<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <html> <head> <link href="https://bactra.org/plain-style.css" rel="stylesheet" type="text/css"> <title>Evolution (of Organisms)</title> </head> <body> <P> <P></P><!-- Access to MathJax through the version I'm hosting on bactra.org !--><!-- but only IF mathmode is activated via meta_mathmode !--> <script> window.MathJax = { tex: { inlineMath: [['$','$'], ['\\(','\\)']], processEscapes: true, autoload: { color: [], colorv2: ['color'] }, packages: {'[+]': ['noerrors']} }, options: { ignoreHtmlClass: 'tex2jax_ignore', processHtmlClass: 'tex2jax_process' }, loader: { load: ['[tex]/noerrors'] }};</script> <cite><a href="http://bactra.org/notebooks">Notebooks</a></cite> <div class="text"><div class="left"><h2>Evolution (of Organisms)</h2> <i><a href="faq.html#5.4">Last update</a>: 21 Apr 2025 21:17</i><br><i><a href="faq.html#5.4">First version</a>: </i> <hr> <P> <P>[A proper discussion of evolution will appear here Any Year Now.] <P><em>Issues in evolution proper</em>: <a href="adaptation.html">adaptation</A>; <a href="complexity.html">complexity</A>; <a href="evo-devo.html">developmental constraints and the evolution of development</A>; <a href="ecology.html">ecology</A> and co-evolution; <a href="evol-game-theory.html">game theory</a>; genetics; sociobiology (in non-human beasties; in human beings, and what exactlyit can and cannot account for); units of selection controversies (genes [Dawkins, Maynard Smith,Williams] vs. gene-complexes [Lewontin, sorta] vs. organisms [Williams thefirst time around] vs. groups [Sober?]) and group-selection arguments (whencan traits which benefit a higher level of selection at the expense of thelower ones evolve? Probably never; the higher level entities don't have enoughcoherence and persistence to act as replicators). <P><em>Query</em>: What is known about the asymptotic distribution of thepopulation under (discrete-time) replicator dynamics? What if the space oftypes in the replicator dynamics is infinite-dimensional? Or the fitnessfunction is subject to stochastic shocks? Or both? (This now has<a href="asymptotics-infinite-stochastic-dyn-sys.html">its own notebook.</a>) <P><em><a href="darwin-machines.html">Extensions of evolution</A></em>: to <a href="seriatim.html">brain function</A>; to <a href="evol-comp.html">computer programming </a>; to <a href="memes.html">culture</A> (memetics); to <a href="evol-econ.html">economics</A>; to <a href="evol-epistem.html">epistemology</A>; to <a href="evol-psych.html">psychology</A>. <P><em>Mathematical modeling</em>: <a href="population-genetics.html">classical population genetics</a> <em>àla</em> Fisher, Haldane and Wright, and its extensions via <ahref="chaos.html">dynamics</A>; <a href="evol-game-theory.html">game theory</a> <em>à la</em> John MaynardSmith. <a href="physical-biology.html">Connections to physics</a>.<a href="agent-based-modeling.html">Agent-based modeling</a>. <P><em>Challenges to neo-Darwinism</em>: Here, as usual, my inclinations areconservative, in that I really don't see what's wrong with the orthodox theory.In any case, there don't seem to be any <em>real</em> alternatives yetadvanced. (Neutral mutations by definition explain the origins of neitheradaptations nor species.) <ul>Recommended, non-technical: <li><a href="dawkins.html">Richard Dawkins</A> <ul> <li><cite>The Blind Watchmaker</cite> <li><cite>Climbing Mount Improbable</cite> <li><cite>The Selfish Gene</cite> </ul> <li><a href="dennett.html">Daniel Dennett</A>, <cite>Darwin's DangerousIdea</cite> <li>Theodosius Dobzhansky, "<ahref="http://www.2think.org/dobzhansky.shtml">Nothing in Biology Makes SenseExcept in the Light of Evolution</a>" [first pub. <cite>American BiologyTeacher</cite> <strong>35</strong> (March 1973): 125--129] <li>Stephen Jay Gould, anything. [But be warned that a lot of what hesays about the Burgess Shale fauna in <cite>Wonderful Life</cite> is disputed--- by his own sources...] <li>John Maynard Smith [As a god to population genetics; disciple ofHaldane] <ul> <li><cite>The Theory of Evolution</cite> [An introductory bookwhich avoids getting tangled up in technical details without sacrificingintellectual rigor or pushing any really strange ideas] <li>and Eörs Szathmáry, <cite>The Origins of Life:From the Birth of Life to the Origin of Language</cite> [<ahref="http://bactra.org/reviews/origins-of-life/">Review: <cite>Major Transitions</cite>Minor</a>] </ul> <li>Jacques Monod, <cite>Chance and Necessity</cite> [<ahref="http://dannyreviews.com/h/Chance_and_Necessity.html">Review by DannyYee</a>] <li>Karl Sigmund, <cite>Games of Life: Explorations in Ecology,Evolution and Behavior</cite> <li><a href="news:talk.origins">talk.origins</A> is where Usenet hashesout creation vs. evolution. (It should be pretty obvious that I am on the sideof the apes.) There's a fine <a href="http://www.talkorigins.org/">website</A>with archives of posts to the newsgroups, the excellent <AHREF="http://www.talkorigins.org/origins/faqs-qa.html">FAQs</A> (read 'embefore attempting to convert the heathen), a nifty <AHREF="http://www.talkorigins.org/origins/fossil-images.html">gallery offossils</A> and the <a href="http://www.ediacara.org/">University ofEdicara</A> <li>Bruce Wallace and Adrian M. Srb, <cite>Adaptation</cite> <li>Jonathan Weiner, <cite>The Beak of the Finch</cite> [Fieldconfirmation of neo-Darwinism, from, nicely enough, the Galapagos. (Pleasedon't start an argument about what it means to confirm a scientific theoryhere.)] </ul> <ul>Recommended, close-ups, non-technical: <li><a href="j-t-bonner.html">John Tyler Bonner</A> <ul> <li><cite>On Development</cite> [Points out that it's a mistaketo think of just the adult form-and-behavior "evolving"; it's really the<em>whole life-cycle,</em> complicating matters considerably...] <li><cite>On the Evolution of Complexity, by Means of NaturalSelection</cite> [<a href="http://bactra.org/reviews/evolution-of-complexity/">Review</A>] </ul> <li>François Jacob, <cite>The