What Evolvability Really Is
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
Evolving Neural Networks That Are Both Modular and Regular: Hyperneat Plus the Connection Cost Technique Joost Huizinga, Jean-Baptiste Mouret, Jeff Clune
Evolving Neural Networks That Are Both Modular and Regular: HyperNeat Plus the Connection Cost Technique Joost Huizinga, Jean-Baptiste Mouret, Jeff Clune To cite this version: Joost Huizinga, Jean-Baptiste Mouret, Jeff Clune. Evolving Neural Networks That Are Both Modular and Regular: HyperNeat Plus the Connection Cost Technique. GECCO ’14: Proceedings of the 2014 Annual Conference on Genetic and Evolutionary Computation, ACM, 2014, Vancouver, Canada. pp.697-704. hal-01300699 HAL Id: hal-01300699 https://hal.archives-ouvertes.fr/hal-01300699 Submitted on 11 Apr 2016 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. To appear in: Proceedings of the Genetic and Evolutionary Computation Conference. 2014 Evolving Neural Networks That Are Both Modular and Regular: HyperNeat Plus the Connection Cost Technique Joost Huizinga Jean-Baptiste Mouret Jeff Clune Evolving AI Lab ISIR, Université Pierre et Evolving AI Lab Department of Computer Marie Curie-Paris 6 Department of Computer Science CNRS UMR 7222 Science University of Wyoming Paris, France University of Wyoming [email protected] [email protected] [email protected] ABSTRACT 1. INTRODUCTION One of humanity’s grand scientific challenges is to create ar- An open and ambitious question in the field of evolution- tificially intelligent robots that rival natural animals in intel- ary robotics is how to produce robots that possess the intel- ligence and agility. -
High Heritability of Telomere Length, but Low Evolvability, and No Significant
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.16.423128; this version posted December 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 High heritability of telomere length, but low evolvability, and no significant 2 heritability of telomere shortening in wild jackdaws 3 4 Christina Bauch1*, Jelle J. Boonekamp1,2, Peter Korsten3, Ellis Mulder1, Simon Verhulst1 5 6 Affiliations: 7 1 Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 8 9747AG Groningen, The Netherlands 9 2 present address: Institute of Biodiversity Animal Health & Comparative Medicine, College 10 of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United 11 Kingdom 12 3 Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, 13 Germany 14 15 16 * Correspondence to: 17 [email protected] 18 19 Running head: High heritability of telomere length bioRxiv preprint doi: https://doi.org/10.1101/2020.12.16.423128; this version posted December 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 20 Abstract 21 Telomere length (TL) and shortening rate predict survival in many organisms. Evolutionary 22 dynamics of TL in response to survival selection depend on the presence of genetic variation 23 that selection can act upon. However, the amount of standing genetic variation is poorly known 24 for both TL and TL shortening rate, and has not been studied for both traits in combination in 25 a wild vertebrate. -
Mating Patterns in a Hybrid Zone of Fire-Bellied Toads
Heredity (2005) 94, 247–257 & 2005 Nature Publishing Group All rights reserved 0018-067X/05 $30.00 www.nature.com/hdy Mating patterns in a hybrid zone of fire-bellied toads (Bombina): inferences from adult and full-sib genotypes BNu¨ rnberger1, NH Barton2, LEB Kruuk2 and TH Vines1,2,3 1Department Biologie II, Ludwig-Maximilians-Universita¨tMu¨nchen, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany; 2Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland We present two novel methods to infer mating patterns from The second approach is based solely on the offspring genetic data. They differ from existing statistical methods of genotypes and relies on the fact that a linear relation exists parentage inference in that they apply to populations that between associations among the offspring and those in the deviate from Hardy–Weinberg and linkage equilibrium, and population of breeding pairs. We apply both methods to a so are suited for the study of assortative mating in hybrid sample from the hybrid zone between the fire-bellied toads zones. The core data set consists of genotypes at several Bombina bombina and B. variegata (Anura: Disco glossidae) loci for a number of full-sib clutches of unknown parentage. in Croatia. Consistently, both approaches provide no Our inference is based throughout on estimates of allelic evidence for a departure from random mating, despite associations within and across loci, such as heterozygote adequate statistical power. Instead, B. variegata-like indivi- deficit and pairwise linkage disequilibrium. In the first duals among the adults contributed disproportionately to the method, the most likely parents of a given clutch are offspring cohort, consistent with their preference for the type determined from the genotypic distribution of the associated of breeding habitat in which this study was conducted. -
