledge...

Variation in reaction norms: Statistical considerations and biological interpretation.

Science.gov (United States)

Morrissey, Michael B; Liefting, Maartje

2016-09-01

Analysis of reaction norms, the functions by which the phenotype produced by a given genotype depends on the environment, is critical to studying many aspects of phenotypic evolution. Different techniques are available for quantifying different aspects of reaction norm variation. We examine what biological inferences can be drawn from some of the more readily applicable analyses for studying reaction norms. We adopt a strongly biologically motivated view, but draw on statistical theory to highlight strengths and drawbacks of different techniques. In particular, consideration of some formal statistical theory leads to revision of some recently, and forcefully, advocated opinions on reaction norm analysis. We clarify what simple analysis of the slope between mean phenotype in two environments can tell us about reaction norms, explore the conditions under which polynomial regression can provide robust inferences about reaction norm shape, and explore how different existing approaches may be used to draw inferences about variation in reaction norm shape. We show how mixed model-based approaches can provide more robust inferences than more commonly used multistep statistical approaches, and derive new metrics of the relative importance of variation in reaction norm intercepts, slopes, and curvatures. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

Czech Academy of Sciences Publication Activity Database

Holland, L. Z.; Albalat, R.; Azumi, K.; Gutierrez, E.B.; Blow, M.J.; Bronner-Fraser, M.; Brunet, F.; Butts, T.; Candiani, S.; Dishaw, L. J.; Ferrier, D.E.K.; Garcia-Fernandez, J.; Gibson-Brown, J.J.; Gissi, C.; Godzik, A.; Hallbook, F.; Hirose, D.; Hosomichi, K.; Ikuta, T.; Inoko, H.; Kasahara, M.; Kasamatsu, J.; Kawashima, T.; Kimura, A.; Kobayashi, M.; Kozmik, Zbyněk; Kubokawa, K.; Laudet, V.; Litman, G.W.; McHardy, A.; Meulemans, D.; Nonaka, M.; Olinski, R.P.; Pancer, Z.; Pennacchio, L.A.; Pestarino, M.; Rast, J.P.; Rigoutsos, I.; Robinson-Rechavi, M.; Roch, G.; Saiga, H.; Sasakura, Y.; Satake, M.; Satou, Y.; Schubert, M.; Sherwood, N.; Shiina, T.; Takatori, N.; Tello, J.; Vopálenský, Pavel; Wada, S.; Xu, A.; Ye, Y.; Yoshida, K.; Yoshizaki, F.; Yu, J.K.; Zhang, Q.; Zmasek, C.M.; De Jong, P.J.; Osoegawa, K.; Putnam, N. H.; Rokhsar, D. S.; Satoh, N.; Holland, P.W.H.

2008-01-01

Roč. 18, č. 7 (2008), s. 1100-1111 ISSN 1088-9051 R&D Projects: GA MŠk(CZ) 1M0520 Institutional research plan: CEZ:AV0Z50520514 Keywords : evolution * amphioxus genome * opsin Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 10.176, year: 2008

Advanced functional evolution equations and inclusions

CERN Document Server

Benchohra, Mouffak

2015-01-01

This book presents up-to-date results on abstract evolution equations and differential inclusions in infinite dimensional spaces. It covers equations with time delay and with impulses, and complements the existing literature in functional differential equations and inclusions. The exposition is devoted to both local and global mild solutions for some classes of functional differential evolution equations and inclusions, and other densely and non-densely defined functional differential equations and inclusions in separable Banach spaces or in Fréchet spaces. The tools used include classical fixed points theorems and the measure-of non-compactness, and each chapter concludes with a section devoted to notes and bibliographical remarks. This monograph is particularly useful for researchers and graduate students studying pure and applied mathematics, engineering, biology and all other applied sciences.

Rotating biological contactors: the Canadian experience

Energy Technology Data Exchange (ETDEWEB)

Cuenca, Manuel A [Ryerson Polytechnical Univ., Toronto, ON (Canada). Chemical Engineering Dept.; Smith, Tom [CMS Rotordisk Inc., Concord, ON (Canada); Vianna, Arlinda C [Servico Nacional de Aprendizagem Industrial (SENAI), Salvador, BA (Brazil)

1994-12-31

In fifteen years, Rotating Biological Contactors (RBC) have become one of the most attractive technologies for secondary wastewater treatment. The present work is a review of the evolution of RBC technology in the last twenty years. In addition, the status of the technology in Canada is described, emphasizing industrial facilities and landfill leachate treatment. An enumeration of the most relevant development areas is included. (author). 34 refs., 3 figs., 7 tabs.

Rotating biological contactors: the Canadian experience

Energy Technology Data Exchange (ETDEWEB)

Cuenca, Manuel A. [Ryerson Polytechnical Univ., Toronto, ON (Canada). Chemical Engineering Dept.; Smith, Tom [CMS Rotordisk Inc., Concord, ON (Canada); Vianna, Arlinda C. [Servico Nacional de Aprendizagem Industrial (SENAI), Salvador, BA (Brazil)

1993-12-31

In fifteen years, Rotating Biological Contactors (RBC) have become one of the most attractive technologies for secondary wastewater treatment. The present work is a review of the evolution of RBC technology in the last twenty years. In addition, the status of the technology in Canada is described, emphasizing industrial facilities and landfill leachate treatment. An enumeration of the most relevant development areas is included. (author). 34 refs., 3 figs., 7 tabs.

Where mathematics, computer science, linguistics and biology meet essays in honour of Gheorghe Păun

CERN Document Server

Mitrana, Victor

2001-01-01

In the last years, it was observed an increasing interest of computer scientists in the structure of biological molecules and the way how they can be manipulated in vitro in order to define theoretical models of computation based on genetic engineering tools. Along the same lines, a parallel interest is growing regarding the process of evolution of living organisms. Much of the current data for genomes are expressed in the form of maps which are now becoming available and permit the study of the evolution of organisms at the scale of genome for the first time. On the other hand, there is an active trend nowadays throughout the field of computational biology toward abstracted, hierarchical views of biological sequences, which is very much in the spirit of computational linguistics. In the last decades, results and methods in the field of formal language theory that might be applied to the description of biological sequences were pointed out.