Possible and the Actual</cite> [Ireally must get around to typing up my notes from his lecture on conserved genesequences] <li>Charles H. Lineweaver, "Paleontological Tests: Human-likeIntelligence is not a Convergent Feature ofEvolution", <a href="http://arxiv.org/abs/0711.1751">arxiv:0711.1751</a> [Avery nice, and simple, way to see the error of some common ways of looking atevolution] <li>John Maynard Smith, <cite>Did Darwin Get It Right? Essays on Games, Sex, and Evolution</cite> <li>Edmund Russell, <cite><a href="http://bactra.org/weblog/algae-2019-12.html#russell">Evolutionary History: Uniting History and Biology to Understand Life on Earth</a></cite> <li>Homer W. Smith, <cite>Kamongo, or, The Lungfish and thePadre</cite> </ul> <ul>Recommended, technical, big picture: <li>John H. Gillespie, <cite>Population Genetics: A ConciseGuide</cite> [<a href="http://bactra.org/reviews/gillespie-pop-gen/">Review: Darwin'sEquations (II)</a>] <li>Peter Godfrey-Smith, <cite>Darwinian Populations andNatural Selection</cite> <li>Josef Hofbauer and Karl Sigmund, <cite>The Theory of Evolution andDynamical Systems: Mathematical Aspects of Selection</cite> <li><a href="john-holland.html">John Holland</a>, <cite><AHREF="evol-comp.html">Adaptation in Natural and Artificial Systems</A></cite> <li>John Maynard Smith, <cite>Evolution and the Theory of Games</cite> [<ahref="http://dannyreviews.com/h/Evolution_and_the_Theory_of_Games.html">Reviewby Danny Yee</a>] </ul> <ul>Recommended, technical, close-ups: <li>Lauren W. Ancel and Walter Fontana, "Plasticity, Evolvability andModularity in RNA," <cite>Journal of Experimental Zoology (Molecular andDevelopmental Evolution),</cite> <strong>288</strong> (2000): 242--283 [<ahref="http://www.santafe.edu/~ancel/PAPERS/jez_plasticity.pdf">Reprint</a>] <li>Richard K. Belew and Melanie Mitchell (eds.), <cite>AdaptiveIndividuals in Evolving Populations: Models and Algorithms</cite> <li>Carl T. Bergstrom and Michael Lachmann, "The fitness value ofinformation", <ahref="http://arxiv.org/abs/q-bio.PE/0510007">q-bio.PE/0510007</a> <li><a href="dawkins.html">Richard Dawkins</A>, <cite>The ExtendedPhenotype</cite> [<a href="http://bactra.org/reviews/extended-phenotype">Review: <em>Not</em>Your Parents' Web of Life</a>] <li>Laura F. Galloway and Julie R. Etterson, "TransgenerationalPlasticity Is Adaptive in the Wild", <ahref="http://dx.doi.org/10.1126/science.1148766"><cite>Science</cite> <strong>318</strong>(2007): 1134--1136</a> <li>Paul H. Harvey and Mark D. Pagel, <cite>The Comparative Method inEvolutionary Biology</cite> [<a href="http://bactra.org/reviews/harvey-pagel/">Review: On theUses of Knowing Where Birds and Bees Come From</a>] <li>David Hull, <cite>Science and Selection: Essays on BiologicalEvolution and Philosophy of Science</cite> <li>Philip Kitcher, <citE>In Mendel's Mirror: Philosophical Reflections on Biology</cite> <li>R. C. Lewontin, <cite>The Genetic Basis of EvolutionaryChange</cite> [An excellent book; but <cite>TheDialectical Biologist</cite> may be safely ignored] <li>C. M. Newman, J. E. Cohen and C. Kipnis, "Neo-darwinian evolution implies punctuated equilibria", <a href="https://doi.org/10.1038/315400a0"><cite>Nature</cite> <strong>315</strong> (1985): 400--401</a> <li>Mark E. J. Newman <ul> <li>"Simple Models of Evolution and Extinction," <ahref="http://arxiv.org/abs/adap-org/9910003">adap-org/9910003</a> <li>MEJN and Gunther J. Eble, "Decline in Extinction Rates andSelf-Similarity in the Fossil Record," <cite>Paleobiology</cite><Strong>25</strong> (1999): 434--439 = <ahref="http://arxiv.org/abs/adap-org/9809004">adap-org/9809004</a> <li>MEJN and Richard G. Palmer, "Models of Extinction: AReview," <a href="http://arxiv.org/abs/adap-org/9908002">adap-org/9908002</a> </ul> <li>Mark Pagel, "Inferring the Historical Patterns of BiologicalEvolution," <cite>Nature</cite> <strong>401</strong> (1999): 877--884[Warning: This paper makes the staggering mistake of confusing likelihood(probability of a model's generating results like the data) with posteriorprobability (probability of the model, given the data). Pagel definitelydoesn't make this elementary blunder elsewhere; I dunno what happened here.] <li>David C. Queller, "The Spaniels of St. Marx and the PanglossianParadox: A Critique of a Rhetorical Programme," <cite>Quarterly Review ofBiology</cite> <strong>70</strong> (1995): 485--489 <li>Karl Sigmund, <cite>The Calculus of Selfishness</cite>[Review: <a href="http://bactra.org/reviews/calculus-of-selfishness.html">Honor AmongThieves</a>] <li>Olivier Rivoire and Stanislas Leibler, "The Value of Informationfor Populations in Varying Environments", <a href="http://arxiv.org/abs/1010.5092">arxiv:1010.5092</a> <li>George C. Willams, <cite>Adaptation and Natural Selection; aCritique of Some Current Evolutionary Thought</cite> [Well, current in 1966,anyway; that it is no longer current is due largerly to this book!] <li>Guoping Zhu, G. Brian Golding and Antony M. Dean, "The SelectiveCause of an Ancient Adaptation", <ahref="http://dx.doi.org/10.1126/science.1106974"><cite>Science</cite> <strong>307</strong>(2005): 1279--1282</a> [Where "ancient" means "about 3.5 billion years old".] </UL> <ul>Recommended, of historical interest: <li><a href="darwin.html">Charles Darwin</A>, <cite>On the Origin ofSpecies, by Means of Natural Selection, or Preservation of Favored Races in theStruggle for Life</cite> [Get the fascimile of the first edition with theintroduction by Ernst Mayr] <li>R. A. Fisher, <cite>The Genetical Theory of NaturalSelection</cite> <li>J. B. S. Haldane, <cite>The Causes of Evolution</cite> [<ahref="http://bactra.org/reviews/causes-of-evolution/">Review: Darwin's Equations</A>] <li>T. H. Huxley, <cite><a href="http://aleph0.clarku.edu/huxley/">TheHuxley File</a></cite> [Nearly complete works, ed. and put on-line by CharlesBlinderman and David Joyce] </ul> <ul>To read, histories of evolutionary thinking and science: <li>Stephen G. Alter, <cite><a