Evolution (of Organisms)

01 May 2008 09:18

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[A proper discussion of evolution will appear here Any Time Now.]

Issues in evolution proper: adaptation; complexity; developmental constraints and the evolution of development; ecology and co-evolution; 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).

Query: 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 its own notebook.)

Extensions of evolution: to brain function; to computer programming ; to culture (memetics); to economics; to epistemology; to psychology.

Mathematical modeling: classical population genetics à la Fisher, Haldane and Wright, and its extensions via dynamics; game theory à la John Maynard Smith. Connections to physics. Agent-based modeling.

Challenges to neo-Darwinism: 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 real alternatives yet advanced. (Neutral mutations by definition explain the origins of neither adaptations nor species.)

Recommended, non-technical:
• John Tyler Bonner
  • On Development [Points out that it's a mistake to think of just the adult form-and-behavior "evolving"; it's really the whole life-cycle, complicating matters considerably...]
  • On the Evolution of Complexity, by Means of Natural Selection [Review]
• Richard Dawkins
  • The Blind Watchmaker
  • Climbing Mount Improbable
  • The Selfish Gene
• Daniel Dennett, Darwin's Dangerous Idea
• Theodosius Dobzhansky, "Nothing in Biology Makes Sense Except in the Light of Evolution" [first pub. American Biology Teacher 35 (March 1973): 125--129]
• Stephen Jay Gould, anything. [But be warned that a lot of what he says about the Burgess Shale fauna in Wonderful Life is disputed --- by his own sources...]
• François Jacob, The Possible and the Actual [I really must get around to typing up my notes from his lecture on conserved gene sequences]
• Charles H. Lineweaver, "Paleontological Tests: Human-like Intelligence is not a Convergent Feature of Evolution", arxiv:0711.1751 [A very nice, and simple, way to see the error of some common ways of looking at evolution]
• John Maynard Smith [As a god to population genetics; disciple of Haldane]
  • Did Darwin Get It Right? Essays on Games, Sex, and Evolution
  • The Theory of Evolution [An introductory book which avoids getting tangled up in technical details without sacrificing intellectual rigor or pushing any really strange ideas]
  • and Eörs Szathmáry, The Origins of Life: From the Birth of Life to the Origin of Language [Review: Major Transitions Minor]
• Jacques Monod, Chance and Necessity [Review by Danny Yee]
• Karl Sigmund, Games of Life: Explorations in Ecology, Evolution and Behavior
• Homer W. Smith, Kamongo, or, The Lungfish and the Padre
• talk.origins 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 website with archives of posts to the newsgroups, the excellent FAQs (read 'em before attempting to convert the heathen), a nifty gallery of fossils and the University of Edicara
• Bruce Wallace and Adrian M. Srb, Adaptation
• Jonathan Weiner, The Beak of the Finch [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.)]