The Biology of Intron Gain and Loss

DEFF Research Database (Denmark)

Jeffares, Daniel C; Mourier, Tobias; Penny, David

2006-01-01

Intron density in eukaryote genomes varies by more than three orders of magnitude, so there must have been extensive intron gain and/or intron loss during evolution. A favored and partial explanation for this range of intron densities has been that introns have accumulated stochastically in large...... on introns depending on the biology of the organism and the gene involved....

A Mixed Exam Format Closes the Gap for Students with a Conflict between Their Religious Belief & the Theory of Evolution

Science.gov (United States)

Stanger-Hall, Kathrin F.; Wenner, Julianne A.

2014-01-01

We assessed the performance of students with a self-reported conflict between their religious belief and the theory of evolution in two sections of a large introductory biology course (N = 373 students). Student performance was measured through pretest and posttest evolution essays and multiple- choice (MC) questions (evolution-related and…

[Molecular biology, darwinism and nomogenesis].

Science.gov (United States)

Vol'kenshteĭn, M V

1987-01-01

The theory of nomogenesis put forward by L. S. Berg in 1922 is discussed. It is shown that side by side with some erroneous anti-darwinian ideas the theory contains a series of important suggestions which anticipate the further development of the synthetic theory of evolution. Berg has foreseen the development of molecular biology. Thus he was the fore-teller of our branch of science. The theory of nomogenesis emphasized the limitations of natural selection which determine the directionality of evolution. Berg treated the speciation as a kind of phase transition. Even the most conscientious critics of Berg have misrepresented the real sense of his works. It is totally groundless to treat nomogenesis as an idealistic of Lamarkian theory. Berg was superior to his critics. However the enthusiasm about nomogenesis in our time shows the inability to separate "the grains from weeds".

Hidden Randomness between Fitness Landscapes Limits Reverse Evolution

Science.gov (United States)

Tan, Longzhi; Serene, Stephen; Xiao Chao, Hui; Gore, Jeff

2012-02-01

Natural populations must constantly adapt to the ever-changing environment. A fundamental question in evolutionary biology is whether adaptations can be reversed by returning the population to its ancestral environment. Traditionally, reverse evolution is defined as restoring an ancestral phenotype (physical characteristics such as body size), and the classic Dollo's Law has hypothesized the impossibility of reversing complex adaptations. However, this ``law'' remains ambiguous unless reverse evolution can be studied at the level of genotypes (the underlying genome sequence). We measured the fitness landscapes of a bacterial antibiotic-resistance gene and analyzed the reversibility of evolution as a global, statistical feature of the landscapes. In both experiments and simulations, we find that an adaptation's reversibility declines as the number of mutations it involves increases, suggesting a probabilistic form of Dollo's Law at the molecular level. We also show computationally that slowly switching between environments facilitates reverse evolution in small populations, where clonal interference is negligible or moderate. This is an analogy to thermodynamics, where the reversibility of a physical process is maximized when conditions are modified infinitely slowly.

Evolution in a Test Tube: Rise of the Wrinkly Spreaders

Science.gov (United States)

Green, Jennifer H.; Koza, Anna; Moshynets, Olena; Pajor, Radoslaw; Ritchie, Margaret R.; Spiers, Andrew J.

2011-01-01

Understanding evolutionary mechanisms is fundamental to a balanced biological education, yet practical demonstrations are rarely considered. In this paper we describe a bacterial liquid microcosm which can be used to demonstrate aspects of evolution, namely adaptive radiation, niche colonisation and competitive fitness. In microcosms inoculated…

Cognitive dissonance as an explanation of the genesis, evolution ...

African Journals Online (AJOL)

The steady erosion of support for this flagrant HIV denialism, together with the rise of neoliberal thinking in the ANC, would lead to the evolution of this biological denialism into a form of treatment denialism. This ideology argued against the widespread provision and use of antiretroviral treatment. Empirical evidence is ...

Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.

Science.gov (United States)

Stoll, Gautier; Viara, Eric; Barillot, Emmanuel; Calzone, Laurence

2012-08-29

Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time. There exist two major types of mathematical modeling approaches: (1) quantitative modeling, representing various chemical species concentrations by real numbers, mainly based on differential equations and chemical kinetics formalism; (2) and qualitative modeling, representing chemical species concentrations or activities by a finite set of discrete values. Both approaches answer particular (and often different) biological questions. Qualitative modeling approach permits a simple and less detailed description of the biological systems, efficiently describes stable state identification but remains inconvenient in describing the transient kinetics leading to these states. In this context, time is represented by discrete steps. Quantitative modeling, on the other hand, can describe more accurately the dynamical behavior of biological processes as it follows the evolution of concentration or activities of chemical species as a function of time, but requires an important amount of information on the parameters difficult to find in the literature. Here, we propose a modeling framework based on a qualitative approach that is intrinsically continuous in time. The algorithm presented in this article fills the gap between qualitative and quantitative modeling. It is based on continuous time Markov process applied on a Boolean state space. In order to describe the temporal evolution of the biological process we wish to model, we explicitly specify the transition rates for each node. For that purpose, we built a language that can be seen as a generalization of Boolean equations. Mathematically, this approach can be translated in a set of ordinary differential

Physics of biological membranes

Science.gov (United States)

Mouritsen, Ole G.

