Understanding Bias in the Introduction of Variation As an Evolutionary
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From Developmental Constraint to Evolvability
From Developmental Constraint to Evolvability How Concepts Figure in Explanation and Disciplinary Identity Ingo Brigandt Department of Philosophy, University of Alberta 2-40 Assiniboia Hall, Edmonton, AB T6G2E7, Canada [email protected] Abstract The concept of developmental constraint was at the heart of develop- mental approaches to evolution of the 1980s. While this idea was widely used to criticize neo-Darwinian evolutionary theory, critique does not yield an alternative framework that offers evolutionary explanations. In current Evo-devo the concept of constraint is of minor importance, whereas notions as evolvability are at the center of attention. The latter clearly defines an explanatory agenda for evolution- ary research, so that one could view the historical shift from ‘developmental con- straint’ towards ‘evolvability’ as the move from a concept that is a mere tool of criticism to a concept that establishes a positive explanatory project. However, by taking a look at how the concept of constraint was employed in the 1980s, I argue that developmental constraint was not just seen as restricting possibilities (‘con- straining’), but also as facilitating morphological change in several ways. Ac- counting for macroevolutionary transformation and the origin of novel form was an aim of these developmental approaches to evolution. Thus, the concept of de- velopmental constraint was part of a positive explanatory agenda long before the advent of Evo-devo as a genuine scientific discipline. In the 1980s, despite the lack of a clear disciplinary identity, this concept coordinated research among pale- ontologists, morphologists, and developmentally inclined evolutionary biologists. I discuss the different functions that scientific concepts can have, highlighting that instead of classifying or explaining natural phenomena, concepts such as ‘devel- opmental constraint’ and ‘evolvability’ are more important in setting explanatory agendas so as to provide intellectual coherence to scientific approaches. -
Population Size and the Rate of Evolution
Review Population size and the rate of evolution 1,2 1 3 Robert Lanfear , Hanna Kokko , and Adam Eyre-Walker 1 Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia 2 National Evolutionary Synthesis Center, Durham, NC, USA 3 School of Life Sciences, University of Sussex, Brighton, UK Does evolution proceed faster in larger or smaller popu- mutations occur and the chance that each mutation lations? The relationship between effective population spreads to fixation. size (Ne) and the rate of evolution has consequences for The purpose of this review is to synthesize theoretical our ability to understand and interpret genomic varia- and empirical knowledge of the relationship between tion, and is central to many aspects of evolution and effective population size (Ne, Box 1) and the substitution ecology. Many factors affect the relationship between Ne rate, which we term the Ne–rate relationship (NeRR). A and the rate of evolution, and recent theoretical and positive NeRR implies faster evolution in larger popula- empirical studies have shown some surprising and tions relative to smaller ones, and a negative NeRR implies sometimes counterintuitive results. Some mechanisms the opposite (Figure 1A,B). Although Ne has long been tend to make the relationship positive, others negative, known to be one of the most important factors determining and they can act simultaneously. The relationship also the substitution rate [5–8], several novel predictions and depends on whether one is interested in the rate of observations have emerged in recent years, causing some neutral, adaptive, or deleterious evolution. Here, we reassessment of earlier theory and highlighting some gaps synthesize theoretical and empirical approaches to un- in our understanding. -
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B. M ü ller, G ü nter P. Wagner, and Werner Callebaut, editors The Evolution of Cognition , edited by Cecilia Heyes and Ludwig Huber, 2000 Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology , edited by Gerd B. M ü ller and Stuart A. Newman, 2003 Environment, Development, and Evolution: Toward a Synthesis , edited by Brian K. Hall, Roy D. Pearson, and Gerd B. M ü ller, 2004 Evolution of Communication Systems: A Comparative Approach , edited by D. Kimbrough Oller and Ulrike Griebel, 2004 Modularity: Understanding the Development and Evolution of Natural Complex Systems , edited by Werner Callebaut and Diego Rasskin-Gutman, 2005 Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution , by Richard A. Watson, 2006 Biological Emergences: Evolution by Natural Experiment , by Robert G. B. Reid, 2007 Modeling Biology: Structure, Behaviors, Evolution , edited by Manfred D. Laubichler and Gerd B. M ü ller, 2007 Evolution of Communicative Flexibility: Complexity, Creativity, and Adaptability in Human and Animal Communication , edited by Kimbrough D. Oller and Ulrike Griebel, 2008 Functions in Biological and Artifi cial Worlds: Comparative Philosophical Perspectives , edited by Ulrich Krohs and Peter Kroes, 2009 Cognitive Biology: Evolutionary and Developmental Perspectives on Mind, Brain, and Behavior , edited by Luca Tommasi, Mary A. Peterson, and Lynn Nadel, 2009 Innovation in Cultural Systems: Contributions from Evolutionary Anthropology , edited by Michael J. O ’ Brien and Stephen J. Shennan, 2010 The Major Transitions in Evolution Revisited , edited by Brett Calcott and Kim Sterelny, 2011 Transformations of Lamarckism: From Subtle Fluids to Molecular Biology , edited by Snait B. -
Interpreting the History of Evolutionary Biology Through a Kuhnian Prism: Sense Or Nonsense?