Recommended, technical:
• Lauren W. Ancel and Walter Fontana, "Plasticity, Evolvability and Modularity in RNA," Journal of Experimental Zoology (Molecular and Developmental Evolution), 288 (2000): 242--283 [Reprint]
• Carl T. Bergstrom and Michael Lachmann, "The fitness value of information", q-bio.PE/0510007
• Charles Darwin, On the Origin of Species, by Means of Natural Selection, or Preservation of Favored Races in the Struggle for Life [Get the fascimile of the first edition with the introduction by Ernst Mayr]
• Richard Dawkins, The Extended Phenotype [Review: Not Your Parents' Web of Life]
• R. A. Fisher, The Genetical Theory of Natural Selection
• Laura F. Galloway and Julie R. Etterson, "Transgenerational Plasticity Is Adaptive in the Wild", Science 318 (2007): 1134--1136
• John Gerhart and Marc Kirschner, Cells, Embryos and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability
• John H. Gillespie, Population Genetics: A Concise Guide [Review: Darwin's Equations (II)]
• J. B. S. Haldane, The Causes of Evolution [Review: Darwin's Equations]
• Paul H. Harvey and Mark D. Pagel, The Comparative Method in Evolutionary Biology [Review: On the Uses of Knowing Where Birds and Bees Come From]
• Josef Hofbauer and Karl Sigmund, The Theory of Evolution and Dynamical Systems: Mathematical Aspects of Selection [Mathematically explicit, i.e., full frontal differentiable manifolds]
• John Holland, Adaptation in Natural and Artificial Systems
• T. H. Huxley, The Huxley File [Nearly complete works, ed. and put on-line by Charles Blinderman and David Joyce]
• R. C. Lewontin, The Genetic Basis of Evolutionary Change [An excellent book; but The Dialectical Biologist may be safely ignored]
• John Maynard Smith, Evolution and the Theory of Games [Review by Danny Yee]
• Mark E. J. Newman
  • "Simple Models of Evolution and Extinction," adap-org/9910003
  • MEJN and Gunther J. Eble, "Decline in Extinction Rates and Self-Similarity in the Fossil Record," Paleobiology 25 (1999): 434--439 = adap-org/9809004
  • MEJN and Richard G. Palmer, "Models of Extinction: A Review," adap-org/9908002
• Martin Nilsson and Nigel Snoad, "Error Thresholds for Quasispecies on Dynamic Fitness Landscapes," Physical Review Letters 84 (2000): 191--194
• Mark Pagel, "Inferring the Historical Patterns of Biological Evolution," Nature 401 (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.]
• David C. Queller, "The Spaniels of St. Marx and the Panglossian Paradox: A Critique of a Rhetorical Programme," Quarterly Review of Biology 70 (1995): 485--489
• George C. Willams, Adaptation and Natural Selection; a Critique of Some Current Evolutionary Thought [Well, current in 1966, anyway; that it is no longer current is due largerly to this book!]
• Guoping Zhu, G. Brian Golding and Antony M. Dean, "The Selective Cause of an Ancient Adaptation", Science 307 (2005): 1279--1282 [Where "ancient" means "about 3.5 billion years old".]