The biological membrane is a complex system consisting of an aqueous biomolecular planar aggregate of predominantly lipid and protein molecules. At physiological temperatures, the membrane may be considered a thin (˜50Å) slab of anisotropic fluid characterized by a high lateral mobility of the various molecular components. A substantial fraction of biological activity takes place in association with membranes. As a very lively piece of condensed matter, the biological membrane is a challenging research topic for both the experimental and theoretical physicists who are facing a number of fundamental physical problems including molecular self-organization, macromolecular structure and dynamics, inter-macromolecular interactions, structure-function relationships, transport of energy and matter, and interfacial forces. This paper will present a brief review of recent theoretical and experimental progress on such problems, with special emphasis on lipid bilayer structure and dynamics, lipid phase transitions, lipid-protein and lipid-cholesterol interactions, intermembrane forces, and the physical constraints imposed on biomembrane function and evolution. The paper advocates the dual point of view that there are a number of interesting physics problems in membranology and, at the same time, that the physical properties of biomembranes are important regulators of membrane function.

Biological and technological effects of some mulberry varieties and ...

African Journals Online (AJOL)

egyptian hak

environment. Evolution 50: 434-437. Mahmoud MAM, Zalat SM, El-Akkad SS & Gilbert F (2008) Genetic variability in the endemic bee Anthophora pauperata among wadis in St Katherine Protectorate. Egyptian Journal of Biology 10: 77-86. Marden JH (1989) Bodybuilding dragonflies: costs and benefits of maximizing flight ...

Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores.

Science.gov (United States)

Bastien, Olivier; Maréchal, Eric

2008-08-07

Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2) following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory) is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure). Homologous sequences were considered as systems 1) having a high redundancy of information reflected by the magnitude of their alignment scores, 2) which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a constant rate, corresponding to the

Biology and Ecology of Alchisme grossa in a Cloud Forest of the Bolivian Yungas

OpenAIRE

Torrico-Bazoberry, Daniel; Caceres-Sanchez, Liliana; Saavedra-Ulloa, Daniela; Flores-Prado, Luis; Niemeyer, Hermann M.; Pinto, Carlos F.

2014-01-01

Treehoppers (Membracidae) exhibit different levels of sociality, from solitary to presocial. Although they are one of the best biological systems to study the evolution of maternal care in insects, information on the biology of species in this group is scarce. This work describes the biology and ecology of Alchisme grossa (Fairmaire) (Hemiptera: Membracidae) in a rain cloud forest of Bolivia. This subsocial membracid utilizes two host-plant species, Brugmansia suaveolens (Humb. & Bonpl. ex Wi...

Systems biology solutions for biochemical production challenges.

Science.gov (United States)

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

2017-06-01

There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Biologically Inspired Technology Using Electroactive Polymers (EAP)

Science.gov (United States)

Bar-Cohen, Yoseph

2006-01-01

Evolution allowed nature to introduce highly effective biological mechanisms that are incredible inspiration for innovation. Humans have always made efforts to imitate nature's inventions and we are increasingly making advances that it becomes significantly easier to imitate, copy, and adapt biological methods, processes and systems. This brought us to the ability to create technology that is far beyond the simple mimicking of nature. Having better tools to understand and to implement nature's principles we are now equipped like never before to be inspired by nature and to employ our tools in far superior ways. Effectively, by bio-inspiration we can have a better view and value of nature capability while studying its models to learn what can be extracted, copied or adapted. Using electroactive polymers (EAP) as artificial muscles is adding an important element to the development of biologically inspired technologies.

An analytically solvable model for rapid evolution of modular structure.

Directory of Open Access Journals (Sweden)

Nadav Kashtan

2009-04-01

Full Text Available Biological systems often display modularity, in the sense that they can be decomposed into nearly independent subsystems. Recent studies have suggested that modular structure can spontaneously emerge if goals (environments change over time, such that each new goal shares the same set of sub-problems with previous goals. Such modularly varying goals can also dramatically speed up evolution, relative to evolution under a constant goal. These studies were based on simulations of model systems, such as logic circuits and RNA structure, which are generally not easy to treat analytically. We present, here, a simple model for evolution under modularly varying goals that can be solved analytically. This model helps to understand some of the fundamental mechanisms that lead to rapid emergence of modular structure under modularly varying goals. In particular, the model suggests a mechanism for the dramatic speedup in evolution observed under such temporally varying goals.

The plant vascular system: Evolution, development and functions

Science.gov (United States)

William J. Lucas; Andrew Groover; Raffael Lichtenberger; Kaori Furuta; Shri-Ram Yadav; Yka Helariutta; Xin-Qiang He; Hiroo Fukuda; Julie Kang; Siobhan M. Brady; John W. Patrick; John Sperry; Akiko Yoshida; Ana-Flor Lopez-Millan; Michael A. Grusak; Pradeep Kachroo

2013-01-01

The emergence of the tracheophyte-based vascular system of land plants had major impacts on the evolution of terrestrial biology, in general, through its role in facilitating the development of plants with increased stature, photosynthetic output, and ability to colonize a greatly expanded range of environmental habitats. Recently, considerable progress has been made...

Cubozoan genome illuminates functional diversification of opsins and photoreceptor evolution

Czech Academy of Sciences Publication Activity Database

Liegertová, Michaela; Pergner, Jiří; Kozmiková, Iryna; Fabian, Peter; Pombinho, António R.; Strnad, Hynek; Pačes, Jan; Vlček, Čestmír; Bartůněk, Petr; Kozmik, Zbyněk

2015-01-01

Roč. 5, Jul 8 (2015) ISSN 2045-2322 R&D Projects: GA ČR GAP305/10/2141; GA MŠk LO1220 Institutional support: RVO:68378050 Keywords : Cubozoan genome * opsins * photoreceptor * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.228, year: 2015

The inception and evolution of a unique masters program in cancer biology, prevention and control.