Interpreting the History of Evolutionary Biology through a Kuhnian Prism: Sense or Nonsense? Koen B. Tanghe Department of Philosophy and Moral Sciences, Universiteit Gent, Belgium Lieven Pauwels Department of Criminology, Criminal Law and Social Law, Universiteit Gent, Belgium Alexis De Tiège Department of Philosophy and Moral Sciences, Universiteit Gent, Belgium Johan Braeckman Department of Philosophy and Moral Sciences, Universiteit Gent, Belgium Traditionally, Thomas S. Kuhn’s The Structure of Scientific Revolutions (1962) is largely identified with his analysis of the structure of scientific revo- lutions. Here, we contribute to a minority tradition in the Kuhn literature by interpreting the history of evolutionary biology through the prism of the entire historical developmental model of sciences that he elaborates in The Structure. This research not only reveals a certain match between this model and the history of evolutionary biology but, more importantly, also sheds new light on several episodes in that history, and particularly on the publication of Charles Darwin’s On the Origin of Species (1859), the construction of the modern evolutionary synthesis, the chronic discontent with it, and the latest expression of that discon- tent, called the extended evolutionary synthesis. Lastly, we also explain why this kind of analysis hasn’t been done before. We would like to thank two anonymous reviewers for their constructive review, as well as the editor Alex Levine. Perspectives on Science 2021, vol. 29, no. 1 © 2021 by The Massachusetts Institute of Technology https://doi.org/10.1162/posc_a_00359 1 Downloaded from http://www.mitpressjournals.org/doi/pdf/10.1162/posc_a_00359 by guest on 30 September 2021 2 Evolutionary Biology through a Kuhnian Prism 1. -
Why Call It Developmental Bias When It Is Just Development? Isaac Salazar-Ciudad1,2,3
Salazar-Ciudad Biology Direct (2021) 16:3 https://doi.org/10.1186/s13062-020-00289-w OPINION Open Access Why call it developmental bias when it is just development? Isaac Salazar-Ciudad1,2,3 Abstract The concept of developmental constraints has been central to understand the role of development in morphological evolution. Developmental constraints are classically defined as biases imposed by development on the distribution of morphological variation. This opinion article argues that the concepts of developmental constraints and developmental biases do not accurately represent the role of development in evolution. The concept of developmental constraints was coined to oppose the view that natural selection is all-capable and to highlight the importance of development for understanding evolution. In the modern synthesis, natural selection was seen as the main factor determining the direction of morphological evolution. For that to be the case, morphological variation needs to be isotropic (i.e. equally possible in all directions). The proponents of the developmental constraint concept argued that development makes that some morphological variation is more likely than other (i.e. variation is not isotropic), and that, thus, development constraints evolution by precluding natural selection from being all-capable. This article adds to the idea that development is not compatible with the isotropic expectation by arguing that, in fact, it could not be otherwise: there is no actual reason to expect that development could lead to isotropic morphological variation. It is then argued that, since the isotropic expectation is untenable, the role of development in evolution should not be understood as a departure from such an expectation. -
IN EVOLUTION JACK LESTER KING UNIVERSITY of CALIFORNIA, SANTA BARBARA This Paper Is Dedicated to Retiring University of California Professors Curt Stern and Everett R
THE ROLE OF MUTATION IN EVOLUTION JACK LESTER KING UNIVERSITY OF CALIFORNIA, SANTA BARBARA This paper is dedicated to retiring University of California Professors Curt Stern and Everett R. Dempster. 1. Introduction Eleven decades of thought and work by Darwinian and neo-Darwinian scientists have produced a sophisticated and detailed structure of evolutionary ,theory and observations. In recent years, new techniques in molecular biology have led to new observations that appear to challenge some of the basic theorems of classical evolutionary theory, precipitating the current crisis in evolutionary thought. Building on morphological and paleontological observations, genetic experimentation, logical arguments, and upon mathematical models requiring simplifying assumptions, neo-Darwinian theorists have been able to make some remarkable predictions, some of which, unfortunately, have proven to be inaccurate. Well-known examples are the prediction that most genes in natural populations must be monomorphic [34], and the calculation that a species could evolve at a maximum rate of the order of one allele substitution per 300 genera- tions [13]. It is now known that a large proportion of gene loci are polymorphic in most species [28], and that evolutionary genetic substitutions occur in the human line, for instance, at a rate of about 50 nucleotide changes per generation [20], [24], [25], [26]. The puzzling observation [21], [40], [46], that homologous proteins in different species evolve at nearly constant rates is very difficult to account for with classical evolutionary theory, and at the very least gives a solid indication that there are qualitative differences between the ways molecules evolve and the ways morphological structures evolve. -
