Syllabus of Readings for Complex Adaptive Systems
and Agent-Based Computational Economics:

4. Biological Evolution

Last Updated: 7 January 2005

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Table of Contents:

• Key Issues in Biological Evolution
• Game Theory Approaches to Biological Evolution

Biological Evolution

A. Key Issues in Biological Evolution

• A Repository of Articles on Evolution (with commentary and author replies) that have appeared in MIT's Boston Review (BR), a political and literary forum, is maintained online by BR. Authors of recent articles include Dennett, Orr, Berwick, Dawkins, Pinker, and Gould.

• Michael Arbib (ed.), The Handbook of Brain Theory and Neural Networks: Second Edition, The MIT Press, Cambridge, MA, 1344 pp., November 2002. ISBN 0-262-01197-2
  From the Publisher: "Dramatically updating and extending the first edition, published in 1995, the second edition of (this book) presents the enormous progress made in recent years in the many subfields related to the two great questions: How does the brain work? and, How can we build intelligent machines? Once again, the heart of the book is a set of almost 300 articles covering the whole spectrum of topics in brain theory and neural networks. ... The second edition greatly increases the coverage of models of fundamental neurobiology, cognitive neuroscience, and neural network approaches to language. It contains 287 articles, compared to the 266 in the first edition. Articles on topics from the first edition have been updated by the original authors or written anew by new authors, and there are 106 articles on new topics."
  Michael A. Arbib is Professor of Computer Science and Neurscience, and Director of the Center for Neural Engineering, at the University of Southern California, Los Angeles.

  Pierre Baldi and Soren Brunak, Bioinformatics: The Machine Learning Approach, The MIT Press, Cambridge, MA, 1998, ISBN 0-262-02442-X.

  From the book blurb: "Bioinformatics is the development and application of computer methods for analysis, interpretation, and prediction, as well as for the design of experiments, in biological applications. ... In this book, Pierre Baldi and Soren Brunak present the key machine learning approaches and apply them to the computational problems encountered in the analysis of biological data. The book is aimed at two types of researchers and students. First are the biologists and biochemists who need to understand new data-driven algorithms, such as neural networks and hidden Markov models, in the context of biological sequences and their molecular structure and function. Second are those with a primary background in physics, mathematics, statistics, or computer science who need to know more about specific applications in molecular biology."

  Rik K. Belew and Melanie Mitchell, Adaptive Individuals in Evolving Populations: Models and Algorithms, Proceedings Volume XXVI, SFI Studies in the Sciences of Complexity, Addison-Wesley, 1996.

  Edited volume of readings by biologists, psychologists, and computer scientists (both classic seminal papers and new contributions) focusing on the complex relationship between the genotypic features underlying the mechanisms of maturation and learning and the adapted behaviors ultimately selected.

  Rodney A. Brooks, "Intelligence Without Representation", Artificial Intelligence 47 (1991), pp. 139-160.

  Brooks argues that intelligent behavior can be generated without having explicit manipulable internal representations.

  Rita Carter, Exploring Consciousness, University of California Press, 320 pp., September 2002. ISBN: 0-520-23737-4

  From the publisher: "Rita Carter ponders the nature, origins, and purpose of consciousness in this fascinating inquiry into the toughest problem facing modern science and philosophy. Building on the foundations of her bestselling book Mapping the Mind, she considers whether consciousness is merely an illusion, a by-product of our brain's workings, some as yet inexplicable feature or property of the material universe, or -- as the latest physics may suggest -- the very fundament of reality. Little, she discovers, is as it first seems. Carter draws from a solid body of knowledge -- empirical findings and theoretical hypotheses -- about consciousness, much of it derived from recent discoveries about the brain."

  Rita Carter is a science writer who has twice been awarded the Medical Journalists' Association prize for outstanding contributions to medical journalism.