href="http://jhupbooks.press.jhu.edu:80/ecom/MasterServlet/GetItemDetailsHandler?iN=9780801872440&qty=1&viewMode=3">Darwinism and the Linguistic Image: Language, Race, and Natural Theology in the Nineteenth Century</a></cite> <li>Peter Bowler, <cite>Evolution: The History of an Idea</cite> <li>Adrian Desmond, <cite>Huxley: From Devil's Disciple to Evolution'sHigh Priest</cite> <li>M. T. Ghiselin, <cite>The Triumph of the Darwinian Method</cite> </ul> <ul>To read, of historical interest: <li>Theodosius Dobzhansky <ul> <li><cite>Mankind Evolving: The Evolution of the HumanSpecies</cite> <li><cite>Genetics and the Origin of Species</cite> </ul> <li>G. Evelyn Hutchinson, <cite>The Ecological Theater and theEvolutionary Play</cite> <li>Konrad Lorenz, <cite>Evolution and Modification of Behavior</cite> </ul> <ul>To read, not otherwise or not yet classified: <li>Marshall Abrams, <cite><a href="https://press.uchicago.edu/ucp/books/book/chicago/E/bo195920308">Evolution and the Machinery of Chance: Philosophy, Probability, and Scientific Practice in Biology</a></cite> <li>P. Ao, "Mathematical Structure of Evolutionary Theory", <ahref="http://arxiv.org/abs/q-bio.QM/0403020">q-bio.QM/0403020</a> ["Here wepostulate three laws which form a mathematical framework to capture the essenceof Darwinian evolutionary dynamics. The second law is most quantitative and isexplicitly expressed by a unique form of stochastic differential equation."Color me skeptical, but I haven't read beyond the abstract.] <li>Wallace Arthur, <cite>Creatures of Accident: The Rise of theAnimal Kingdom</cite> <li>John C. Avise, <cite><a href="http://cambridge.org/9780521674171">Evolutionary Pathways in Nature: A Phylogenetic Approach</a></cite> <li>J. B. Beltman and P. Haccou, "Speciation through the learning ofhabitat features", <ahref="http://dx.doi.org/10.1016/j.tpb.2005.01.001"><cite>Theoretical PopulationBiology</cite> <strong>67</strong> (2005): 189--202</a> <li>Ioana Bena, Michel Droz and Andrzej Pekalski, "Complex populationdynamics as a competition between multiple time-scalephenomena", <ahref="http://arxiv.org/abs/q-bio.PE/0703033">q-bio.PE/0703033</a> <li>Carl T. Bergstrom and Rustom Antia, "How do adaptive immunesystems control pathogens while avoidingautoimmunity?", <ahref="http://dx.doi.org/10.1016/j.tree.2005.11.008"><cite>Trends in Ecology andEvolution</cite> <strong>21</strong> (2006): 22--28</a>[<ahref="http://octavia.zoology.washington.edu/disease/BergstromAndAntia06.pdf">PDFreprint</a> via Carl] <li>C. T. Bergstrom and M. Rosvall, "The transmission sense of information", <a href="http://arxiv.org/abs/0810.4168">arxiv:0810.4168</a> <li>Daniel R. Brooks and Deborah A. McLennan, <cite><ahref="http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/14753.ctl">The Nature ofDiversity: An Evolutionary Voyage of Discovery</a></cite> <li>Erick Chastain, Rustom Antia, Carl T. Bergstrom, "Defensive complexity and the phylogenetic conservation of immune control", <a href="http://arxiv.org/abs/1211.2878">arxiv:1211.2878</a> <li>Kim Christensen, Simone A. di Collobiano, Matt Hall, and HenrikJ. Jensen, "Tangled Nature: a model of evolutionary ecology," <ahref="http://arxiv.org/abs/cond-mat/0104116">cond-mat/0104116</a> <li>Dale H. Clayton, Sarah E. Bush and Kevin P. Johnson, <cite><a href="http://press.uchicago.edu/ucp/books/book/chicago/C/bo21515934">Coevolution of Life on Hosts: Integrating Ecology and History</a></cite> <li>Charles C. Cockell, <cite><a href="http://www.cambridge.org/0521817366">Impossible Extinction: Natural Catastrophes and the Supremacy of the Microbial World</a></cite> <li>Claude Combes, <cite>The Art of Being a Parasite</cite>[<a href="http://dannyreviews.com/h/Parasite.html">Review by Danny Yee</a>] <li>Vincent Courtillot, <cite><a href="http://www.cambridge.org/0521583926">Evolutionary Catastrophes: The Science of Mass Extinction</a></cite> <li>Depew and Weber, <cite>Darwinism Evolving: Systems Dynamics and theGenealogy of Evolution</cite> [Beware of genealogies which aren't actuallyabout families. <ahref="http://www.nybooks.com/articles/article-preview?article_id=1982">Review</a>by John Maynard Smith.] <li>Michael Doebli, <cite><a href="http://press.princeton.edu/titles/9484.html">Adaptive Diversification</a></cite> <li>Nikolay V. Dokholyan and Eugene I. Shakhnovich, "Understandinghierarchical protein evolution from first principles," <ahref="http://arxiv.org/abs/cond-mat/0104469">cond-mat/0104469</a> <li>Gunther Eble, "On the Dual Nature of Chance in Evolutionary Biology andPaleobiology," <ahref="http://www.santafe.edu/sfi/publications/Abstracts/98-09-085abs.html">SFIWorking Paper 98-09-085</a> <li>Manfred Eigen, <cite>The Hypercycle, a Principle of Natural Self-organization</cite> <li>David E. Fastovsky and David B. Weishampel, <cite><a href="http://www.cambridge.org/0521811724">The Evolution and Extinction of the Dinosaurs</a></cite> <li>A. Feigl, "Essential conditions for evolution of communicationwithin aspecies", <a href="http://dx.doi.org/10.1016/j.jtbi.2008.07.005"><cite>Journalof Theoretical Biology</cite><strong>254</strong> (2008): 768--778</a>, <a href="http://arxiv.org/abs/0803.0412">arxiv:0803.0412</a> <li> Luca Ferraro, Andrea Giansanti, Giovanni Giuliano and VittorioRosato, "Co-expression of statistically over-represented peptides in proteomes:a key to phylogeny?", <ahref="http://arxiv.org/abs/q-bio.MN/0410011">q-bio.MN/0410011</a> <li>Walter Fontana and Peter Schuster, "Continuity in Evolution: On theNature of Transitions," <ahref="http://www.santafe.edu/sfi/publications/Abstracts/98-04-030abs.html">SFIWorking Paper 98-04-030</a> <li>Barbara Forrest and Paul R. Gross, <cite>Creationism's TrojanHorse: The Wedge of Intelligent Design</cite> <li>Steven A. Frank, "Wright's adaptive landscape versus Fisher's fundamental theorem", <a href="http://arxiv.org/abs/1102.3709">arxiv:1102.3709</a> <li>Sergey Gavrilets, <cite>Fitness Landscapes and the Origin ofSpecies</cite> <li>Diane P. Genereuz and Carl T. Bergstrom, "Evolution in Action:Understanding