Mendelism, Plant Breeding and Experimental Cultures: Agriculture and the Development of Genetics in France Christophe Bonneuil
Mendelism, plant breeding and experimental cultures: Agriculture and the development of genetics in France Christophe Bonneuil To cite this version: Christophe Bonneuil. Mendelism, plant breeding and experimental cultures: Agriculture and the development of genetics in France. Journal of the History of Biology, Springer Verlag, 2006, vol. 39 (n° 2 (juill. 2006)), pp.281-308. hal-00175990 HAL Id: hal-00175990 https://hal.archives-ouvertes.fr/hal-00175990 Submitted on 3 Oct 2007 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Mendelism, plant breeding and experimental cultures: Agriculture and the development of genetics in France Christophe Bonneuil Centre Koyré d’Histoire des Sciences et des Techniques, CNRS, Paris and INRA-TSV 57 rue Cuvier. MNHN. 75005 Paris. France Journal of the History of Biology, vol. 39, no. 2 (juill. 2006), 281-308. This is an early version; please refer to the original publication for quotations, photos, and original pagination Abstract The article reevaluates the reception of Mendelism in France, and more generally considers the complex relationship between Mendelism and plant breeding in the first half on the twentieth century. It shows on the one side that agricultural research and higher education institutions have played a key role in the development and institutionalization of genetics in France, whereas university biologists remained reluctant to accept this approach on heredity. -
The Role of Mutation Bias in Adaptive Molecular Evolution: Insights from 2 Convergent Changes in Protein Function 3
bioRxiv preprint doi: https://doi.org/10.1101/580175; this version posted March 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 1 The role of mutation bias in adaptive molecular evolution: insights from 2 convergent changes in protein function 3 4 5 Jay F. Storz1*, Chandrasekhar Natarajan1, Anthony V. Signore1, Christopher C. Witt2,3, David M. 6 McCandlish4, Arlin Stoltzfus5* 7 8 1School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 9 2Department of Biology, University of New Mexico, Albuquerque, NM 87131 10 3Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131 11 4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724 12 5Office of Data and Informatics, Material Measurement Laboratory, NIST, and Institute for Bioscience 13 and Biotechnology Research, Rockville, MD 20850 14 15 *Corresponding authors: Jay F. Storz ([email protected]), Arlin Stoltzfus ([email protected]) 16 17 18 Abstract 19 An underexplored question in evolutionary genetics concerns the extent to which mutational bias in the 20 production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the 21 genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG 22 dinucleotides: If the DNA nucleotide cytosine (C) is immediately 5’ to guanine (G) on the same coding 23 strand, then – depending on methylation status – point mutations at both sites occur at an elevated rate 24 relative to mutations at non-CpG sites. -
Explanatory Unification and the Early Synthesis 597
Brit. J. Phil. Sci. 56 (2005), 595–609 Explanatory Unification and the Early Synthesis Anya Plutynski ABSTRACT The object of this paper is to reply to Morrison’s ([2000]) claim that while ‘structural unity’ was achieved at the level of the mathematical models of population genetics in the early synthesis, there was explanatory disunity. I argue to the contrary, that the early synthesis effected by the founders of theoretical population genetics was unifying and explanatory both. Defending this requires a reconsideration of Morrison’s notion of explanation. In Morrison’s view, all and only answers to ‘why’ questions which include the ‘cause or mechanism’ for some phenomenon count as explanatory. In my view, mathematical demonstrations that answer ‘how possibly’ and ‘why necessarily’ ques- tions may also count as explanatory. The authors of the synthesis explained how evolution was possible on a Mendelian system of inheritance, answered skepticism about the sufficiency of selection, and thus explained why and how a Darwinian research program was warranted. While today we take many of these claims as obvious, they required argument, and part of the explanatory work of the formal sciences is providing such arguments. Surely, Fisher and Wright had competing views as to the optimal means of generating adaptation. Nevertheless, they had common opponents and a common unifying and explanatory goal that their mathematical demonstrations served. 1 Introduction: Morrison’s challenge 2 Fisher v. Wright revisited 3 The early synthesis 4 Conclusion: unification and explanation reconciled 1 Introduction: Morrison’s challenge Morrison ([2000]) has recently argued that unification and explanation are often at odds in science. -
Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology Anna Hiatt