  Luigi Luca Cavalli-Sforza, Francesco Cavalli-Sforza, Sarah Thorne, and Heather Mimnaugh, eds., The Great Human Diasporas: The History of Diversity and Evolution, Perseus, October 1996, 300 pp., ISBN: 0-201-44231-0.

  From Booknews, Inc.: "Population geneticist Cavalli-Sforza summarizes his 40 years of research on the connections between current genetic data and the evolutionary past for general readers. He outlines the fundamentals of evolutionary theory, shows how archaeological and genetic data were used to track human migrations during the spread of agriculture, and probes issues of eugenics, genetic engineering, and the existence of a single ancestral language."

  B. Charlesworth, Evolution in Age-Structured Populations, Cambridge University Press, 1980.

  Robert James Collins, Studies in Artificial Evolution, Ph.D. Dissertation, Artificial Life Laboratory, Department of Computer Science, UCLA, 1992.

  Reputed to be the first alife dissertation.

  Antonio R. Damasio, Looking for Spinoza: Joy, Sorrow, and the Feeling Brain, Viking Press, 528 pp., September 2002. ISBN: 0-670-03151-8

  From Publisher's Weekley (Copyright 2003 Reed Business Information, Inc.): "The third in a series that began with Descarte's Error, this book deftly combines recent advances in neuroscience with charged meditations on foundational 17th-century philosopher Baruch Spinoza, and the result is Damasio's fullest report so far on the nature of feelings. ... Damasio makes a useful distinction between emotions, which are publicly observable body states, and feelings, which are mental states observable only to the person having them. ... Damasio goes on to connect his own views to Spinoza's and to sympathize with that thinker's `secular religiosity,' which identified God with nature. He ends by discussing spiritual feelings, which he relates to the `sense that the organism is functioning with the greatest possible perfection.'"

  Antonio R. Damasio is the Van Allen Professor and Head of the Department of Neurology at the University of Iowa Medical Center and Adjunct Professor at the Salk Institute in San Diego.

  Kevin Davies Cracking the Genome: Inside the Race to Unlock Human DNA, Free Press, New York, N.Y., 288 pp., February 2001. ISBN 0-743-20479-4

  From the Editors of Scientific American: "The massive effort of recent years to decode the human genome, Davies writes, `is, at the very least, an extraordinary technological achievement, and is at best perhaps the defining moment in the evolution of mankind.' Davies... gives a clear account of the `epic battle' between the public Human Genome Project and the private Celera Genomics to be the first to sequence the genome. He examines difficult issues that arise from the program, among them the legal issue of gene patenting and the moral issue of genetic engineering. And he foresees that `the explosion in genomic information fueled by the sequence will revolutionize the diagnosis and treatment of countless diseases."

  Kevin Davies is the founding editor of Nature Genetics and executive editor of Current Biology.

  Richard Dawkins, The Blind Watchmaker, W.W. Norton, New York, 1987.

  An enthusiastic defense of Darwin.

  Terrence W. Deacon, The Symbolic Species: The Co-Evolution of Language and the Brain, W. W. Norton and Co., New York, N.Y., 527 pp., April 1998. ISBN 0-393-31574-4

  From the publisher: "This revolutionary book provides fresh answers to long-standing questions of human origins and consciousness. Drawing on his breakthrough research in comparative neuroscience, Terrence Deacon offers a wealth of insights into the significance of symbolic thinking: from the co-evolutionary exchange between language and brains over two million years of hominid evolution to the ethical repercussions that followed man's newfound access to other people's thoughts and emotions. Informing these insights is a new understanding of how Darwinian processes underlie the brain's development and function as well as its evolution. In contrast to much contemporary neuroscience that treats the brain as no more or less than a computer, Deacon provides a new clarity of vision into the mechanisms of mind. It injects a renewed sense of adventure into the experience of being human."

  Terrence W. Deacon is associate professor of biological anthropology at Boston University and also conducts research at the McLean Hospital at the Harvard Medical School.