Science.gov (United States)

Cousin, Carolyn; Blancato, Jan

2010-09-01

The University of the District of Columbia (UDC) and the Lombardi Comprehensive Cancer Center (LCCC), Georgetown University Medical Center established a Masters Degree Program in Cancer Biology, Prevention and Control at UDC that is jointly administered and taught by UDC and LCCC faculty. The goal of the Masters Degree Program is to educate students as master-level cancer professionals capable of conducting research and service in cancer biology, prevention, and control or to further advance the education of students to pursue doctoral studies. The Program's unique nature is reflected in its philosophy "the best cancer prevention and control researchers are those with a sound understanding of cancer biology". This program is a full-time, 2-year, 36-credit degree in which students take half of their coursework at UDC and half of their coursework at LCCC. During the second year, students are required to conduct research either at LCCC or UDC. Unlike most cancer biology programs, this unique Program emphasizes both cancer biology and cancer outreach training.

Domain organizations of modular extracellular matrix proteins and their evolution.

Science.gov (United States)

Engel, J

1996-11-01

Multidomain proteins which are composed of modular units are a rather recent invention of evolution. Domains are defined as autonomously folding regions of a protein, and many of them are similar in sequence and structure, indicating common ancestry. Their modular nature is emphasized by frequent repetitions in identical or in different proteins and by a large number of different combinations with other domains. The extracellular matrix is perhaps the largest biological system composed of modular mosaic proteins, and its astonishing complexity and diversity are based on them. A cluster of minireviews on modular proteins is being published in Matrix Biology. These deal with the evolution of modular proteins, the three-dimensional structure of domains and the ways in which these interact in a multidomain protein. They discuss structure-function relationships in calcium binding domains, collagen helices, alpha-helical coiled-coil domains and C-lectins. The present minireview is focused on some general aspects and serves as an introduction to the cluster.

How Biology Teachers Can Respond to Intelligent Design

Science.gov (United States)

Mackenzie, Jim

2010-01-01

Teachers of biology and related subjects are increasingly meeting objections from students and their parents to the teaching of evolution and the exclusion of what is called the theory of Intelligent Design. This paper attempts to draw together arguments and evidence which may be used by such teachers. Four lessons are drawn from the 1982…

Prospects for the study of evolution in the deep biosphere

Directory of Open Access Journals (Sweden)

Jennifer F Biddle

2012-01-01

Full Text Available Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Manhes et al. 2011, Martiny et al. 2006. Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI theme team on Evolution (www.darkenergybiosphere.org.

Prospects for the Study of Evolution in the Deep Biosphere

Science.gov (United States)

Biddle, Jennifer F.; Sylvan, Jason B.; Brazelton, William J.; Tully, Benjamin J.; Edwards, Katrina J.; Moyer, Craig L.; Heidelberg, John F.; Nelson, William C.

2012-01-01

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org). PMID:22319515

Systems Biology — the Broader Perspective

Directory of Open Access Journals (Sweden)

Jonathan Bard

2013-06-01

Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

Ontogeny and Evolution Through the Lens of the Developmental Systems Theory (DST

Directory of Open Access Journals (Sweden)

Vicente Dressino

2017-09-01

Full Text Available The Developmental Systems Theory (DST intends to make a conceptual summary that links ontogenic development to evolution. This theory’s background may be found in the works of Waddington and Bertalanffy, who provided the foundations for the canalization of development and the biological systems theory, respectively. The aim of this work is to make a preliminary conceptual analysis of DST as a theoretical framework for developmental biology in particular and for evolutionary biology in general. For that purpose, we will take into account some of the concepts and proposals that constitute this framework, and we will work with secondary data obtained from the bibliography. We conclude that: 1. DST is able to argue against the gene centrist vision about the explanations that try to justify biological and evolutionary development; 2. DST argues coherently in favor of the role of Epigenetics in ontogeny and evolution; 3. In connection to that, the role of natural selection is restricted to a secondary plane; 4. DST proposes that the nature/nurture dichotomy must be overcome; and 5. DST constitutes a possible methodological research program composed of a series of not necessarily related hypothesis, theories, and methods that may be confirmed in a relatively independent manner from the rest of the theoretical network.

2011 Archaea: Ecology, Metabolism, & Molecular Biology

Energy Technology Data Exchange (ETDEWEB)

Keneth Stedman

2011-08-05

Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

Analysis of biological spectrum of Divčibare flora

Directory of Open Access Journals (Sweden)

Popović Ivana

2006-01-01

Full Text Available One of the essential analyses which is performed during the floristic study of a region is the analysis of the biological spectrum. The analysis of the biological spectrum of the flora includes the determination of the type of life form for each taxon described in the flora of the study region. If it is considered that life form is a specific structural-functional response to the environmental effects and the result of the adaptation during the species evolution, it is clear that the basic characteristics of the site are more or less reflected in any life form. This fact is confirmed by the analysis of the biological spectrum of Divčibare flora. The study results are in correlation with the results of the analysis of the biological spectrum of the flora of Serbia and the Balkan Peninsula.

Inequity aversion and the evolution of cooperation

OpenAIRE

Ahmed, Asrar; Karlapalem, Kamalakar

2014-01-01

Evolution of cooperation is a widely studied problem in biology, social science, economics, and artificial intelligence. Most of the existing approaches that explain cooperation rely on some notion of direct or indirect reciprocity. These reciprocity based models assume agents recognize their partner and know their previous interactions, which requires advanced cognitive abilities. In this paper we are interested in developing a model that produces cooperation without requiring any explicit m...

Regenesis how synthetic biology will reinvent nature and ourselves

CERN Document Server

Church, George M

2012-01-01

Imagine a future in which human beings have become immune to all viruses, in which bacteria can custom-produce everyday items, like a drinking cup, or generate enough electricity to end oil dependency. Building a house would entail no more work than planting a seed in the ground. These scenarios may seem far-fetched, but pioneering geneticist George Church and science writer Ed Regis show that synthetic biology is bringing us ever closer to making such visions a reality. In "Regenesis," Church and Regis explorethe possibilities--and perils--of the emerging field of synthetic biology. Synthetic biology, in which living organisms are selectively altered by modifying substantial portions of their genomes, allows for the creation of entirely new species of organisms. Until now, nature has been the exclusive arbiter of life, death, and evolution; with synthetic biology, we now have the potential to write our own biological future. Indeed, as Church and Regis show, it even enables us to revisit crucial points in th...