To read:
• P. Ao, "Mathematical Structure of Evolutionary Theory", q-bio.QM/0403020 ["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.]
• Wallace Arthur, Creatures of Accident: The Rise of the Animal Kingdom
• John C. Avise, Evolutionary Pathways in Nature: A Phylogenetic Approach [blurb]
• Ellen Baake and Wilfried Gabriel, "Biological Evolution through Mutation, Selection, and Drift: An Introductory Review," cond-mat/9907372
• Ellen Baake, Hans-Otto Georgii, "Mutation, selection, and ancestry in branching models: a variational approach", q-bio.PE/0611018
• Richard K. Belew and Melanie Mitchell (eds.), Adaptive Individuals in Evolving Populations: Models and Algorithms
• J. B. Beltman and P. Haccou, "Speciation through the learning of habitat features", Theoretical Population Biology 67 (2005): 189--202
• Ioana Bena, Michel Droz and Andrzej Pekalski, "Complex population dynamics as a competition between multiple time-scale phenomena", q-bio.PE/0703033
• Carl T. Bergstrom and Rustom Antia, "How do adaptive immune systems control pathogens while avoiding autoimmunity?", Trends in Ecology and Evolution 21 (2006): 22--28 [PDF reprint via Carl]
• Peter Bowler, Evolution: The History of an Idea
• R. A. Blythe and A. J. McKane, "Stochastic Models of Evolution in Genetics, Ecology and Linguistics", cond-mat/0703478
• Daniel R. Brooks and Deborah A. McLennan, The Nature of Diversity: An Evolutionary Voyage of Discovery [Blurb]
• Sean B. Carroll, From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design
• Nicolas Champagnat, Régis Ferrière, Sylvie Méléar, "Individual-based probabilistic models of adaptive evolution and various scaling approximations", math.PR/0510453 ["We are interested in modelling Darwinian evolution, resulting from the interplay of phenotypic variation and natural selection through ecological interactions. Our models are rooted in the microscopic, stochastic description of a population of discrete individuals characterized by one or several adaptive traits. The population is modelled as a stochastic point process whose generator captures the probabilistic dynamics over continuous time of birth, mutation, and death, as influenced by each individual's trait values, and interactions between individuals. An offspring usually inherits the trait values of her progenitor, except when a mutation causes the offspring to take an instantaneous mutation step at birth to new trait values. We look for tractable large population approximations. By combining various scalings on population size, birth and death rates, mutation rate, mutation step, or time, a single microscopic model is shown to lead to contrasting macroscopic limits, of different nature: deterministic, in the form of ordinary, integro-, or partial differential equations, or probabilistic, like stochastic partial differential equations or superprocesses. In the limit of rare mutations, we show that a possible approximation is a jump process, justifying rigorously the so-called trait substitution sequence."]
• Nicolas Champagnat and Amaury Lambert, "Evolution of discrete populations and the canonical diffusion of adaptive dynamics", math.PR/0601643
• Kim Christensen, Simone A. di Collobiano, Matt Hall, and Henrik J. Jensen, "Tangled Nature: a model of evolutionary ecology," cond-mat/0104116
• Freddy Bugge Christiansen, Theories of Population Variation in Genes and Genomes [blurb, intro]
• Jens Christian Claussen and Arne Traulsen, "Non-Gaussian fluctuations arising from finite populations: Exact results for the evolutionary Moran process", Physical Review E 71 (2005): 025101
• Charles C. Cockell, Impossible Extinction: Natural Catastrophes and the Supremacy of the Microbial World [blurb]
• Elisheva Cohen, David A. Kessler and Herbert Levine, "Recombination dramatically speeds up evolution of finite populations", q-bio.PE/0410015
• Claude Combes, The Art of Being a Parasite [Review by Danny Yee]
• Vincent Courtillot, Evolutionary Catastrophes: The Science of Mass Extinction [blurb]
• Depew and Weber, Darwinism Evolving: Systems Dynamics and the Genealogy of Evolution [Beware of genealogies which aren't actually about families. Review by John Maynard Smith.]
• Fabio Dercole and Sergio Rinaldi, Analysis of Evolutionary Processes: The Adaptive Dynamics Approach and Its Applications [Blurb, ch. 1]
• Adrian Desmond, Huxley: From Devil's Disciple to Evolution's High Priest
• Theodosius Dobzhansky
  • Mankind Evolving: The Evolution of the Human Species
  • Genetics and the Origin of Species
• Nikolay V. Dokholyan and Eugene I. Shakhnovich, "Understanding hierarchical protein evolution from first principles," cond-mat/0104469
• Rick Durrett and Jason Schweinsberg, "A coalescent model for the effect of advantageous mutations on the genealogy of a population", math.PR/0411071
• Gunther Eble
  • "On the Dual Nature of Chance in Evolutionary Biology and Paleobiology," SFI Working Paper 98-09-085