  Daniel C. Dennett, Darwin's Dangerous Idea: Evolution and the Meaning of Life, Touchstone Books, 1996, ISBN: 068482471X.

  Also of interest: the two-part critique of this book by Stephen Jay Gould (June 12 and June 26, 1997) as well as Dennett's reply and Gould's rebuttal (August 14, 1997), and further comments by Steven Pinker followed by Gould's rebuttal (October 9, 1997), all originally appearing in, and now archived by, the NY Review of Books.

  Daniel C. Dennett, Freedom Evolves, Viking Press, 347 pp., February 2003. ISBN: 0-670-03186-0

  From the publisher: "In this new book, Dennett shows that evolution is the key to resolving the ancient problems of moral and political freedom. Like the planet's atmosphere on which life depends, the conditions on which our freedom depends had to evolve, and like the atmosphere, they continue to evolve - and could be extinguished. According to Dennett, biology provides the perspective from which we can distinguish the varieties of freedom that matter. Throughout the history of life on this planet, an interacting web and internal and external conditions have provided the frameworks for the design of agents that are more free than their parts - from the unwitting gropings of the simplest life forms to the more informed activities of animals to the moral dilemmas that confront human beings living in societies."

  Daniel C. Dennett is a University Professor and the Director of the Center for Cognitive Studies at Tufts University.

  Lee Alan Dugatkin, The Imitation Factor: Evolution Beyond the Gene, Free Press, 243 pp., January 2001. ISBN: 0-684-86453-3.

  From Booklist: "Dugatkin, biologist and science writer, spares the reader what he calls `the nasty mathematics' backing up his findings but provides a fascinating look at how the act of imitating affects evolution and culture. He offers interesting examples to prove theories on sexual and mating habits of barn swallows, scorpion flies, stalk-eyed flies, guppies, and humans as they imitate the behavior of others of their species and, thereby, transmit physical and cultural traits."

  Brian Goodwin, How the Leopard Changed Its spots, Scribner, N.Y., 1994.

  Stephen Jay Gould, The Structure of Evolutionary Theory, Harvard University Press, Cambridge, MA, 1464 pp., March 2002. ISBN: 0-674-00613-5

  From Publishers Weekly (Copyright 2002 Cahners Business Information, Inc.): "The culmination of about 25 years of research and study, this book traces the history of evolutionary thought and charts a path for its future. After Darwin wrote The Origin of Species in 1859, scientists created a synthesis of genetics, ecology and paleontology to explain how natural selection could produce change and form new species. Gould thinks that this `modern synthesis' has hardened into a dogma stifling the science. Gould claims that an obsession with `selfish genes' and simplistic versions of natural selection blinds researchers to the significance of new discoveries about how evolution really works. The rules by which embryos develop, for example, create constraints that channel the flow of evolution. Asteroid impacts and other catastrophes can send evolution off on unpredictable trajectories. And selection, Gould contends, may act not just on individuals or their genes, but on entire species or groups of species, and in ways we've only begun to understand. This book presents Gould in all his incarnations: as a digressive historian, original thinker and cunning polemiscist. It is certainly not a perfect work. Gould gives short shrift to the tremendous discoveries spurred by `Darwinian fundamentalism,' while he sometimes overplays the importance of hazy theoretical arguments that support his own claims. But even Gould's opponents will recognize this as the magnum opus of one of the world's leading evolutionary thinkers."

  Until his death in 2002, Stephen Jay Gould was the Alexander Agassiz Professor of Zoology at Harvard University.

  Steve Grand, Creation: Life and How to Make It, Harvard University Press, Cambridge, MA, 230 pp., October 2001. ISBN: 0-647-00654-2.

  From Publishers Weekly: "Blending aspects of philosophy, computer science, artificial intelligence, biology, and computer gaming, Grand attempts to define life, discuss the nature of the human soul, and demonstrate how it is possible to create entities that demand to be called both living and intelligent. ... He argues persuasively that life, both real and artificial, is an emergent property, arising inevitably from the interactions of its component parts and, as such, is something much greater than and qualitatively different from the sum of its parts. This view leads Grand to assert that most scientists working in the field of artificial intelligence are taking the wrong tack when they attempt to program intelligence into machines."