Perceptions of High School Biology Teachers in Christian Schools on Relationships between Religious Beliefs and Teaching Evolution

Science.gov (United States)

Mangahas, Ana Marie E.

2017-01-01

This mixed method study explored Christian teachers' beliefs in religious schools on evolution, their attitudes toward evolution, and their perceptions on the effect of those beliefs on the teaching of evolutionary content. Teachers (N = 52) from Association for Christian Schools International (ACSI) accredited schools in California and Hawaii…

The Origin and Evolution of Life in Pakistani High School Biology

Science.gov (United States)

Asghar, Anila; Wiles, Jason R.; Alters, Brian

2010-01-01

This study seeks to inform science education practitioners and researchers in the West about apparent attempts to reconcile science and religion in Pakistan's public school curriculum. We analysed the national high school science curriculum and biology textbooks (English) used in the Government schools in Pakistan, where Islamic faith is the…

Biology meets Physics: Reductionism and Multi-scale Modeling of Morphogenesis

DEFF Research Database (Denmark)

Green, Sara; Batterman, Robert

2017-01-01

A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism ...... modeling in developmental biology. In such contexts, the relation between models at different scales and from different disciplines is neither reductive nor completely autonomous, but interdependent....... from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes a step back in asking whether bottom......-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the “tyranny of scales” problem present a challenge to reductive explanations in both physics and biology. The problem refers to the scale...

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

OpenAIRE

Smith, Stephen A; Beaulieu, Jeremy M; Donoghue, Michael J

2009-01-01

Abstract Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylog...

Ultrastructure, macromolecules, and evolution

CERN Document Server

Dillon, Lawrence S

1981-01-01

Thus far in the history of biology, two, and only two, fundamental principles have come to light that pervade and unify the entire science-the cell theory and the concept of evolution. While it is true that recently opened fields of inves­ tigation have given rise to several generalizations of wide impact, such as the universality of DNA and the energetic dynamics of ecology, closer inspection reveals them to be part and parcel of either of the first two mentioned. Because in the final analysis energy can act upon an organism solely at the cellular level, its effects may be perceived basically to represent one facet of cell me­ tabolism. Similarly, because the DNA theory centers upon the means by which cells build proteins and reproduce themselves, it too proves to be only one more, even though an exciting, aspect of the cell theory. In fact, if the matter is given closer scrutiny, evolution itself can be viewed as being a fundamental portion of the cell concept, for its effects arise only as a consequence ...

Genetic diversity, virulence and fitness evolution in an obligate fungal parasite of bees.

Science.gov (United States)

Evison, S E F; Foley, K; Jensen, A B; Hughes, W O H

2015-01-01

Within-host competition is predicted to drive the evolution of virulence in parasites, but the precise outcomes of such interactions are often unpredictable due to many factors including the biology of the host and the parasite, stochastic events and co-evolutionary interactions. Here, we use a serial passage experiment (SPE) with three strains of a heterothallic fungal parasite (Ascosphaera apis) of the Honey bee (Apis mellifera) to assess how evolving under increasing competitive pressure affects parasite virulence and fitness evolution. The results show an increase in virulence after successive generations of selection and consequently faster production of spores. This faster sporulation, however, did not translate into more spores being produced during this longer window of sporulation; rather, it appeared to induce a loss of fitness in terms of total spore production. There was no evidence to suggest that a greater diversity of competing strains was a driver of this increased virulence and subsequent fitness cost, but rather that strain-specific competitive interactions influenced the evolutionary outcomes of mixed infections. It is possible that the parasite may have evolved to avoid competition with multiple strains because of its heterothallic mode of reproduction, which highlights the importance of understanding parasite biology when predicting disease dynamics. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

Science.gov (United States)

Colautti, Robert I; Lau, Jennifer A

2015-05-01

Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

Conference on chemical evolution and the origin of life: Self-organization of the macromolecules of life

International Nuclear Information System (INIS)

1993-10-01

The formation of biomolecules was a necessary step in the evolution of life on earth. This interdisciplinary conference emphasized the role of replication in processes of self-organization of biological macromolecules. The present document contains abstracts of the 26 contributions to the conference on chemical evolution. The individual contributions have been indexed separately for the database

Using synthetic biology to make cells tomorrow's test tubes.

Science.gov (United States)

Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

2016-04-18

The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.

Historical Contingency in Controlled Evolution

Science.gov (United States)

Schuster, Peter

2014-12-01

A basic question in evolution is dealing with the nature of an evolutionary memory. At thermodynamic equilibrium, at stable stationary states or other stable attractors the memory on the path leading to the long-time solution is erased, at least in part. Similar arguments hold for unique optima. Optimality in biology is discussed on the basis of microbial metabolism. Biology, on the other hand, is characterized by historical contingency, which has recently become accessible to experimental test in bacterial populations evolving under controlled conditions. Computer simulations give additional insight into the nature of the evolutionary memory, which is ultimately caused by the enormous space of possibilities that is so large that it escapes all attempts of visualization. In essence, this contribution is dealing with two questions of current evolutionary theory: (i) Are organisms operating at optimal performance? and (ii) How is the evolutionary memory built up in populations?

2nd Colombian Congress on Computational Biology and Bioinformatics

CERN Document Server

Cristancho, Marco; Isaza, Gustavo; Pinzón, Andrés; Rodríguez, Juan

2014-01-01

This volume compiles accepted contributions for the 2nd Edition of the Colombian Computational Biology and Bioinformatics Congress CCBCOL, after a rigorous review process in which 54 papers were accepted for publication from 119 submitted contributions. Bioinformatics and Computational Biology are areas of knowledge that have emerged due to advances that have taken place in the Biological Sciences and its integration with Information Sciences. The expansion of projects involving the study of genomes has led the way in the production of vast amounts of sequence data which needs to be organized, analyzed and stored to understand phenomena associated with living organisms related to their evolution, behavior in different ecosystems, and the development of applications that can be derived from this analysis.  .