antibiotic resistance" [forthcoming bookchapter] <li>Ulrich Gerland and Terence Hwa, "On the Selection and Evolution ofRegulatory DNA Motifs," <ahref="http://arxiv.org/abs/physics/0112039">physics/0112039</a> <li>Thomas J. Givnish and Kenneth J. Sytsma (eds.), <cite>MolecularEvolution and Adaptive Radiation</cite> <li>Stephen Jay Gould, <cite>The Structure of Evolutionary Theory</cite> <li>B. Rosemary Grant and Peter R. Grant, <cite>Evolutionary Dynamicsof a Natural Population: The Large Cactus Finch of the Galapagos</cite> <li>Dan Graur and William Martin, "Reading the entrails of chickens:molecular timescales of evolution and the illusion of precision",<cite>Trends in Genetics</cite> <strong>20</strong> (2004): 80--86[<ahref="http://www2.hawaii.edu/~khayes/Journal_Club/Journal_Club04/graurandmartin2004.pdf ">PDFreprint</a>] <li>Eva Jablonka and Marion J. Lamb, <cite><a href="http://mitpress.mit.edu/0262101076">Evolution in FourDimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in theHistory of Life</a></cite> <li>Ronald A. Jenner, <cite><a href="https://doi.org/10.1017/9781316226667">Ancestors in Evolutionary Biology: Linear Thinking about Branching Trees</a></cite> <li>Marc Kirschner and John Gerhart, <cite>The Plausibility ofLife</cite>[<a href="http://radio.weblogs.com/0100167/2005/12/26.html#a463">Capsule reviewby Frenando Pereira</a>] <li>Kevin N. Lala , Tobias Uller , Nathalie Feiner , Marcus Feldman and Scott F. Gilbert, <cite><a href="https://doi.org/10.1515/9780691262406">Evolution Evolving: The Developmental Origins of Adaptation and Biodiversity</a></cite> <li>Laura Landweber and Erik Winfree (ed.), <cite>Evolution asComputation</cite> [The dual subject to <a href="evol-comp.html">evolutionarycomputation</a>, as were] <li>Daniel J. Lawson and Henrik Jeldtoft Jensen, "Evolution asDiffusion in typespace", <a href="http://arxiv.org/abs/q-bio.PE/0609009">q-bio.PE/0609009</a> <li>George Levine, <cite><a href="https://www.jstor.org/stable/j.ctt7pgq4">Darwin Loves You: Natural Selection and the Re-Enchantment of the World</a></cite> <li>Elisabeth Lloyd, <cite>The Structure and Confirmation ofEvolutionary Theory</cite> <li>Long, <cite>Rise of the Fishes</cite> <li>David J. C. MacKay, "Rate of Information Acquisition by a Speciessubjected to Natural Selection" [<ahref="http://www.inference.phy.cam.ac.uk/mackay/Evolution.html">link</a>] <li>Joshua S. Madin, John Alroy, Martin Aberhan, Franz T. Fürsich,Wolfgang Kiessling, Matthew A. Kosnik, Peter J. Wagner, "StatisticalIndependence of Escalatory Ecological Trends in Phanerozoic MarineInvertebrates", <a href="http://dx.doi.org/10.1126/science.1123591"><cite>Science</cite> <strong>312</strong>(2006): 897--900</a> <li>Marc Mangel, <citE><a href="http://cambridge.org/9780521537483">The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology</a></cite> <li>Ernst Mayr <UL> <li><cite>Growth of Biological Thought</cite> <li><cite>Populations, Species and Evolution</cite> <li><cite>This Is Biology</cite> <li><cite>What Evolution Is</cite> </UL> <li>Margaret McFall-Ngai, "Adaptive Immunity: Care for the community",<ahref="http://dx.doi.org/10.1038/445153a"><cite>Nature</cite> <strong>445</strong>(2007): 153</a> <li>Géza Meszéna, Mats Gyllenberg, Frans J. Jacobs andJohan A. J. Metz, "Link between Population Dynamics and Dynamics of DarwinianEvolution",<a href="http://dx.doi.org/10.1103/PhysRevLett.95.078105"><cite>Physical ReviewLetters</cite> <strong>95</strong> (2005): 078105</a> <li>Richard E. Michod, <cite>Darwinian Dynamics: EvolutionaryTransitions in Fitness and Individuality</cite> <li>Stephen P. Miller, Mark Lunzer, and Antony M. Dean, "DirectDemonstration of an Adaptive Constraint", <a href="http://dx.doi.org/10.1126/science.1133479"><cite>Science</cite> <strong>314</strong> (2006):458--461</a> <li>Mitton, <cite>Selection in Natural Populations</cite> <li>Karl J. Niklas, <cite>The Evolutionary Biology of Plants</cite> [<ahref="http://dannyreviews.com/h/Plant_Evolution.html">Ringing endorsement</a>from Danny Yee --- "the most rewarding book on evolution I have read foryears."] <li>F. John Odling-Smee, Kevin N. Laland and Marcus W. Feldman, <cite><a href="https://www.jstor.org/stable/j.ctt24hqpd">Niche Construction: The Neglected Process in Evolution</a></cite> <li>Karen M. Page and Martin A. Nowak, "Unifying EvolutionaryDynamics", <a href="http://dx.doi.org/10.1006/jtbi.2002.3112"><cite>Journal ofTheoretical Biology</cite> <strong>219</strong> (2002): 93--98</a> [Thanksto David Krakauer] <li>John Pepper, "Relatedness in Trait Group Models of SocialEvolution," SFI Working Paper 00-07-034 <li>Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander J. Tans, "Empirical fitness landscapes reveal accessible evolutionary paths",<ahref="http://dx.doi.org/10.1038/nature05451"><cite>Nature</cite> <strong>445</strong>(2007): 383--386</a> <li>Angela Potochnik, "Optimality Modeling and Explanatory Generality",<a href="http://philsci-archive.pitt.edu/archive/00003011/">phil-sci/3011</a> <li>José M. Ranz and Carlos A. Machado, "Uncovering evolutionarypatterns of gene expression usingmicroarrays", <ahref="http://dx.doi.org/10.1016/j.tree.2005.09.002"><cite>Trends in Ecology andEvolution</cite> <strong>21</strong> (2006): 29--37</a> <li>Alex Rosenberg, <cite><ahref="http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/193615.ctl">Darwinian Reductionism: Or, How to Stop Worrying and Love Molecular Biology</a></cite> <li>Scott W. Roy and Walter Gilbert, "Complex early genes",<a href="http://dx.doi.org/10.1073/pnas.0408355101"><citE>Proceedings of theNational Academy of Sciences</cite> (USA) <strong>102</strong> (2005):1986--1991</a> <li>Paul Schmid-Hempel, <cite><a href="https://doi.org/10.1093/oso/9780198832140.001.0001">Evolutionary Parasitology: The Integrated Study of Infections, Immunology, Ecology, and Genetics</a></cite> <li>Veit Schämmle and E. Brigatti, "Speciational view ofmacroevolution: are micro and macroevolution