  S. R. Hameroff, A. W. Kaszniak, and A. C. Scott (eds.), Toward a Science of Consciousness 2, MIT Press, 1998, 0-262-08262-4.

  From the book blurb: "What is Consciousness? Recent attempts to answer this question have motivated two interdisciplinary conferences sponsored by the University of Arizona in Tucson. ... This volume presents a selection of invited papers from the second conference, held in April 1996."

  D. L. Hartl and A. C. Clark, Principles of Population Genetics, 2nd edition, Sinauer, Sunderland, MA, 1989.

  William D. Hamilton, Narrow Roads of Gene Land: The Collected Papers of W. D. Hamilton (Evolution of Sex,2), Getty Center for Education in the Arts, 512 pages, February 2001, ISBN: 0-198-50336-9.

  From the publisher: "The range and fundamental importance of Hamilton's contributions to theoretical biology have given him an enviable status throughout the world. Most of the papers are classics, still regarded as fresh and relevant today, yet many are in inaccessible places. The introductions are completely new, and give the humanas well as the scientific background to the work and resulting paper."

  Marc D. Hauser, Wild Minds: What Animals Really Think, Henry Holt and Company, 315 pages, March 2000, ISBN: 0-805-05669-6.

  Marc D. Hauser argues that the only way to understand how animals think, and what they think about, is to see the minds of animals as a specialized collection of mental tools that are each designed to solve particular social and ecological problems. In particular, he argues that all animals, including humans, share a universal toolkit that allows them to recognize objects, count how many there are, and find their way in a spatial world. He also argues that specialized tools have arisen among animals in response to unique sets of social or ecological problems that these animals have confronted. He defends his arguments by drawing upon extensive observations and experiments on animals in the wild and in captivity, using evolutionary theory and methodological techniques from ethology, cognitive science, neurobiology, linguistics, and infant development.
  

  Marc D. Hauser is Professor of Psychology at Harvard University.

  Henrik Jeldtoft Jensen, Self-Organized Criticality: Emergent Complex Behavior in Physical and Biological Systems, Cambridge University Press, 1998, 168 pp., $32.95 (paperback, Barnesandnoble.com). ISBN 0-521-48371-9

  From the publisher: "Self-organized criticality (SOC) is based upon the idea that complex behavior can develop spontaneously in certain multi-body systems whose dynamics vary abruptly. This book is a clear and concise introduction to the field of self-organized criticality, and contains an overview of the main research results. The author presents and analyzes computer models to describe a number of systems, and he explains the different mathematical formalisms developed to understand SOC. The final chapter assesses the impact of this field of study, and highlights some key areas of new research."

  Stuart Kauffman, Origins of Order: Self-Organization and Selection in Evolution, Oxford U Press, N.Y., 1993.

  From the Preface: "This book is an attempt to focus attention on new themes in developmental and evolutionary biology. It is, in fact, an attempt to include Darwinism in a broader context. ...One might have thought, more than a century (after Darwin), that we would understand the construction requirements which permit complex systems to adapt. But we do not. Nor do we understand the extent to which selection can achieve systems able to adapt successfully. This book explores these broad themes."

  Evelyn Fox Keller, The Century of the Gene, Harvard University Press, 192 pp., January 2001. ISBN: 0-674-00372-1.

  From the publisher: "In a book that promises to change the way we think and talk about genes and genetic determinism, Evelyn Fox Keller, one of our most gifted historians and philosophers of science, provides a powerful, profound analysis of the achievements of genetics and molecular biology in the twentieth century, the century of the gene. Not just a chronicle of biology's progress from gene to genome in one hundred years, (this book) also calls our attention to the surprising ways these advances challenge the familiar picture of the gene most of us still entertain... (A) new awareness is absolutely critical: that understanding the components of a system (be they individual genes, proteins, or even molecules) may tell us little about the interactions among these components."