Developing of the future: scaffolded Darwinism in societal evolution.

Science.gov (United States)

Andersson, Claes; Törnberg, Anton; Törnberg, Petter

2014-08-01

We sympathize with the project of a synthetic approach for devising a "theory of intentional change" and agree that Darwinism should be central in such a theory. But Darwinism is not the only process of evolution that needs to be included. Evolutionary biology itself has taken such a turn recently, with the emergence of developmental evolutionary approaches.

The impact of a scheduling change on ninth grade high school performance on biology benchmark exams and the California Standards Test

Science.gov (United States)

Leonardi, Marcelo

The primary purpose of this study was to examine the impact of a scheduling change from a trimester 4x4 block schedule to a modified hybrid schedule on student achievement in ninth grade biology courses. This study examined the impact of the scheduling change on student achievement through teacher created benchmark assessments in Genetics, DNA, and Evolution and on the California Standardized Test in Biology. The secondary purpose of this study examined the ninth grade biology teacher perceptions of ninth grade biology student achievement. Using a mixed methods research approach, data was collected both quantitatively and qualitatively as aligned to research questions. Quantitative methods included gathering data from departmental benchmark exams and California Standardized Test in Biology and conducting multiple analysis of covariance and analysis of covariance to determine significance differences. Qualitative methods include journal entries questions and focus group interviews. The results revealed a statistically significant increase in scores on both the DNA and Evolution benchmark exams. DNA and Evolution benchmark exams showed significant improvements from a change in scheduling format. The scheduling change was responsible for 1.5% of the increase in DNA benchmark scores and 2% of the increase in Evolution benchmark scores. The results revealed a statistically significant decrease in scores on the Genetics Benchmark exam as a result of the scheduling change. The scheduling change was responsible for 1% of the decrease in Genetics benchmark scores. The results also revealed a statistically significant increase in scores on the CST Biology exam. The scheduling change was responsible for .7% of the increase in CST Biology scores. Results of the focus group discussions indicated that all teachers preferred the modified hybrid schedule over the trimester schedule and that it improved student achievement.

The impact of genomics on research in diversity and evolution of archaea.

Science.gov (United States)

Mardanov, A V; Ravin, N V

2012-08-01

Since the definition of archaea as a separate domain of life along with bacteria and eukaryotes, they have become one of the most interesting objects of modern microbiology, molecular biology, and biochemistry. Sequencing and analysis of archaeal genomes were especially important for studies on archaea because of a limited availability of genetic tools for the majority of these microorganisms and problems associated with their cultivation. Fifteen years since the publication of the first genome of an archaeon, more than one hundred complete genome sequences of representatives of different phylogenetic groups have been determined. Analysis of these genomes has expanded our knowledge of biology of archaea, their diversity and evolution, and allowed identification and characterization of new deep phylogenetic lineages of archaea. The development of genome technologies has allowed sequencing the genomes of uncultivated archaea directly from enrichment cultures, metagenomic samples, and even from single cells. Insights have been gained into the evolution of key biochemical processes in archaea, such as cell division and DNA replication, the role of horizontal gene transfer in the evolution of archaea, and new relationships between archaea and eukaryotes have been revealed.

[Thermodynamic theory of evolution and aging].

Science.gov (United States)

Gladyshev, G P

2012-01-01

Life in the Universe emerges and develops under certain conditions in accordance with the general laws of nature, in particular, in accordance with the law of temporal hierarchies, the second law of thermodynamics and the principle of stability of matter. Biological evolution and organism's aging are accompanied by a change in the chemical and supramolecular compositions of living bodies. As shown by the author in 1977 these well-known changes have the thermodynamic nature (origin). Phenomenological hierarchical thermodynamics of near-equilibrium quasi-closed systems allows us to explain and predict the evolutionary transformation in the living world. From a viewpoint of power-consuming substance of biological objects the phenomenon of life, first, is the struggle for power-consuming chemicals. The accumulation of this substance in biological systems is associated with the aspiration of the specific Gibbs function of formation of supramolecular structures of living organisms to a minimum. The development of classical science opens up new horizons to explore the real world and contributes to the success of gerontology and geriatrics. This paper is a brief review containing new results.

SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

Science.gov (United States)

Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J

2013-01-01

We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases.

On the role of sparseness in the evolution of modularity in gene regulatory networks.

Science.gov (United States)

Espinosa-Soto, Carlos

2018-05-01

Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases.

A Biologist in Wonderland: The Texas Biology Textbook Adoption Hearings.

Science.gov (United States)

McInerney, Joseph D.

1991-01-01

Examines Texas adoption process, described by author as having an inordinate impact on textbook market. Creationist opposition to evolution content in biological textbooks is well organized. Author presents 10 arguments made at hearing by creationists that he describes as a monument to scientific illiteracy. Asserts that creationists' confusion of…

The biology of Phytophthora infestans at its center of origin

NARCIS (Netherlands)

Grünwald, N.J.; Flier, W.G.

2005-01-01

The central highlands of Mexico are considered to be a center of genetic diversity for both the potato late blight pathogen and for tuber-bearing Solanum spp. Recent work conducted in Mexico and South America sheds new light on the biology and evolution of Phytophthora infestans and other related

Art and brain: insights from neuropsychology, biology and evolution.