decoupled?", <ahref="http://arxiv.org/abs/q-bio.PE/0509032">q-bio.PE/0509032</a> <li>William A. Searcy and Stephen Nowicki, <cite><a href="http://www.pupress.princeton.edu/titles/8110.html">The Evolution ofAnimal Communication: Reliability and Deception in Signaling Systems</a></cite> <li>Homer William Smith, <cite>From Fish to Philosopher</cite> [Anybook which is listed under both "Consciousness" and "Kidneys" in thelibrary of Congress classification is worth looking up] <li>Elliott Sober <ul> <li><cite>The Nature of Selection</cite> [<ahref="http://dannyreviews.com/h/The_Nature_of_Selection.html">Review by DannyYee</a>] <li><cite><a href="http://cambridge.org/9780521692748">Evidence and Evolution: The Logic Behind theScience</a></cite> </ul> <li>Ricard V. Solé, Isaac Salazar-Ciudad and JordiGarcia-Fernández, "Landscapes, Gene Networks and Pattern Formation: Onthe Cambrian Explosion," <ahref="http://www.santafe.edu/sfi/publications/Abstracts/00-08-046abs.html">SFIWorking Paper 00-08-046</a> <li>Stanley, <cite>Extinction</cite> <li>Jun Sun and Michael W. Deem, "Spontaneous Emergence of Modularityin a Model of Evolving Individuals", <ahref="http://dx.doi.org/10.1103/PhysRevLett.99.228107"><cite>Physical ReviewLetters</cite> <strong>99</strong> (2007): 228107</a> <li>Guido Tiana, Boris E. Shakhnovich, Nikolay V. Dokholyan and EugeneI. Shakhnovich, "Imprint of evolution on protein structures", <ahref="http://dx.doi.org/10.1073/pnas.0306638101"><cite>PNAS</cite><strong>101</strong> (2004): 2846--2851</a> <li>Daniel P. Todes, <cite>Darwin Without Malthus: The Struggle forExistence in Russian Evolutionary Thought</cite> <li>Annie E. Tsong, Brian B. Tuch, Hao Li and Alexander D. Johnson,Lines 1–500 of 554. Load more
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <html> <head> <link href="https://bactra.org/plain-style.css" rel="stylesheet" type="text/css"> <title>Evolution (of Organisms)</title> </head> <body> <P> <P></P><!-- Access to MathJax through the version I'm hosting on bactra.org !--> <!-- but only IF mathmode is activated via meta_mathmode !--> <script> window.MathJax = { tex: { inlineMath: [['$','$'], ['\\(','\\)']], processEscapes: true, autoload: { color: [], colorv2: ['color'] }, packages: {'[+]': ['noerrors']} }, options: { ignoreHtmlClass: 'tex2jax_ignore', processHtmlClass: 'tex2jax_process' }, loader: { load: ['[tex]/noerrors'] } }; </script> <cite><a href="http://bactra.org/notebooks">Notebooks</a></cite> <div class="text"> <div class="left"> <h2>Evolution (of Organisms)</h2> <i><a href="faq.html#5.4">Last update</a>: 21 Apr 2025 21:17</i> <br><i><a href="faq.html#5.4">First version</a>: </i> <hr> <P> <P>[A proper discussion of evolution will appear here Any Year Now.] <P><em>Issues in evolution proper</em>: <a href="adaptation.html">adaptation</A>; <a href="complexity.html">complexity</A>; <a href="evo-devo.html">developmental constraints and the evolution of development</A>; <a href="ecology.html">ecology</A> and co-evolution; <a href="evol-game-theory.html">game theory</a>; genetics; sociobiology (in non-human beasties; in human beings, and what exactly it can and cannot account for); units of selection controversies (genes [Dawkins, Maynard Smith, Williams] vs. gene-complexes [Lewontin, sorta] vs. organisms [Williams the first time around] vs. groups [Sober?]) and group-selection arguments (when can traits which benefit a higher level of selection at the expense of the lower ones evolve? Probably never; the higher level entities don't have enough coherence and persistence to act as replicators). <P><em>Query</em>: What is known about the asymptotic distribution of the population under (discrete-time) replicator dynamics? What if the space of types in the replicator dynamics is infinite-dimensional? Or the fitness function is subject to stochastic shocks? Or both? (This now has <a href="asymptotics-infinite-stochastic-dyn-sys.html">its own notebook.</a>) <P><em><a href="darwin-machines.html">Extensions of evolution</A></em>: to <a href="seriatim.html">brain function</A>; to <a href="evol-comp.html">computer programming </a>; to <a href="memes.html">culture</A> (memetics); to <a href="evol-econ.html">economics</A>; to <a href="evol-epistem.html">epistemology</A>; to <a href="evol-psych.html">psychology</A>. <P><em>Mathematical modeling</em>: <a href="population-genetics.html">classical population genetics</a> <em>à la</em> Fisher, Haldane and Wright, and its extensions via <a href="chaos.html">dynamics</A>; <a href="evol-game-theory.html">game theory</a> <em>à la</em> John Maynard Smith. <a href="physical-biology.html">Connections to physics</a>. <a href="agent-based-modeling.html">Agent-based modeling</a>. <P><em>Challenges to neo-Darwinism</em>: Here, as usual, my inclinations are conservative, in that I really don't see what's wrong with the orthodox theory. In any case, there don't seem to be any <em>real</em> alternatives yet advanced. (Neutral mutations by definition explain the origins of neither adaptations nor species.) <ul>Recommended, non-technical: <li><a href="dawkins.html">Richard Dawkins</A> <ul> <li><cite>The Blind Watchmaker</cite> <li><cite>Climbing Mount Improbable</cite> <li><cite>The Selfish Gene</cite> </ul> <li><a href="dennett.html">Daniel Dennett</A>, <cite>Darwin's Dangerous Idea</cite> <li>Theodosius Dobzhansky, "<a href="http://www.2think.org/dobzhansky.shtml">Nothing in Biology Makes Sense Except in the Light of Evolution</a>" [first pub. <cite>American Biology Teacher</cite> <strong>35</strong> (March 1973): 125--129] <li>Stephen Jay Gould, anything. [But be warned that a lot of what he says about the Burgess Shale fauna in <cite>Wonderful Life</cite> is disputed --- by his own sources...] <li>John Maynard Smith [As a god to population genetics; disciple of Haldane] <ul> <li><cite>The Theory of Evolution</cite> [An introductory book which avoids getting tangled up in technical details without sacrificing intellectual rigor or pushing any really strange ideas] <li>and Eörs Szathmáry, <cite>The Origins of Life: From the Birth of Life to the Origin of Language</cite> [<a href="http://bactra.org/reviews/origins-of-life/">Review: <cite>Major Transitions</cite> Minor</a>] </ul> <li>Jacques Monod, <cite>Chance and Necessity</cite> [<a href="http://dannyreviews.com/h/Chance_and_Necessity.html">Review by Danny Yee</a>] <li>Karl Sigmund, <cite>Games of Life: Explorations in Ecology, Evolution and Behavior</cite> <li><a href="news:talk.origins">talk.origins</A> is where Usenet hashes out creation vs. evolution. (It should be pretty obvious that I am on the side of the apes.) There's a fine <a href="http://www.talkorigins.org/">website</A> with archives of posts to the newsgroups, the excellent <A HREF="http://www.talkorigins.org/origins/faqs-qa.html">FAQs</A> (read 'em before attempting to convert the heathen), a nifty <A HREF="http://www.talkorigins.org/origins/fossil-images.html">gallery of fossils</A> and the <a href="http://www.ediacara.org/">University of Edicara</A> <li>Bruce Wallace and Adrian M. Srb, <cite>Adaptation</cite> <li>Jonathan Weiner, <cite>The Beak of the Finch</cite> [Field confirmation of neo-Darwinism, from, nicely enough, the Galapagos. (Please don't start an argument about what it means to confirm a scientific theory here.)] </ul> <ul>Recommended, close-ups, non-technical: <li><a href="j-t-bonner.html">John Tyler Bonner</A> <ul> <li><cite>On Development</cite> [Points out that it's a mistake to think of just the adult form-and-behavior "evolving"; it's really the <em>whole life-cycle,</em> complicating matters considerably...] <li><cite>On the Evolution of Complexity, by Means of Natural Selection</cite> [<a href="http://bactra.org/reviews/evolution-of-complexity/">Review</A>] </ul> <li>François Jacob, <cite>The Possible and the Actual</cite> [I really must get around to typing up my notes from his lecture on conserved gene sequences] <li>Charles H. Lineweaver, "Paleontological Tests: Human-like Intelligence is not a Convergent Feature of Evolution", <a href="http://arxiv.org/abs/0711.1751">arxiv:0711.1751</a> [A very nice, and simple, way to see the error of some common ways of looking at evolution] <li>John Maynard Smith, <cite>Did Darwin Get It Right? Essays on Games, Sex, and Evolution</cite> <li>Edmund Russell, <cite><a href="http://bactra.org/weblog/algae-2019-12.html#russell">Evolutionary History: Uniting History and Biology to Understand Life on Earth</a></cite> <li>Homer W. Smith, <cite>Kamongo, or, The Lungfish and the Padre</cite> </ul> <ul>Recommended, technical, big picture: <li>John H. Gillespie, <cite>Population Genetics: A Concise Guide</cite> [<a href="http://bactra.org/reviews/gillespie-pop-gen/">Review: Darwin's Equations (II)</a>] <li>Peter Godfrey-Smith, <cite>Darwinian Populations and Natural Selection</cite> <li>Josef Hofbauer and Karl Sigmund, <cite>The Theory of Evolution and Dynamical Systems: Mathematical Aspects of Selection</cite> <li><a href="john-holland.html">John Holland</a>, <cite><A HREF="evol-comp.html">Adaptation in Natural and Artificial Systems</A></cite> <li>John Maynard Smith, <cite>Evolution and the Theory of Games</cite> [<a href="http://dannyreviews.com/h/Evolution_and_the_Theory_of_Games.html">Review by Danny Yee</a>] </ul> <ul>Recommended, technical, close-ups: <li>Lauren W. Ancel and Walter Fontana, "Plasticity, Evolvability and Modularity in RNA," <cite>Journal of Experimental Zoology (Molecular and Developmental Evolution),</cite> <strong>288</strong> (2000): 242--283 [<a href="http://www.santafe.edu/~ancel/PAPERS/jez_plasticity.pdf">Reprint</a>] <li>Richard K. Belew and Melanie Mitchell (eds.), <cite>Adaptive Individuals in Evolving Populations: Models and Algorithms</cite> <li>Carl T. Bergstrom and Michael Lachmann, "The fitness value of information", <a href="http://arxiv.org/abs/q-bio.PE/0510007">q-bio.PE/0510007</a> <li><a href="dawkins.html">Richard Dawkins</A>, <cite>The Extended Phenotype</cite> [<a href="http://bactra.org/reviews/extended-phenotype">Review: <em>Not</em> Your Parents' Web of Life</a>] <li>Laura F. Galloway and Julie R. Etterson, "Transgenerational Plasticity Is Adaptive in the Wild", <a href="http://dx.doi.org/10.1126/science.1148766"><cite>Science</cite> <strong>318</strong> (2007): 1134--1136</a> <li>Paul H. Harvey and Mark D. Pagel, <cite>The Comparative Method in Evolutionary Biology</cite> [<a href="http://bactra.org/reviews/harvey-pagel/">Review: On the Uses of Knowing Where Birds and Bees Come From</a>] <li>David Hull, <cite>Science and Selection: Essays on Biological Evolution and Philosophy of Science</cite> <li>Philip Kitcher, <citE>In Mendel's Mirror: Philosophical Reflections on Biology</cite> <li>R. C. Lewontin, <cite>The Genetic Basis of Evolutionary Change</cite> [An excellent book; but <cite>The Dialectical Biologist</cite> may be safely ignored] <li>C. M. Newman, J. E. Cohen and C. Kipnis, "Neo-darwinian evolution implies punctuated equilibria", <a href="https://doi.org/10.1038/315400a0"><cite>Nature</cite> <strong>315</strong> (1985): 400--401</a> <li>Mark E. J. Newman <ul> <li>"Simple Models of Evolution and Extinction," <a href="http://arxiv.org/abs/adap-org/9910003">adap-org/9910003</a> <li>MEJN and Gunther J. Eble, "Decline in Extinction Rates and Self-Similarity in the Fossil Record," <cite>Paleobiology</cite> <Strong>25</strong> (1999): 434--439 = <a href="http://arxiv.org/abs/adap-org/9809004">adap-org/9809004</a> <li>MEJN and Richard G. Palmer, "Models of Extinction: A Review," <a href="http://arxiv.org/abs/adap-org/9908002">adap-org/9908002</a> </ul> <li>Mark Pagel, "Inferring the Historical Patterns of Biological Evolution," <cite>Nature</cite> <strong>401</strong> (1999): 877--884 [Warning: This paper makes the staggering mistake of confusing likelihood (probability of a model's generating results like the data) with posterior probability (probability of the model, given the data). Pagel definitely doesn't make this elementary blunder elsewhere; I dunno what happened here.] <li>David C. Queller, "The Spaniels