  Evelyn Fox Keller is Professor of History and Philosophy of Science at MIT.

  Christopher Langton, ed., Artificial Life, Volume 6, SFI Studies in the Sciences of Complexity, Addison-Wesley, 1989. [The proceedings of the first conference on alife, held in Los Alamos (1987).]

  Christopher Langton, Charles Taylor, Doyne Farmer, and Steen Rasmussen, eds., Artificial Life II, Volume 10, SFI Studies in the Sciences of Complexity, Addison-Wesley, California, 1992. [The proceedings of the second conference on artificial life, held in Santa Fe (1990).]

  Christopher Langton, ed., Artificial Life II, Video Proceedings, Addison-Wesley, 1992. [An interesting video presentation of the second conference on artificial life, held in Santa Fe (1990).]

  Christopher Langton et al., eds., Artificial Life III, Volume 17, Santa Fe Institute Studies in the Sciences of Complexity, Addison-Wesley, 1994. [Proceedings of the third conference on artificial life, held in Santa Fe (1992).]

  Christopher Langton and T. Shimohara, eds., Artificial Life V, MIT Press/Bradford Books, MA, 1996, 0-262-62111-8. [Proceedings of the fifth conference on artificial life, held in Japan (1996).]

  Rodolfo R. Llinas, I of the Vortex: From Neurons to Self, The MIT Press, Cambridge, MA, 264 pp., April 2002. ISBN 0-262-12233-2

  From the publisher: "In (this book), Rodolfo Llinas, a founding father of modern brain science, presents an original view of the evolution and nature of mind. According to Llinas, the `mindness state' evolved to allow predictive interactions between mobile creatures and their environment. To move through the environment safely, a creature must anticipate the outcome of each movement on the basis of incoming sensory data. Thus the capacity to predict is most likely the ultimate brain function. One could even say that Self is the centralization of prediction. At the heart of Llinas's theory is the concept of oscillation. Many neurons possess electrical activity, manifested as oscillating variations in the minute voltages across the cell membrane. On the crests of these oscillations occur larger electrical events that are the basis for neuron-to-neuron communication. Like cicadas chirping in unison, a group of neurons oscillating in phase can resonate with a distant group of neurons. This simultaneity of neuronal activity is the neurobiological root of cognition. Although the internal state that we call the mind is guided by the senses, it is also generated by the oscillations within the brain. Thus, in a certain sense, one could say that we live in a kind of virtual reality."

  Rodolfo R. Llinas is the Thomas and Susanne Murphy Professor of Neuroscience and Chairman of the Department of Physiology and Neuroscience at the New York University School of Medicine.

  Lynn Margulis, Dorion Sagan, and Philip Morrison, Slanted Truths: Essays on Gaia, Symbiosis, and Evolution, Copernicus Books, 1997, 368 pp., $28.00 (hard cover). ISBN 0-387-94927-5

  From the publisher: "Lynn Margulis and Dorion Sagan here present their fourth book as a writing team, a collection of their essays on Gaia theory, symbiosis, individuality, and the way science is practiced nowadays. Lynn Margulis is most famous for her now-widely-accepted proposition that the cells of higher plants and animals are not individuals but symbiotic unions of more primitive cells. In these essays, perhaps more clearly than in any of Margulis and Sagan's previous books, we can see how her seemingly disparate interests combine into a coherent and very provocative scientific world-view about the tendency of life to form complex communities."

  Ernst Mayr, This is Biology: The Science of the Living World, Belknap Press, 352 pages, September 1998 (Reprint Edition), ISBN: 0-674-88469-8.

  From an amazon.com editorial review: "Though biology is a relatively young science, born in the 19th century, its roots go back to the days of Aristotle. Mayr traces its development from the ancient Greeks to the advent of modern molecular techniques. Woven throughout this history of the science is an explanation of its relation to other sciences and to the humanities, particularly history and ethics."