12 Evolvability of Real Functions
i i i i Evolvability of Real Functions PAUL VALIANT , Brown University We formulate a notion of evolvability for functions with domain and range that are real-valued vectors, a compelling way of expressing many natural biological processes. We show that linear and fixed-degree polynomial functions are evolvable in the following dually-robust sense: There is a single evolution algorithm that, for all convex loss functions, converges for all distributions. It is possible that such dually-robust results can be achieved by simpler and more-natural evolution algorithms. Towards this end, we introduce a simple and natural algorithm that we call wide-scale random noise and prove a corresponding result for the L2 metric. We conjecture that the algorithm works for a more general class of metrics. 12 Categories and Subject Descriptors: F.1.1 [Computation by Abstract Devices]: Models of Computa- tion—Self-modifying machines; G.1.6 [Numerical Analysis]: Optimization—Convex programming; I.2.6 [Artificial Intelligence]: Learning—Concept learning;J.3[Computer Applications]: Life and Medical Sciences—Biology and genetics General Terms: Algorithms, Theory Additional Key Words and Phrases: Evolvability, optimization ACM Reference Format: Valiant, P. 2014. Evolvability of real functions. ACM Trans. Comput. Theory 6, 3, Article 12 (July 2014), 19 pages. DOI:http://dx.doi.org/10.1145/2633598 1. INTRODUCTION Since Darwin first assembled the empirical facts that pointed to evolution as the source of the hugely diverse and yet finely honed mechanisms of life, there has been the mys- tery of how the biochemical mechanisms of evolution (indeed, how any mechanism) can apparently consistently succeed at finding innovative solutions to the unexpected problems of life. -
3718 Issue63july2010 1.Pdf
Issue 63.qxd:Genetic Society News 1/10/10 14:41 Page 1 JULYJULLYY 2010 | ISSUEISSUE 63 GENETICSGENNETICSS SOCIETYSOCIEETY NENEWSEWS In this issue The Genetics Society NewsNewws is edited by U Genetics Society PresidentPresident Honoured Honoured ProfProf David Hosken and items ittems for future future issues can be sent to thee editor,editor, preferably preferably U Mouse Genetics Meeting by email to [email protected],D.J.Hosken@@exeter.ac.uk, or U SponsoredSponsored Meetings Meetings hardhard copy to Chair in Evolutionary Evoolutionary Biology, Biology, UniversityUniversity of Exeter,Exeter, Cornwall Cornnwall Campus, U The JBS Haldane LectureLecture Tremough,Tremough, Penryn, TR10 0 9EZ UK.UK. The U Schools Evolutionn ConferenceConference Newsletter is published twicet a year,year, with copy dates of 1st June andand 26th November.November. U TaxiTaxi Drivers The British YeastYeaste Group Group descend on Oxford Oxford for their 2010 meeting: m see the reportreport on page 35. 3 Image © Georgina McLoughlin Issue 63.qxd:Genetic Society News 1/10/10 14:41 Page 2 A WORD FROM THE EDITOR A word from the editor Welcome to issue 63. In this issue we announce a UK is recognised with the award of a CBE in the new Genetics Society Prize to Queen’s Birthday Honours, tells us about one of Welcome to my last issue as join the medals and lectures we her favourite papers by Susan Lindquist, the 2010 editor of the Genetics Society award. The JBS Haldane Mendel Lecturer. Somewhat unusually we have a News, after 3 years in the hot Lecture will be awarded couple of Taxi Drivers in this issue – Brian and seat and a total of 8 years on annually to recognise Deborah Charlesworth are not so happy about the committee it is time to excellence in communicating the way that the print media deals with some move on before I really outstay aspects of genetics research to scientific issues and Chris Ponting bemoans the my welcome! It has been a the public. -
The University of Chicago Epistasis, Contingency, And
THE UNIVERSITY OF CHICAGO EPISTASIS, CONTINGENCY, AND EVOLVABILITY IN THE SEQUENCE SPACE OF ANCIENT PROTEINS A DISSERTATION SUBMITTED TO THE FACULTY OF THE DIVISION OF THE BIOLOGICAL SCIENCES AND THE PRITZKER SCHOOL OF MEDICINE IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN BIOCHEMISTRY AND MOLECULAR BIOPHYSICS BY TYLER NELSON STARR CHICAGO, ILLINOIS AUGUST 2018 Table of Contents List of Figures .................................................................................................................... iv List of Tables ..................................................................................................................... vi Acknowledgements ........................................................................................................... vii Abstract .............................................................................................................................. ix Chapter 1 Introduction ......................................................................................................1 1.1 Sequence space and protein evolution .............................................................1 1.2 Deep mutational scanning ................................................................................2 1.3 Epistasis ...........................................................................................................3 1.4 Chance and determinism ..................................................................................4 1.5 Evolvability ......................................................................................................6 -
