Why We Don't Want Another "Synthesis"
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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. -
Natural Necessity Natural Selection
NATURAL SELECTION NATURAL NECESSITY See Laws of Nature NATURAL SELECTION In modern evolutionary biology, a set of objects is Adaptationism said to experience a selection process precisely when At the close of his introduction to those objects vary in/itness (see Fitness). For exam On the Origin oj' ple, if zebras that run fast are fitter than zehras that Species, Darwin [1859] 1964, 6 says that natural selection is "the main but not the exclusive" cause run slow (perhaps because faster zebras are better ofevolution. In reaction to misinterpretations ofhis able to avoid lion predation), a selection process is theory, Darwin felt compelled to reemphasize, in the set in motion. If the trait that exhibits variation hook's last edition, that there was more to evolution in fit~ess is heritable-meaning, in our example, that faster parents tend to have faster offspring than natural selection. It remains a matter of con troversy in evolutionary biology how important and slower parents tend to have slower offspring then the selection process is apt to chancre trait natural selection has been in the history of life. frequencies in the population, leading fitte';. traits This is the poinl of biological substance that pres to increase in frequency and less fit traits to decline ently divides adaptationists and anti-adaptationists. The debate over adaptationism also has a separate (Lewontin 1970). This change is the one that selec tion is "apt" to engender, rather than the one that methodological dimension, with critics insisting that adaptive hypotheses be tested more rigorously must occur, because evolutionary theory describes <Gould and Lewontin 1979; Sober 1993). -
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 Evolution of Universal Adaptations of Life Is Driven by Universal Properties of Matter: Energy, Entropy, and Interaction [Version 2; Peer Review: 3 Approved]
F1000Research 2020, 9:626 Last updated: 23 SEP 2021 OPINION ARTICLE The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction [version 2; peer review: 3 approved] Irun R. Cohen 1, Assaf Marron 2 1Department of Immunology, Weizmann Institute of Science, Rehovot, 76100, Israel 2Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel v2 First published: 18 Jun 2020, 9:626 Open Peer Review https://doi.org/10.12688/f1000research.24447.1 Second version: 30 Jul 2020, 9:626 https://doi.org/10.12688/f1000research.24447.2 Reviewer Status Latest published: 02 Sep 2020, 9:626 https://doi.org/10.12688/f1000research.24447.3 Invited Reviewers 1 2 3 Abstract The evolution of multicellular eukaryotes expresses two sorts of version 3 adaptations: local adaptations like fur or feathers, which characterize (revision) species in particular environments, and universal adaptations like 02 Sep 2020 microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms version 2 driving the universal adaptations of multicellulars should themselves (revision) report report be universal, and propose a mechanism based on properties of matter 30 Jul 2020 and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. version 1 Metabolic networks channel some of this energy to form cooperating, 18 Jun 2020 report report interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it 1. -
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. -
Mimicry, Saltational Evolution, and the Crossing of Fitness Valleys
CHAPTER 16 Mimicry, Saltational Evolution, and the Crossing of Fitness Valleys Olof Leimar, Birgitta S. Tullberg, and James Mallet 16.1 Introduction saltationism. In terms of Adaptive Landscapes, if the mimic-to-be resides on one adaptive peak and The relative contribution of gradual and saltational the model on another, mimicry evolves in a single change to evolution has been debated ever since mutational leap, and the issue of natural selection Darwin (1859) emphasized gradualism in his the- only enters through the constraint that the peak ory of evolution by natural selection. The phe- jumped to should be higher than the starting peak. nomenon of mimicry was an important example This would apply both to Müllerian mimicry, where in this debate. In mimicry evolution, members of the starting point is an aposematic species, and to a population or species become similar in appear- Batesian mimicry, where the starting adaptive peak ance to an aposematic model species and thereby of the palatable mimic-to-be is determined by func- gain increased protection from predation. The num- tions other than aposematism, for instance crypsis ber of steps in the approach to mimicry could be or other protective coloration, like flash coloration few or many and their sizes either large or small. (Cott 1940; Ruxton et al. 2004), or partner choice. In 1915, Punnett published an influential book on In response to claims like those by Punnett (1915), mimicry in butterflies, in which he summed up and as part of his efforts to unify gradualism and his strong opposition to gradualistic accounts of Mendelian genetics, Fisher (1927, 1930) presented mimicry evolution. -
The Origin of Historical Kinds in Biology and Culture Günter P. Wagne
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 24 April 2019 doi:10.20944/preprints201904.0266.v1 Extending the Explanatory Scope of Evolutionary Theory: The Origin of Historical Kinds in Biology and Culture Günter P. Wagner and Gary Tomlinson Yale University Abstract Since its inception, evolutionary theory has experienced a number of extensions. The most important of these took the forms of the Modern Evolutionary Synthesis (MES), embracing genetics and population biology in the early 20th century, and the Extended Evolutionary Synthesis (EES) of the last thirty years, embracing, among other factors, non-genetic forms of inheritance. While we appreciate the motivation for this recent extension, we argue that it does not go far enough, since it restricts itself to widening explanations of adaptation by adding mechanisms of inheritance and variation. A more thoroughgoing extension is needed, one that widens the explanatory scope of evolutionary theory. In addition to adaptation and its various mechanisms, evolutionary theory must recognize as a distinct intellectual challenge the origin of what we call “historical kinds.” Under historical kinds we include any process that acquires a quasi-independent and traceable lineage-history in biological and cultural evolution. We develop the notion of a historical kind in a series of paradigmatic exemplars, from genes and homologues to rituals and music, and we propose a preliminary characterization. Keywords: historical individuals, extended evolutionary synthesis, evolutionary innovation, culture 1. Introduction For the last several decades, a set of concerns has exerted increasing pressure on the modern evolutionary synthesis (MES) of the mid-twentieth century, with the goal of widening the explanatory powers of evolutionary theory. -
Soft Inheritance: Challenging the Modern Synthesis
Genetics and Molecular Biology, 31, 2, 389-395 (2008) Copyright © 2008, Sociedade Brasileira de Genética. Printed in Brazil www.sbg.org.br Review Article Soft inheritance: Challenging the Modern Synthesis Eva Jablonka1 and Marion J. Lamb2 1The Cohn Institute for the History and Philosophy of Science and Ideas, Tel-Aviv University, Tel-Aviv, Israel. 211 Fernwood, Clarence Road, London, United Kingdom. Abstract This paper presents some of the recent challenges to the Modern Synthesis of evolutionary theory, which has domi- nated evolutionary thinking for the last sixty years. The focus of the paper is the challenge of soft inheritance - the idea that variations that arise during development can be inherited. There is ample evidence showing that phenotypic variations that are independent of variations in DNA sequence, and targeted DNA changes that are guided by epigenetic control systems, are important sources of hereditary variation, and hence can contribute to evolutionary changes. Furthermore, under certain conditions, the mechanisms underlying epigenetic inheritance can also lead to saltational changes that reorganize the epigenome. These discoveries are clearly incompatible with the tenets of the Modern Synthesis, which denied any significant role for Lamarckian and saltational processes. In view of the data that support soft inheritance, as well as other challenges to the Modern Synthesis, it is concluded that that synthesis no longer offers a satisfactory theoretical framework for evolutionary biology. Key words: epigenetic inheritance, hereditary variation, Lamarckism, macroevolution, microevolution. Received: March 18, 2008; Accepted: March 19, 2008. Introduction 1. Heredity occurs through the transmission of germ- There are winds of change in evolutionary biology, line genes. -
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.