  Ernst Mayr and William B. Provine (eds.), The Evolutionary Synthesis: Perspectives on the Unification of Biology, Harvard University Press, 1998, 504 pp., $19.95 (paperback, Amazon.com). ISBN 0-674-27226-9

  From the publisher: "Biology was forged into a single, coherent science only within living memory. In this volume the thinkers responsible for the `modern synthesis' of evolutionary biology and genetics come together to analyze that remarkable event. In a new Preface, Ernst Mayr calls attention to the fact that scientists in different biological disciplines varied considerably in their degree of acceptance of Darwin's theories. Mayr shows us that these differences were played out in four separate periods: 1859 to 1899, 1900 to 1915, 1916 to 1936, and 1937 to 1947. He thus enables us to understand fully why the synthesis was necessary and why Darwin's original theory -- that evolutionary change is due to the combination of variation and selection -- is as solid at the end of the twentieth century as it was in 1859."

  Jean-Arcady Meyer, Alain Berthoz, Dario Floreano, Herbert L. Roitblat, and Stewart W. Wilson (eds.), From Animals to Animats 6, Proceedings of the Sixth International Conference on Simulation of Adaptive Behavior, MIT Press, October 2000, 500 pages, ISBN: 0-262-63200-4.

  From the publisher: "The Animals to Animats Conference brings together researchers from ethology, psychology, ecology, artificial intelligence, artificial life, robotics, engineering, and related fields to further understanding of the behaviors and underlying mechanisms that allow natural and synthetic agents (animats) to adapt and survive in uncertain environments. The work presented focuses on well-defined models -- robotic, computer-simulation, and mathematical -- that help to characterize and compare various organizational principles or architectures underlying adaptive behavior in both natural animals and animats."

  R. E. Michod and B. R. Levin, eds., The Evolution of Sex, Sinauer Associates, 1988.

  Includes papers by J. M. Smith, W. Hamilton, M. Rose, J. Felzenstein, J. Crow, R. Trivers, G. Williams, M. Uyenoyama, among others.

  Geoffrey F. Miller, The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature, Doubleday, April 2000, 520 pp., ISBN 0-385-49516-1.

  From an Amazon.com Editorial Review: "In The Mating Mind, (the author) takes Darwin's `other' evolutionary theory -- of sexual rather than natural selection -- and uses it to build a theory about how the human mind has developed the sophistication of a peacock's tail to encourage sexual choice and the refining of art, morality, music, and literature. While many evolutionary psychologists see the mind as a Swiss army knife, and cognitive science sees it as a computer, Miller compares it to an entertainment system, evolved to stimulate other brains."

  Randolph M. Nesse (ed.), Evolution and the Capacity for Commitment, Russell Sage Foundation Series on Trust, New York, N.Y., 352 pp., November 2001. ISBN 0-871-54622-1

  From the book jacket (Edward O. Wilson, University Research Professor, Harvard University): "Nothing is more basic to the human condition than the capacity for commitment, and nothing is more important to the capacity than its biological underpinnings and evolution. Randolph Nesse, serving as editor and connecting essayist, and the other authors of (this volume) are among the leaders in and around this newly emerging field of scholarship."

  Randolph M. Nesse is professor of psychiatry and professor of psychology at the University of Michigan.

  Steven Pinker, The Blank Slate: The Modern Denial of Human Nature, Viking Press, 528pp., September 2002. ISBN: 0-670-03151-8.

  From Publishers Weekly (Copyright 2002 Cahners Business Information, Inc.): Drawing on decades of research in the `sciences of human nature,' (Pinker) attacks the notion that an infant's mind is a blank slate, arguing instead that human beings have an inherited universal structure shaped by the demands made upon the species for survival, albeit with plenty of room for cultural and individual variation. For those who have been following the sciences in question including cognitive science, neuroscience, behavioral genetics and evolutionary psychology much of the evidence will be familiar, yet Pinker's clear and witty presentation, complete with comic strips and allusions to writers from Woody Allen to Emily Dickinson, keeps the material fresh. What might amaze is the persistent, often vitriolic resistance to these findings Pinker presents and systematically takes apart, decrying the hold of the `blank slate' and other orthodoxies on intellectual life."