  • "The Role of Development in Evolutionary Radiations," in M. L. McKinney (ed.), Biodiversity Dynamics = SFI Working Paper 98-09-084
• Manfred Eigen, The Hypercycle, a Principle of Natural Self-organization
• Bryan K. Epperson, Geographical Genetics
• A. Eriksson, B. Haubold, and B. Mehlig, "Statistics of selectively neutral genetic variation," physics/0111205
• David E. Fastovsky and David B. Weishampel, The Evolution and Extinction of the Dinosaurs [blurb]
• Luca Ferraro, Andrea Giansanti, Giovanni Giuliano and Vittorio Rosato, "Co-expression of statistically over-represented peptides in proteomes: a key to phylogeny?", q-bio.MN/0410011
• Walter Fontana and Peter Schuster, "Continuity in Evolution: On the Nature of Transitions," SFI Working Paper 98-04-030
• Barbara Forrest and Paul R. Gross, Creationism's Trojan Horse: The Wedge of Intelligent Design
• Sergey Gavrilets, Fitness Landscapes and the Origin of Species
• Diane P. Genereuz and Carl T. Bergstrom, "Evolution in Action: Understanding antibiotic resistance" [forthcoming book chapter; PDF]
• Ulrich Gerland and Terence Hwa, "On the Selection and Evolution of Regulatory DNA Motifs," physics/0112039
• M. T. Ghiselin, The Triumph of the Darwinian Method
• John H. Gillespie, The Causes of Molecular Evolution
• Thomas J. Givnish and Kenneth J. Sytsma (eds.), Molecular Evolution and Adaptive Radiation
• Stephen Jay Gould
  • Full House
  • Ontogeny and Phylogeny
  • The Structure of Evolutionary Theory
• B. Rosemary Grant and Peter R. Grant, Evolutionary Dynamics of a Natural Population: The Large Cactus Finch of the Galapagos
• Dan Graur and William Martin, "Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision", Trends in Genetics 20 (2004): 80--86 [PDF reprint]
• Joachim Hermisson, Oliver Redner, Holger Wagner and Ellen Baake, "Mutation-Selection Balance: Ancestry, Load, and Maximum Principle," cond-mat/0202432
• Hofbauer and Sigmund, Evolutionary Games and Replicator Dynamics
• David Hull, Science and Selection: Essays on Biological Evolution and Philosophy of Science
• G. Evelyn Hutchinson, The Ecological Theater and the Evolutionary Play
• Eva Jablonka and Marion J. Lamb, Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life [Blurb]
• Kavita Jain and Joachim Krug, "Evolutionary trajectories in rugged fitness landscapes", q-bio.PE/0501028 = Journal of Statistical Mechanics: Theory and Experiment (2005): P04008
• P. D. Jarvis, J. D. Bashford and J. G. Sumner, "Path integral formulation of phylogenetic branching processes", q-bio.PE/0411047
• Marc Kirschner and John Gerhart, The Plausibility of Life [Capsule review by Frenando Pereira]
• Laura Landweber and Erik Winfree (ed.), Evolution as Computation [The dual subject to evolutionary computation, as were]
• Daniel J. Lawson and Henrik Jeldtoft Jensen, "Evolution as Diffusion in type space", q-bio.PE/0609009
• George Levine, Darwin Loves You: Natural Selection and the Re-Enchantment of the World
• Konrad Lorenz, Evolution and Modification of Behavior
• Elisabeth Lloyd, The Structure and Confirmation of Evolutionary Theory
• Long, Rise of the Fishes
• David J. C. MacKay, "Rate of Information Acquisition by a Species subjected to Natural Selection" [link]
• Marc Mangel, The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology [blurb]
• John Maynard Smith, Evolutionary Genetics [Review by Danny Yee]
• Ernst Mayr
  • Growth of Biological Thought
  • Populations, Species and Evolution
  • This Is Biology
  • What Evolution Is
• Margaret McFall-Ngai, "Adaptive Immunity: Care for the community", Nature 445 (2007): 153
• Géza Meszéna, Mats Gyllenberg, Frans J. Jacobs and Johan A. J. Metz, "Link between Population Dynamics and Dynamics of Darwinian Evolution", Physical Review Letters 95 (2005): 078105
• Richard E. Michod, Darwinian Dynamics: Evolutionary Transitions in Fitness and Individuality
• Jacek Miekisz, "Evolutionary game theory and population dynamics", q-bio.PE/0703062 [51 pp. lecture notes]
• Stephen P. Miller, Mark Lunzer, and Antony M. Dean, "Direct Demonstration of an Adaptive Constraint", Science 314 (2006): 458--461
• Mitton, Selection in Natural Populations
• Karl J. Niklas, The Evolutionary Biology of Plants [Ringing endorsement from Danny Yee --- "the most rewarding book on evolution I have read for years."]
• Martin Nilsson, "Optimal Mutation Rates on Static Fitness Landscpes", physics/0005018
• Karen M. Page and Martin A. Nowak, "Unifying Evolutionary Dynamics", Journal of Theoretical Biology 219 (2002): 93--98 [Thanks to David Krakauer]
• John Pepper, "Relatedness in Trait Group Models of Social Evolution," SFI Working Paper 00-07-034
• Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander J. Tans, "Empirical fitness landscapes reveal accessible evolutionary paths", Nature 445 (2007): 383--386
• Angela Potochnik, "Optimality Modeling and Explanatory Generality", phil-sci/3011