Science.gov (United States)

Zaidel, Dahlia W

2010-02-01

Art is a uniquely human activity associated fundamentally with symbolic and abstract cognition. Its practice in human societies throughout the world, coupled with seeming non-functionality, has led to three major brain theories of art. (1) The localized brain regions and pathways theory links art to multiple neural regions. (2) The display of art and its aesthetics theory is tied to the biological motivation of courtship signals and mate selection strategies in animals. (3) The evolutionary theory links the symbolic nature of art to critical pivotal brain changes in Homo sapiens supporting increased development of language and hierarchical social grouping. Collectively, these theories point to art as a multi-process cognition dependent on diverse brain regions and on redundancy in art-related functional representation.

Present Day Biology seen in the Looking Glass of Physics of Complexity

Science.gov (United States)

Schuster, P.

Darwin's theory of variation and selection in its simplest form is directly applicable to RNA evolution in vitro as well as to virus evolution, and it allows for quantitative predictions. Understanding evolution at the molecular level is ultimately related to the central paradigm of structural biology: sequence⇒ structure ⇒ function. We elaborate on the state of the art in modeling and understanding evolution of RNA driven by reproduction and mutation. The focus will be laid on the landscape concept—originally introduced by Sewall Wright—and its application to problems in biology. The relation between genotypes and phenotypes is the result of two consecutive mappings from a space of genotypes called sequence space onto a space of phenotypes or structures, and fitness is the result of a mapping from phenotype space into non-negative real numbers. Realistic landscapes as derived from folding of RNA sequences into structures are characterized by two properties: (i) they are rugged in the sense that sequences lying nearby in sequence space may have very different fitness values and (ii) they are characterized by an appreciable degree of neutrality implying that a certain fraction of genotypes and/or phenotypes cannot be distinguished in the selection process. Evolutionary dynamics on realistic landscapes will be studied as a function of the mutation rate, and the role of neutrality in the selection process will be discussed.

The painted turtle, Chrysemys picta: a model system for vertebrate evolution, ecology, and human health.

Science.gov (United States)

Valenzuela, Nicole

2009-07-01

Painted turtles (Chrysemys picta) are representatives of a vertebrate clade whose biology and phylogenetic position hold a key to our understanding of fundamental aspects of vertebrate evolution. These features make them an ideal emerging model system. Extensive ecological and physiological research provide the context in which to place new research advances in evolutionary genetics, genomics, evolutionary developmental biology, and ecological developmental biology which are enabled by current resources, such as a bacterial artificial chromosome (BAC) library of C. picta, and the imminent development of additional ones such as genome sequences and cDNA and expressed sequence tag (EST) libraries. This integrative approach will allow the research community to continue making advances to provide functional and evolutionary explanations for the lability of biological traits found not only among reptiles but vertebrates in general. Moreover, because humans and reptiles share a common ancestor, and given the ease of using nonplacental vertebrates in experimental biology compared with mammalian embryos, painted turtles are also an emerging model system for biomedical research. For example, painted turtles have been studied to understand many biological responses to overwintering and anoxia, as potential sentinels for environmental xenobiotics, and as a model to decipher the ecology and evolution of sexual development and reproduction. Thus, painted turtles are an excellent reptilian model system for studies with human health, environmental, ecological, and evolutionary significance.

Evolution of the serum resistance-associated SRA gene in African trypanosomes

Czech Academy of Sciences Publication Activity Database

Lai, D. H.; Wang, Q.P.; Lukeš, Julius; Lun, Z.R.

2009-01-01

Roč. 54, č. 7 (2009), s. 1275-1278 ISSN 1001-6538 R&D Projects: GA MŠk 2B06129 Institutional research plan: CEZ:AV0Z60220518 Keywords : SRA * SRAbc * evolution * African trypanosomes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.898, year: 2009

Hominid evolution: genetics versus memetics

Science.gov (United States)

Carter, Brandon

2012-01-01

The last few million years on planet Earth have witnessed two remarkable phases of hominid development, starting with a phase of biological evolution characterized by rather rapid increase of the size of the brain. This has been followed by a phase of even more rapid technological evolution and concomitant expansion of the size of the population that began when our own particular ‘sapiens’ species emerged, just a few hundred thousand years ago. The present investigation exploits the analogy between the neo-Darwinian genetic evolution mechanism governing the first phase, and the memetic evolution mechanism governing the second phase. From the outset of the latter until very recently - about the year 2000 - the growth of the global population N was roughly governed by an equation of the form dN/Ndt=N/T*, in which T* is a coefficient introduced (in 1960) by von Foerster, who evaluated it empirically as about 200 000 million years. It is shown here how the value of this hitherto mysterious timescale governing the memetic phase is explicable in terms of what happened in the preceding genetic phase. The outcome is that the order of magnitude of the Foerster timescale can be accounted for as the product of the relevant (human) generation timescale, about 20 years, with the number of bits of information in the genome, of the order of 10 000 million. Whereas the origin of our ‘homo’ genus may well have involved an evolutionary hard step, it transpires that the emergence of our particular ‘sapiens’ species was rather an automatic process.

From frog integument to human skin: dermatological perspectives from frog skin biology

NARCIS (Netherlands)

Haslam, I.S.; Roubos, E.W.; Mangoni, M.L.; Yoshizato, K.; Vaudry, H.; Kloepper, J.E.; Pattwell, D.M.; Maderson, P.F.A.; Paus, R.