DNA Evidence: Probability, Population Genetics, and the Courts David H
Penn State Law eLibrary Journal Articles Faculty Works 1993 DNA Evidence: Probability, Population Genetics, and the Courts David H. Kaye Penn State Law Follow this and additional works at: http://elibrary.law.psu.edu/fac_works Part of the Criminal Law Commons, Evidence Commons, and the Science and Technology Law Commons Recommended Citation David H. Kaye, DNA Evidence: Probability, Population Genetics, and the Courts, 7 Harv. J.L. & Tech. 101 (1993). This Article is brought to you for free and open access by the Faculty Works at Penn State Law eLibrary. It has been accepted for inclusion in Journal Articles by an authorized administrator of Penn State Law eLibrary. For more information, please contact [email protected]. Volume 7, Fall Issue, 1993 DNA EVIDENCE: PROBABILITY, POPULATION GENETICS, AND THE COURTS David H. Kaye* INTRODUCTION Courts, attorneys, scientists, statisticians, journalists, and government 4 agencies have been explaining,' examining, 2 promoting,3 proselytizing, denigrating,5 and otherwise struggling with DNA identification evidence at least since 1985.6 In the first wave of cases, expert testimony for the * Regents' Professor, Arizona State University College of Law, Box 877906, Tempe, AZ 85287-7906 (602 965-2922, [email protected]). A version of this paper was presented at the 1992 Joint Statistical Meetings of the American Statistical Association, the Biometric Society, and the Institute of Mathematical Statistics. I am grateful to Herman Cheroff for comments on that paper and to Colin Aitken, Richard Lempert, Bruce Weir, and especially Bernard Devlin for comments on later drafts. The errors that remain despite this guidance are entirely my own. -
Evolution Is a Quantitative Science
Book Review/Science in the Media Evolution Is a Quantitative Science John F. Y. Brookfield* Institute of Genetics, School of Biology, University of Nottingham, Nottingham, United Kingdom Evolutionary genetics is a mature field ing in evolutionary genetics must be of endeavour, and some of biology’s included in all bioinformatics and geno- greatest minds have contributed to the mics courses. Educators will find that theory of population genetics. Initially, foundation in Elements of Evolutionary Genet- they faced a problem, in that following the ics, by Brian and Deborah Charlesworth. rediscovery of Mendel’s results in the early This thorough and accurate textbook years of the 20th century, some saw an represents a remarkable achievement. The unbridgeable gulf between the sudden rigour of the approach is impeccable changes in appearance seen in the mutant throughout, and the text makes clear just forms of peas studied by Mendel, and the how many areas of biology, such as sex, gradual and subtle changes to evolving genome structure, migration and popula- populations envisaged by Darwin. The so- tion variation, and adaptive evolution called Neo-Darwinian synthesis linked itself, can be understood only through these ideas by considering the likely effect the application of formal models in which of Darwinian natural selection on varia- evolutionary processes are considered in a tions in Mendelian genes, variations which precise way. Most telling, however, is the would not necessarily have major effects consistently quantitative approach to data on organisms’ phenotypes. Unusually, for and their interpretation. While a full biology, this theory was developed, pri- appreciation of the book will require some marily by Fisher, Haldane and Wright, mathematical understanding, the steps prior to the existence of data sets to which required are clearly dealt with in appen- it could realistically be applied. -
Editor-In-Chief Professor Brian Charlesworth Editors Dr Joan