• William B. Provine
  • The Origins of Theoretical Population Genetics
  • Sewall Wright and Evolutionary Biology
• José M. Ranz and Carlos A. Machado, "Uncovering evolutionary patterns of gene expression using microarrays", Trends in Ecology and Evolution 21 (2006): 29--37
• Alex Rosenberg, Darwinian Reductionism: Or, How to Stop Worrying and Love Molecular Biology [Blurb]
• Scott W. Roy and Walter Gilbert, "Complex early genes", Proceedings of the National Academy of Sciences (USA) 102 (2005): 1986--1991
• Tor Schoenmeyr and Claus O. Wilke, "Finite genome size can halt Muller's ratchet," physics/0109058
• Veit Schämmle and E. Brigatti, "Speciational view of macroevolution: are micro and macroevolution decoupled?", q-bio.PE/0509032 ["We introduce a simple computational model that, with a microscopic dynamics driven by natural selection and mutation alone, allows the description of true speciation events. A statistical analysis of the so generated evolutionary tree captures realistic features showing power laws for frequency distributions in time and size. Albeit these successful predictions, the difficulty in obtaining punctuated dynamics with mass extinctions suggests the necessity of decoupling micro and macro-evolutionary mechanisms in agreement with some ideas of Gould's and Eldredge's theory of punctuated equilibrium."]
• William A. Searcy and Stephen Nowicki, The Evolution of Animal Communication: Reliability and Deception in Signaling Systems [Blurb, intro]
• Homer William Smith, From Fish to Philosopher [Any book which is listed under both "Consciousness" and "Kidneys" in the library of Congress classification is worth looking up]
• Nigel Snoad, Limits to Evolvability in Changing Environments [Ph.D. thesis, Australian National University, 2000]
• Elliott Sober
  • The Nature of Selection [Review by Danny Yee]
  • Evidence and Evolution: The Logic Behind the Science [blurb]
• Ricard V. Solé, Isaac Salazar-Ciudad and Jordi Garcia-Fernández, "Landscapes, Gene Networks and Pattern Formation: On the Cambrian Explosion," SFI Working Paper 00-08-046
• Stanley, Extinction
• Mark Stegeman and Paul Rhode, "Stochastic Darwinian equilibria in small and large populations", Games and Economic Behavior 49 (2004): 171--214
• Jun Sun and Michael W. Deem, "Spontaneous Emergence of Modularity in a Model of Evolving Individuals", Physical Review Letters 99 (2007): 228107
• Gergely J Szollosi, Imre Derenyi, "Hierarchical meanfield theory of evolutionary games on structured populations", arxiv:0704.0357
• Simon Tavaré "Ancestral Inference in Population Genetics"
• Guido Tiana, Boris E. Shakhnovich, Nikolay V. Dokholyan and Eugene I. Shakhnovich, "Imprint of evolution on protein structures", PNAS 101 (2004): 2846--2851
• Daniel P. Todes, Darwin Without Malthus: The Struggle for Existence in Russian Evolutionary Thought
• Arne Traulsen, Jens Christian Claussen, and Christoph Hauert, "Coevolutionary Dynamics: From Finite to Infinite Populations", Physical Review Letters 95 (2005): 238701
• Arne Traulsen, Jorge M. Pacheco and Lorens A. Imhof, "Stochasticity and evolutionary stability", q-bio.PE/0609021 = Physical Review E 74 (2006): 021905
• Annie E. Tsong, Brian B. Tuch, Hao Li and Alexander D. Johnson, "Evolution of alternative transcriptional circuits with identical logic", Nature 443 (2006): 415--420
• J. Scott Turner, The Tinkerer's Accomplice: How Design Emerges From Life Itself
• Erik van Nimwegen, The Statistical Dynamics of Epochal Evolution [Ph.D. thesis, University of Utrecht, 1999; on-line]
• Geerat J. Vermeij
  • Evolution and Escalation: An Ecological History of Life
  • "Historical contingency and the purported uniqueness of evolutionary innovations", PNAS 103 (2006): 1804--1809
  • Nature: An Economic History [Review in American Scientist]
• Christian von Mering, Evgeny M. Zdobnov, Sophia Tsoka, Francesca D. Ciccarelli, Jose B. Pereira-Leal, Christos A. Ouzoounis and Peer Bork, "Genome evolution reveals biochemical networks and functional modules", PNAS 100 (2003): 15428--15433
• Andreas Wagner, Robustness and Evolvability in Living Systems [Blurb, chapter 1]
• Gunter P. Wagner, Chris Amemiya and Frank Ruddle, "Hox cluster duplications and the opportunity for evolutionary novelties", PNAS 100 (2003): 14603--14606
• Denis M. Walsh, "Fit and Diversity: Explaining Adaptive Evolution", Philosophy of Science 70 (2003): 280--301
• Richard A. Watson, Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution [Blurb]
• Claus O. Wilke
  • "Adaptive evolution on neutral networks," physics/0101021
  • "Selection for Fitness vs. Selection for Robustness in RNA Secondary Structure Folding," physics/0103022
• Claus O. Wilke and D. Allan Drummond, "Population genetics of translational robustness", q-bio.PE/0509031
• Claus O. Wilke, Christopher Ronnewinkel and Thomas Martinetz, "Dynamic Fitness Landscapes in Molecular Evolution," physics/9912012