Bryn Mawr College Scholarship, Research, and Creative Work at Bryn Mawr College Biology Faculty Research and Scholarship Biology 2013 Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology Anna Hiatt Gregory K. Davis Bryn Mawr College, [email protected] Caleb Trujillo Mark Terry Donald P. French See next page for additional authors Let us know how access to this document benefits ouy . Follow this and additional works at: http://repository.brynmawr.edu/bio_pubs Part of the Biology Commons Custom Citation Hiatt A, Davis GK, Trujillo C, Terry M, French DP, Price RM and Perez KE . "Getting to evo-devo: concepts and challenges for students learning evolutionary developmental biology". CBE-Life Sciences Education 12 (2013): 494-508. This paper is posted at Scholarship, Research, and Creative Work at Bryn Mawr College. http://repository.brynmawr.edu/bio_pubs/10 For more information, please contact [email protected]. Authors Anna Hiatt, Gregory K. Davis, Caleb Trujillo, Mark Terry, Donald P. French, Rebecca M. Price, and Kathryn E. Perez This article is available at Scholarship, Research, and Creative Work at Bryn Mawr College: http://repository.brynmawr.edu/ bio_pubs/10 CBE—Life Sciences Education Vol. 12, 494–508, Fall 2013 Article Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology Anna Hiatt,*† Gregory K. Davis,‡ Caleb Trujillo,§ Mark Terry, Donald P. French,* Rebecca M. Price,¶ and Kathryn E. Perez** *Department of Zoology, Oklahoma -
Chapter 2: Why Would We Call for a New Evolutionary Synthesis? the Variation Issue and the Explanatory Alternatives
Chapter 2: Why would we call for a new evolutionary synthesis? The variation issue and the explanatory alternatives. Philippe Huneman It is pervasively claimed that the framework of evolutionary theory, the Modern Synthesis (MS), which has been built between the 1930s and the 1950s through the synthesis of Mendelian genetics and Darwinian theory, has to be deeply revised, changed, “extended” (Pigliucci and Muller 2011, Odling-Smee Laland and Feldman 2003, Danchin et al 2011) or “expanded” (Gould 2002). Empirical and conceptual reasons are supposedly converging to support such a move. Supporters of a new Synthesis (e.g. Gilbert, Opitz and Raff 1996, Pigliucci and Muller 2011, Odling-Smee Laland and Feldman 2003, Danchin et al 2011, Jablonka and Lamb 2005, Oyama, Griffiths and Gray 2001 etc.) may disagree on many things but they generally think that the Modern Synthesis, as a scientific theory through which explanations for biological phylogeny, adaptation and diversity should be sought, gave too much importance to natural selection or that its focus on genes, exemplified by the textbook definition of evolution as a change in genotypic frequencies, was exaggerate. In this paper I pose the question what kind of empirical findings would be likely to force a dramatic theoretical change, meaning that the core claims of MS regarding natural selection and genetics. I will focus on one strain of critiques, that targeted the explanatory weight of natural selection as selection for the fittest traits (provided that variant traits arise by mutation and recombination). I will distinguish several critiques, according to their content and to the strength of the challenge: whereas some challenges necessitate a complete rethinking of the core concepts of evolutionary theory, others are solved by adding or amending the main concepts or modeling assumptions. -
Statement About Pnas Paper “The New Mutation Theory of Phenotypic Evolution”
July 30, 2007 (revised) Brief Historical Perspectives of the Paper “THE NEW MUTATION THEORY OF PHENOTYPIC EVOLUTION” Proceedings of the National Academy of Sciences, USA, 104:12235-12242, Published July 17, 2007 online. Masatoshi Nei The following is the author’s account of the history of development of the mutation theory of phenotypic evolution and related matters. Darwinism (1) Charles Darwin proposed that evolution occurs by natural selection in the presence of fluctuating variation. (2) At his time, the mechanism of generation of new variation was not known, and he assumed that new variation is generated by climatic changes, inheritance of acquired characters, spontaneous variations, etc. However, he believed that new variation occurs in random direction and evolutionary change is caused by natural selection. (3) He assumed that enormous phenotypic diversity among different phyla and classes is the result of accumulation of gradual evolution by natural selection. Saltationism Several biologists such as Thomas Huxley, William Bateson, and Hugo de Vries argued that the extent of variation between species is much greater than that within 1 species and therefore saltational or macromutational change is necessary to form new species rather than gradual evolution as proposed by Darwin. In this view a new species can be produced by a single macromutation, and therefore natural selection is unimportant. This view was strengthened when de Vries discovered several new forms of evening primroses which were very different from the parental species (Oenothera lamarckiana) and appeared to be new species. This discovery suggested that new species can arise by a single step of macromutation. However, it was later shown that O.