RSBL_8_1_cover.qxd 1/12/12 12:14 PM Page 2 Editor-in-Chief GUIDANCE FOR AUTHORS Professor Brian Charlesworth Selection criteria Editors Categories The criteria for selection are scientific excellence, originality and Papers published in Biology Letters will be categorised by subject, Dr Joan Herbers interest across disciplines within biology. Papers are assessed by the which include Editorial Board for suitability before full peer-review. Their Dr Paul Sniegowski • animal behaviour • marine biology recommendations are passed to the Editor. The Editor is responsible Publishing Editor for all editorial decisions and he makes these decisions based on the • biomechanics • molecular evolution Charlotte Wray reports received from the referees and the Editorial Board. • community ecology • neurobiology • conservation biology • palaeontology Editorial Board Publishing format • pathogen biology Biology Letters are published regularly online and in bimonthly print • evolutionary biology Brian Charlesworth, Editor-in-Chief Alex Kacelnik School of Biological Sciences, University of Edinburgh Department of Zoology, Oxford University issues. Along with all Royal Society journals, we are committed to • phylogeny Joan Herbers, Editor Laurent Keller • evolutionary developmental Department of Evolution, Ecology and Organismal Biology, Ohio State University Department of Ecology and Evolution, University of Lausanne archiving and providing perpetual access. Although the printed biology Paul Sniegowski, Editor Nicole King • physiology Department of Biology, University of Pennsylvania Department of Molecular and Cell Biology, University of California, Berkeley version of Biology Letters is limited to 2500 words, there is the Tom Little • genome biology • population ecology Leticia Avilés Institute of Evolutionary Biology, University of Edinburgh Department of Zoology, University of British Columbia Martine Maan facility for Electronic Supplementary Material (ESM). -
Reconciling Explanations for the Evolution of Evolvability
Reconciling Explanations for the Evolution of Evolvability Bryan Wilder and Kenneth O. Stanley To Appear In: Adaptive Behavior journal. London: SAGE, 2015. Abstract Evolution's ability to find innovative phenotypes is an important ingredient in the emergence of complexity in nature. A key factor in this capability is evolvability, or the propensity towards phenotypic variation. Numerous explanations for the origins of evolvability have been proposed, often differing in the role that they attribute to adaptive processes. To provide a new perspective on these explanations, experiments in this paper simulate evolution in gene regulatory networks, revealing that the type of evolvability in question significantly impacts the dynamics that follow. In particular, while adaptive processes result in evolvable individuals, processes that are either neutral or that explicitly encourage divergence result in evolvable populations. Furthermore, evolvability at the population level proves the most critical factor in the production of evolutionary innovations, suggesting that nonadaptive mechanisms are the most promising avenue for investigating and understanding evolvability. These results reconcile a large body of work across biology and inform attempts to reproduce evolvability in artificial settings. Keywords: Evolvability, evolutionary computation, gene regulatory networks Introduction Something about the structure of biological systems allows evolution to find new innovations. An important question is whether such evolvability (defined roughly as the propensity to introduce novel 1 phenotypic variation) is itself a product of selection. In essence, is evolvability evolvable (Pigliucci, 2008)? Much prior work has attempted to encourage evolvability in artificial systems in the hope of reproducing the open-ended dynamics of biological evolution (Reisinger & Miikkulainen, 2006; Grefenstette, 1999; Bedau et al., 2000; Channon, 2006; Spector, Klein, & Feinstein, 2007; Standish, 2003). -
Evolutionary Developmental Biology 573
EVOC20 29/08/2003 11:15 AM Page 572 Evolutionary 20 Developmental Biology volutionary developmental biology, now often known Eas “evo-devo,” is the study of the relation between evolution and development. The relation between evolution and development has been the subject of research for many years, and the chapter begins by looking at some classic ideas. However, the subject has been transformed in recent years as the genes that control development have begun to be identified. This chapter looks at how changes in these developmental genes, such as changes in their spatial or temporal expression in the embryo, are associated with changes in adult morphology. The origin of a set of genes controlling development may have opened up new and more flexible ways in which evolution could occur: life may have become more “evolvable.” EVOC20 29/08/2003 11:15 AM Page 573 CHAPTER 20 / Evolutionary Developmental Biology 573 20.1 Changes in development, and the genes controlling development, underlie morphological evolution Morphological structures, such as heads, legs, and tails, are produced in each individual organism by development. The organism begins life as a single cell. The organism grows by cell division, and the various cell types (bone cells, skin cells, and so on) are produced by differentiation within dividing cell lines. When one species evolves into Morphological evolution is driven another, with a changed morphological form, the developmental process must have by developmental evolution changed too. If the descendant species has longer legs, it is because the developmental process that produces legs has been accelerated, or extended over time.