Evolution (of Organisms)

25 Oct 2024 09:27

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

Issues in evolution proper: adaptation; complexity; developmental constraints and the evolution of development; ecology and co-evolution; game theory; 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:
• 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...]
• John Maynard Smith [As a god to population genetics; disciple of Haldane]
  • 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
• 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, close-ups, 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]
• 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, Did Darwin Get It Right? Essays on Games, Sex, and Evolution
• Edmund Russell, Evolutionary History: Uniting History and Biology to Understand Life on Earth
• Homer W. Smith, Kamongo, or, The Lungfish and the Padre

Recommended, technical, big picture:
• John H. Gillespie, Population Genetics: A Concise Guide [Review: Darwin's Equations (II)]
• Peter Godfrey-Smith, Darwinian Populations and Natural Selection
• Josef Hofbauer and Karl Sigmund, The Theory of Evolution and Dynamical Systems: Mathematical Aspects of Selection
• John Holland, Adaptation in Natural and Artificial Systems
• John Maynard Smith, Evolution and the Theory of Games [Review by Danny Yee]

Recommended, technical, close-ups:
• 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]
• Richard K. Belew and Melanie Mitchell (eds.), Adaptive Individuals in Evolving Populations: Models and Algorithms
• Carl T. Bergstrom and Michael Lachmann, "The fitness value of information", q-bio.PE/0510007
• Richard Dawkins, The Extended Phenotype [Review: Not Your Parents' Web of Life]
• Laura F. Galloway and Julie R. Etterson, "Transgenerational Plasticity Is Adaptive in the Wild", Science 318 (2007): 1134--1136
• 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]
• David Hull, Science and Selection: Essays on Biological Evolution and Philosophy of Science
• Philip Kitcher, In Mendel's Mirror: Philosophical Reflections on Biology
• R. C. Lewontin, The Genetic Basis of Evolutionary Change [An excellent book; but The Dialectical Biologist may be safely ignored]
• C. M. Newman, J. E. Cohen and C. Kipnis, "Neo-darwinian evolution implies punctuated equilibria", Nature 315 (1985): 400--401
• 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
• 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
• Karl Sigmund, The Calculus of Selfishness [Review: Honor Among Thieves]
• Olivier Rivoire and Stanislas Leibler, "The Value of Information for Populations in Varying Environments", arxiv:1010.5092
• 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".]

Recommended, of historical interest:
• 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]
• R. A. Fisher, The Genetical Theory of Natural Selection
• J. B. S. Haldane, The Causes of Evolution [Review: Darwin's Equations]
• T. H. Huxley, The Huxley File [Nearly complete works, ed. and put on-line by Charles Blinderman and David Joyce]

To read, histories of evolutionary thinking and science:
• Stephen G. Alter, Darwinism and the Linguistic Image: Language, Race, and Natural Theology in the Nineteenth Century
• Peter Bowler, Evolution: The History of an Idea
• Adrian Desmond, Huxley: From Devil's Disciple to Evolution's High Priest
• M. T. Ghiselin, The Triumph of the Darwinian Method

To read, of historical interest:
• Theodosius Dobzhansky
  • Mankind Evolving: The Evolution of the Human Species
  • Genetics and the Origin of Species
• G. Evelyn Hutchinson, The Ecological Theater and the Evolutionary Play
• Konrad Lorenz, Evolution and Modification of Behavior

To read, not otherwise or not yet classified:
• Marshall Abrams, Evolution and the Machinery of Chance: Philosophy, Probability, and Scientific Practice in Biology
• 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
• 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]
• C. T. Bergstrom and M. Rosvall, "The transmission sense of information", arxiv:0810.4168
• Daniel R. Brooks and Deborah A. McLennan, The Nature of Diversity: An Evolutionary Voyage of Discovery
• Erick Chastain, Rustom Antia, Carl T. Bergstrom, "Defensive complexity and the phylogenetic conservation of immune control", arxiv:1211.2878
• Kim Christensen, Simone A. di Collobiano, Matt Hall, and Henrik J. Jensen, "Tangled Nature: a model of evolutionary ecology," cond-mat/0104116
• Dale H. Clayton, Sarah E. Bush and Kevin P. Johnson, Coevolution of Life on Hosts: Integrating Ecology and History
• Charles C. Cockell, Impossible Extinction: Natural Catastrophes and the Supremacy of the Microbial World
• Claude Combes, The Art of Being a Parasite [Review by Danny Yee]
• Vincent Courtillot, Evolutionary Catastrophes: The Science of Mass Extinction
• 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.]
• Michael Doebli, Adaptive Diversification
• Nikolay V. Dokholyan and Eugene I. Shakhnovich, "Understanding hierarchical protein evolution from first principles," cond-mat/0104469
• Gunther Eble, "On the Dual Nature of Chance in Evolutionary Biology and Paleobiology," SFI Working Paper 98-09-085
• Manfred Eigen, The Hypercycle, a Principle of Natural Self-organization
• David E. Fastovsky and David B. Weishampel, The Evolution and Extinction of the Dinosaurs
• A. Feigl, "Essential conditions for evolution of communication within a species", Journal of Theoretical Biology 254 (2008): 768--778, arxiv:0803.0412
• 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
• Steven A. Frank, "Wright's adaptive landscape versus Fisher's fundamental theorem", arxiv:1102.3709
• 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]
• Ulrich Gerland and Terence Hwa, "On the Selection and Evolution of Regulatory DNA Motifs," physics/0112039
• Thomas J. Givnish and Kenneth J. Sytsma (eds.), Molecular Evolution and Adaptive Radiation
• Stephen Jay Gould, 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]
• Eva Jablonka and Marion J. Lamb, Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life
• Ronald A. Jenner, Ancestors in Evolutionary Biology: Linear Thinking about Branching Trees
• Marc Kirschner and John Gerhart, The Plausibility of Life [Capsule review by Frenando Pereira]
• Kevin N. Lala , Tobias Uller , Nathalie Feiner , Marcus Feldman and Scott F. Gilbert, Evolution Evolving: The Developmental Origins of Adaptation and Biodiversity
• 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
• 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]
• 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", Science 312 (2006): 897--900
• Marc Mangel, The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology
• 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
• 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."]
• F. John Odling-Smee, Kevin N. Laland and Marcus W. Feldman, Niche Construction: The Neglected Process in Evolution
• 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
• 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
• Scott W. Roy and Walter Gilbert, "Complex early genes", Proceedings of the National Academy of Sciences (USA) 102 (2005): 1986--1991
• Paul Schmid-Hempel, Evolutionary Parasitology: The Integrated Study of Infections, Immunology, Ecology, and Genetics
• Veit Schämmle and E. Brigatti, "Speciational view of macroevolution: are micro and macroevolution decoupled?", q-bio.PE/0509032
• William A. Searcy and Stephen Nowicki, The Evolution of Animal Communication: Reliability and Deception in Signaling Systems
• 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]
• Elliott Sober
  • The Nature of Selection [Review by Danny Yee]
  • Evidence and Evolution: The Logic Behind the Science
• 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
• Jun Sun and Michael W. Deem, "Spontaneous Emergence of Modularity in a Model of Evolving Individuals", Physical Review Letters 99 (2007): 228107
• 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
• 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
• 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
• 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