of St. Marx and the Panglossian Paradox: A Critique of a Rhetorical Programme," <cite>Quarterly Review of Biology</cite> <strong>70</strong> (1995): 485--489 <li>Karl Sigmund, <cite>The Calculus of Selfishness</cite> [Review: <a href="http://bactra.org/reviews/calculus-of-selfishness.html">Honor Among Thieves</a>] <li>Olivier Rivoire and Stanislas Leibler, "The Value of Information for Populations in Varying Environments", <a href="http://arxiv.org/abs/1010.5092">arxiv:1010.5092</a> <li>George C. Willams, <cite>Adaptation and Natural Selection; a Critique of Some Current Evolutionary Thought</cite> [Well, current in 1966, anyway; that it is no longer current is due largerly to this book!] <li>Guoping Zhu, G. Brian Golding and Antony M. Dean, "The Selective Cause of an Ancient Adaptation", <a href="http://dx.doi.org/10.1126/science.1106974"><cite>Science</cite> <strong>307</strong> (2005): 1279--1282</a> [Where "ancient" means "about 3.5 billion years old".] </UL> <ul>Recommended, of historical interest: <li><a href="darwin.html">Charles Darwin</A>, <cite>On the Origin of Species, by Means of Natural Selection, or Preservation of Favored Races in the Struggle for Life</cite> [Get the fascimile of the first edition with the introduction by Ernst Mayr] <li>R. A. Fisher, <cite>The Genetical Theory of Natural Selection</cite> <li>J. B. S. Haldane, <cite>The Causes of Evolution</cite> [<a href="http://bactra.org/reviews/causes-of-evolution/">Review: Darwin's Equations</A>] <li>T. H. Huxley, <cite><a href="http://aleph0.clarku.edu/huxley/">The Huxley File</a></cite> [Nearly complete works, ed. and put on-line by Charles Blinderman and David Joyce] </ul> <ul>To read, histories of evolutionary thinking and science: <li>Stephen G. Alter, <cite><a href="http://jhupbooks.press.jhu.edu:80/ecom/MasterServlet/GetItemDetailsHandler?iN=9780801872440&qty=1&viewMode=3">Darwinism and the Linguistic Image: Language, Race, and Natural Theology in the Nineteenth Century</a></cite> <li>Peter Bowler, <cite>Evolution: The History of an Idea</cite> <li>Adrian Desmond, <cite>Huxley: From Devil's Disciple to Evolution's High Priest</cite> <li>M. T. Ghiselin, <cite>The Triumph of the Darwinian Method</cite> </ul> <ul>To read, of historical interest: <li>Theodosius Dobzhansky <ul> <li><cite>Mankind Evolving: The Evolution of the Human Species</cite> <li><cite>Genetics and the Origin of Species</cite> </ul> <li>G. Evelyn Hutchinson, <cite>The Ecological Theater and the Evolutionary Play</cite> <li>Konrad Lorenz, <cite>Evolution and Modification of Behavior</cite> </ul> <ul>To read, not otherwise or not yet classified: <li>Marshall Abrams, <cite><a href="https://press.uchicago.edu/ucp/books/book/chicago/E/bo195920308">Evolution and the Machinery of Chance: Philosophy, Probability, and Scientific Practice in Biology</a></cite> <li>P. Ao, "Mathematical Structure of Evolutionary Theory", <a href="http://arxiv.org/abs/q-bio.QM/0403020">q-bio.QM/0403020</a> ["Here we postulate three laws which form a mathematical framework to capture the essence of Darwinian evolutionary dynamics. The second law is most quantitative and is explicitly expressed by a unique form of stochastic differential equation." Color me skeptical, but I haven't read beyond the abstract.] <li>Wallace Arthur, <cite>Creatures of Accident: The Rise of the Animal Kingdom</cite> <li>John C. Avise, <cite><a href="http://cambridge.org/9780521674171">Evolutionary Pathways in Nature: A Phylogenetic Approach</a></cite> <li>J. B. Beltman and P. Haccou, "Speciation through the learning of habitat features", <a href="http://dx.doi.org/10.1016/j.tpb.2005.01.001"><cite>Theoretical Population Biology</cite> <strong>67</strong> (2005): 189--202</a> <li>Ioana Bena, Michel Droz and Andrzej Pekalski, "Complex population dynamics as a competition between multiple time-scale phenomena", <a href="http://arxiv.org/abs/q-bio.PE/0703033">q-bio.PE/0703033</a> <li>Carl T. Bergstrom and Rustom Antia, "How do adaptive immune systems control pathogens while avoiding autoimmunity?", <a href="http://dx.doi.org/10.1016/j.tree.2005.11.008"><cite>Trends in Ecology and Evolution</cite> <strong>21</strong> (2006): 22--28</a> [<a href="http://octavia.zoology.washington.edu/disease/BergstromAndAntia06.pdf">PDF reprint</a> via Carl] <li>C. T. Bergstrom and M. Rosvall, "The transmission sense of information", <a href="http://arxiv.org/abs/0810.4168">arxiv:0810.4168</a> <li>Daniel R. Brooks and Deborah A. McLennan, <cite><a href="http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/14753.ctl">The Nature of Diversity: An Evolutionary Voyage of Discovery</a></cite> <li>Erick Chastain, Rustom Antia, Carl T. Bergstrom, "Defensive complexity and the phylogenetic conservation of immune control", <a href="http://arxiv.org/abs/1211.2878">arxiv:1211.2878</a> <li>Kim Christensen, Simone A. di Collobiano, Matt Hall, and Henrik J. Jensen, "Tangled Nature: a model of evolutionary ecology," <a href="http://arxiv.org/abs/cond-mat/0104116">cond-mat/0104116</a> <li>Dale H. Clayton, Sarah E. Bush and Kevin P. Johnson, <cite><a href="http://press.uchicago.edu/ucp/books/book/chicago/C/bo21515934">Coevolution of Life on Hosts: Integrating Ecology and History</a></cite> <li>Charles C. Cockell, <cite><a href="http://www.cambridge.org/0521817366">Impossible Extinction: Natural Catastrophes and the Supremacy of the Microbial World</a></cite> <li>Claude Combes, <cite>The Art of Being a Parasite</cite> [<a href="http://dannyreviews.com/h/Parasite.html">Review by Danny Yee</a>] <li>Vincent Courtillot, <cite><a href="http://www.cambridge.org/0521583926">Evolutionary Catastrophes: The Science of Mass Extinction</a></cite> <li>Depew and Weber, <cite>Darwinism Evolving: Systems Dynamics and the Genealogy of Evolution</cite> [Beware of genealogies which aren't actually about families. <a href="http://www.nybooks.com/articles/article-preview?article_id=1982">Review</a> by John Maynard Smith.] <li>Michael Doebli, <cite><a href="http://press.princeton.edu/titles/9484.html">Adaptive