2014-01-01

For over a century, frogs have been studied across various scientific fields, including physiology, embryology, neuroscience, (neuro)endocrinology, ecology, genetics, behavioural science, evolution, drug development, and conservation biology. In some cases, frog skin has proven very successful as a

Biologically inspired technologies using artificial muscles

Science.gov (United States)

Bar-Cohen, Yoseph

2005-01-01

After billions of years of evolution, nature developed inventions that work, which are appropriate for the intended tasks and that last. The evolution of nature led to the introduction of highly effective and power efficient biological mechanisms that are scalable from micron to many meters in size. Imitating these mechanisms offers enormous potentials for the improvement of our life and the tools we use. Humans have always made efforts to imitate nature and we are increasingly reaching levels of advancement where it becomes significantly easier to imitate, copy, and adapt biological methods, processes and systems. Some of the biomimetic technologies that have emerged include artificial muscles, artificial intelligence, and artificial vision to which significant advances in materials science, mechanics, electronics, and computer science have contributed greatly. One of the newest fields of biomimetics is the electroactive polymers (EAP) that are also known as artificial muscles. To take advantage of these materials, efforts are made worldwide to establish a strong infrastructure addressing the need for comprehensive analytical modeling of their operation mechanism and develop effective processing and characterization techniques. The field is still in its emerging state and robust materials are not readily available however in recent years significant progress has been made and commercial products have already started to appear. This paper covers the state-of-the-art and challenges to making artificial muscles and their potential biomimetic applications.

Hologenomics: Systems-Level Host Biology.

Science.gov (United States)

Theis, Kevin R

2018-01-01

The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.

Biological Principles and Threshold Concepts for Understanding Natural Selection. Implications for Developing Visualizations as a Pedagogic Tool

Science.gov (United States)

Tibell, Lena A. E.; Harms, Ute

2017-11-01

Modern evolutionary theory is both a central theory and an integrative framework of the life sciences. This is reflected in the common references to evolution in modern science education curricula and contexts. In fact, evolution is a core idea that is supposed to support biology learning by facilitating the organization of relevant knowledge. In addition, evolution can function as a pivotal link between concepts and highlight similarities in the complexity of biological concepts. However, empirical studies in many countries have for decades identified deficiencies in students' scientific understanding of evolution mainly focusing on natural selection. Clearly, there are major obstacles to learning natural selection, and we argue that to overcome them, it is essential to address explicitly the general abstract concepts that underlie the biological processes, e.g., randomness or probability. Hence, we propose a two-dimensional framework for analyzing and structuring teaching of natural selection. The first—purely biological—dimension embraces the three main principles variation, heredity, and selection structured in nine key concepts that form the core idea of natural selection. The second dimension encompasses four so-called thresholds, i.e., general abstract and/or non-perceptual concepts: randomness, probability, spatial scales, and temporal scales. We claim that both of these dimensions must be continuously considered, in tandem, when teaching evolution in order to allow development of a meaningful understanding of the process. Further, we suggest that making the thresholds tangible with the aid of appropriate kinds of visualizations will facilitate grasping of the threshold concepts, and thus, help learners to overcome the difficulties in understanding the central theory of life.

Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores

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Maréchal Eric

2008-08-01

Full Text Available Abstract Background Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2 following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. Results We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure. Homologous sequences were considered as systems 1 having a high redundancy of information reflected by the magnitude of their alignment scores, 2 which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a

Homeostasis as the Mechanism of Evolution

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John S. Torday

2015-09-01

Full Text Available Homeostasis is conventionally thought of merely as a synchronic (same time servo-mechanism that maintains the status quo for organismal physiology. However, when seen from the perspective of developmental physiology, homeostasis is a robust, dynamic, intergenerational, diachronic (across-time mechanism for the maintenance, perpetuation and modification of physiologic structure and function. The integral relationships generated by cell-cell signaling for the mechanisms of embryogenesis, physiology and repair provide the needed insight to the scale-free universality of the homeostatic principle, offering a novel opportunity for a Systems approach to Biology. Starting with the inception of life itself, with the advent of reproduction during meiosis and mitosis, moving forward both ontogenetically and phylogenetically through the evolutionary steps involved in adaptation to an ever-changing environment, Biology and Evolution Theory need no longer default to teleology.

Biology, ecology and evolution of the family Gigasporaceae, arbuscular mycorrhizal fungi (Glomeromycota)

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Souza, Francisco Adriano de

2005-01-01

Research described in this thesis focused on biological, ecological and evolutionary aspects of Arbuscular Mycorrhizal Fungi (AMF), and in particular of the family Gigasporaceae (Gigaspora and Scutellospora, genera). This study had two major objectives. The first objective was to obtain better

Evolution of SUMO Function and Chain Formation in Insects.

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Ureña, Enric; Pirone, Lucia; Chafino, Silvia; Pérez, Coralia; Sutherland, James D; Lang, Valérie; Rodriguez, Manuel S; Lopitz-Otsoa, Fernando; Blanco, Francisco J; Barrio, Rosa; Martín, David

2016-02-01

SUMOylation, the covalent binding of Small Ubiquitin-like Modifier (SUMO) to target proteins, is a posttranslational modification that regulates critical cellular processes in eukaryotes. In insects, SUMOylation has been studied in holometabolous species, particularly in the dipteran Drosophila melanogaster, which contains a single SUMO gene (smt3). This has led to the assumption that insects contain a single SUMO gene. However, the analysis of insect genomes shows that basal insects contain two SUMO genes, orthologous to vertebrate SUMO1 and SUMO2/3. Our phylogenetical analysis reveals that the SUMO gene has been duplicated giving rise to SUMO1 and SUMO2/3 families early in Metazoan evolution, and that later in insect evolution the SUMO1 gene has been lost after the Hymenoptera divergence. To explore the consequences of this loss, we have examined the characteristics and different biological functions of the two SUMO genes (SUMO1 and SUMO3) in the hemimetabolous cockroach Blattella germanica and compared them with those of Drosophila Smt3. Here, we show that the metamorphic role of the SUMO genes is evolutionary conserved in insects, although there has been a regulatory switch from SUMO1 in basal insects to SUMO3 in more derived ones. We also show that, unlike vertebrates, insect SUMO3 proteins cannot form polySUMO chains due to the loss of critical lysine residues within the N-terminal part of the protein. Furthermore, the formation of polySUMO chains by expression of ectopic human SUMO3 has a deleterious effect in Drosophila. These findings contribute to the understanding of the functional consequences of the evolution of SUMO genes. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Emergence of communication in socio-biological networks

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