Diversification</a></cite> <li>Nikolay V. Dokholyan and Eugene I. Shakhnovich, "Understanding hierarchical protein evolution from first principles," <a href="http://arxiv.org/abs/cond-mat/0104469">cond-mat/0104469</a> <li>Gunther Eble, "On the Dual Nature of Chance in Evolutionary Biology and Paleobiology," <a href="http://www.santafe.edu/sfi/publications/Abstracts/98-09-085abs.html">SFI Working Paper 98-09-085</a> <li>Manfred Eigen, <cite>The Hypercycle, a Principle of Natural Self-organization</cite> <li>David E. Fastovsky and David B. Weishampel, <cite><a href="http://www.cambridge.org/0521811724">The Evolution and Extinction of the Dinosaurs</a></cite> <li>A. Feigl, "Essential conditions for evolution of communication within a species", <a href="http://dx.doi.org/10.1016/j.jtbi.2008.07.005"><cite>Journal of Theoretical Biology</cite> <strong>254</strong> (2008): 768--778</a>, <a href="http://arxiv.org/abs/0803.0412">arxiv:0803.0412</a> <li> Luca Ferraro, Andrea Giansanti, Giovanni Giuliano and Vittorio Rosato, "Co-expression of statistically over-represented peptides in proteomes: a key to phylogeny?", <a href="http://arxiv.org/abs/q-bio.MN/0410011">q-bio.MN/0410011</a> <li>Walter Fontana and Peter Schuster, "Continuity in Evolution: On the Nature of Transitions," <a href="http://www.santafe.edu/sfi/publications/Abstracts/98-04-030abs.html">SFI Working Paper 98-04-030</a> <li>Barbara Forrest and Paul R. Gross, <cite>Creationism's Trojan Horse: The Wedge of Intelligent Design</cite> <li>Steven A. Frank, "Wright's adaptive landscape versus Fisher's fundamental theorem", <a href="http://arxiv.org/abs/1102.3709">arxiv:1102.3709</a> <li>Sergey Gavrilets, <cite>Fitness Landscapes and the Origin of Species</cite> <li>Diane P. Genereuz and Carl T. Bergstrom, "Evolution in Action: Understanding antibiotic resistance" [forthcoming book chapter] <li>Ulrich Gerland and Terence Hwa, "On the Selection and Evolution of Regulatory DNA Motifs," <a href="http://arxiv.org/abs/physics/0112039">physics/0112039</a> <li>Thomas J. Givnish and Kenneth J. Sytsma (eds.), <cite>Molecular Evolution and Adaptive Radiation</cite> <li>Stephen Jay Gould, <cite>The Structure of Evolutionary Theory</cite> <li>B. Rosemary Grant and Peter R. Grant, <cite>Evolutionary Dynamics of a Natural Population: The Large Cactus Finch of the Galapagos</cite> <li>Dan Graur and William Martin, "Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision", <cite>Trends in Genetics</cite> <strong>20</strong> (2004): 80--86 [<a href="http://www2.hawaii.edu/~khayes/Journal_Club/Journal_Club04/graurandmartin2004.pdf ">PDF reprint</a>] <li>Eva Jablonka and Marion J. Lamb, <cite><a href="http://mitpress.mit.edu/0262101076">Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life</a></cite> <li>Ronald A. Jenner, <cite><a href="https://doi.org/10.1017/9781316226667">Ancestors in Evolutionary Biology: Linear Thinking about Branching Trees</a></cite> <li>Marc Kirschner and John Gerhart, <cite>The Plausibility of Life</cite> [<a href="http://radio.weblogs.com/0100167/2005/12/26.html#a463">Capsule review by Frenando Pereira</a>] <li>Kevin N. Lala , Tobias Uller , Nathalie Feiner , Marcus Feldman and Scott F. Gilbert, <cite><a href="https://doi.org/10.1515/9780691262406">Evolution Evolving: The Developmental Origins of Adaptation and Biodiversity</a></cite> <li>Laura Landweber and Erik Winfree (ed.), <cite>Evolution as Computation</cite> [The dual subject to <a href="evol-comp.html">evolutionary computation</a>, as were] <li>Daniel J. Lawson and Henrik Jeldtoft Jensen, "Evolution as Diffusion in type space", <a href="http://arxiv.org/abs/q-bio.PE/0609009">q-bio.PE/0609009</a> <li>George Levine, <cite><a href="https://www.jstor.org/stable/j.ctt7pgq4">Darwin Loves You: Natural Selection and the Re-Enchantment of the World</a></cite> <li>Elisabeth Lloyd, <cite>The Structure and Confirmation of Evolutionary Theory</cite> <li>Long, <cite>Rise of the Fishes</cite> <li>David J. C. MacKay, "Rate of Information Acquisition by a Species subjected to Natural Selection" [<a href="http://www.inference.phy.cam.ac.uk/mackay/Evolution.html">link</a>] <li>Joshua S. Madin, John Alroy, Martin Aberhan, Franz T. Fürsich, Wolfgang Kiessling, Matthew A. Kosnik, Peter J. Wagner, "Statistical Independence of Escalatory Ecological Trends in Phanerozoic Marine Invertebrates", <a href="http://dx.doi.org/10.1126/science.1123591"><cite>Science</cite> <strong>312</strong> (2006): 897--900</a> <li>Marc Mangel, <citE><a href="http://cambridge.org/9780521537483">The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology</a></cite> <li>Ernst Mayr <UL> <li><cite>Growth of Biological Thought</cite> <li><cite>Populations, Species and Evolution</cite> <li><cite>This Is Biology</cite> <li><cite>What Evolution Is</cite> </UL> <li>Margaret McFall-Ngai, "Adaptive Immunity: Care for the community", <a href="http://dx.doi.org/10.1038/445153a"><cite>Nature</cite> <strong>445</strong> (2007): 153</a> <li>Géza Meszéna, Mats Gyllenberg, Frans J. Jacobs and Johan A. J. Metz, "Link between Population Dynamics and Dynamics of Darwinian Evolution", <a href="http://dx.doi.org/10.1103/PhysRevLett.95.078105"><cite>Physical Review Letters</cite> <strong>95</strong> (2005): 078105</a> <li>Richard E. Michod, <cite>Darwinian Dynamics: Evolutionary Transitions in Fitness and Individuality</cite> <li>Stephen P. Miller, Mark Lunzer, and Antony M. Dean, "Direct Demonstration of an Adaptive Constraint", <a href="http://dx.doi.org/ 10.1126/science.1133479"><cite>Science</cite> <strong>314</strong> (2006): 458--461</a> <li>Mitton, <cite>Selection in Natural Populations</cite> <li>Karl J. Niklas, <cite>The Evolutionary Biology of Plants</cite> [<a href="http://dannyreviews.com/h/Plant_Evolution.html">Ringing endorsement</a> from Danny Yee --- "the most rewarding book on evolution I have read for years."] <li>F. John Odling-Smee, Kevin N. Laland and Marcus W. 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