  Steven Pinker is the Peter de Florez Professor of Psychology, Department of Brain and Cognitive Sciences, MIT, Cambridge, MA.

  P. Prusinkiewicz and Aristid Lindenmayer, The Algorithmic Beauty of Plants, Springer-Verlag, New York, 1990

  Description of L-Systems, coupled with astounding pictures.

  Steven R. Quartz and Terrence J. Sejnowski, Liars, Lovers, and Heroes: What the New Brain Science Reveals About How We Become Who We Are, William Morrow and Co., 336pp., October 2002. ISBN: 0-688-16218-5.

  From the publisher: "This exciting, timely book combines cutting-edge findings in neuroscience with examples from history and recent headlines to offer new insights into who we are. Introducing the new science of cultural biology, born of advances in brain imaging, computer modeling, and genetics, Drs. Quartz and Sejnowski demystify the dynamic engagement between brain and world that makes us something far beyond the sum of our parts. The authors show how our humanity unfolds in precise stages as brain and world engage on increasingly complex levels. Their discussion embraces shaping forces as ancient as climate change over millennia and events as recent as the terrorism and heroism of September 11 and offers intriguing answers to some of our most enduring questions, including why we live together, love, kill -- and sometimes lay down our lives for others."

  Steven R. Quartz is Director of the Social Cognitive Neuroscience Laboratory at the California Institute of Technology, and Terrence J. Sejnowski is Director of the Computational Neurobiology Laboratory at the Salk Institute.

  Thomas Ray, "An Approach to the Synthesis of Life", pp. 371-401 in C. Langton, ed., Artificial Life II, op. cit..

  Matt Ridley, Evolution, Blackwell, Cambridge, MA, 1993.

  Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Harpercollins, October 2000, 352 pp., ISBN 0-060-93290-2.

  From an Amazon.com Editorial Review: "Science writer Matt Ridley has found a way to tell someone else's story without being accused of plagiarism. ... Each chapter pries one gene out of its chromosome and focuses on its role in our development and adult life, but also goes further, exploring the implications of genetic research and our quickly changing attitudes towards this information. Genome shies away from the `tedious biochemical middle managers' that only a nerd could love and instead goes for the A-material: genes associated with cancer, intelligence, sex (of course), and more."

  Don Ross, Andrew Brook, and David Thompson (eds.), Dennett's Philosophy, MIT Press, September 2000, 448 pages, ISBN: 0-262-18200-9.

  From the publisher: "The influential philosopher Daniel Dennett is best known for his distinctive theory of mental content, his elucidation of how the complex components of mental processing seem to come together in the relatively coherent narratives that we tell ourselves about ourselves and in his vivid accounts of how to think about minds in their evolutionary setting. The essays in this collection step back to ask: Do the complex components of Dennett's work on intentionality, consciousness, evolution, and ethics themselves come together into a coherent philosophical system? ... In the concluding essay ... Dennett offers his own thoughts on the comprehensiveness of his philosophy."

  Don Ross is Senior Lecturer in Economics and Director of the Philosophy, Politics, and Economics Program at the University of Cape Town. Andrew Brook is Professor of Philosophy and Director of the Cognitive Science Program at Carleton University, Canada.

  Vaclav Smil, The Earth's Biosphere, The MIT Press, Cambridge, MA, 360 pp., July 2002. ISBN 0-262-19472-4

  From the publisher: "In his latest book, Vaclav Smil tells the story of the Earth's biosphere from its near- and long-term future. He explains the workings of its parts and what is known about their interactions. With essay-like flair, he examines the biosphere's physics, chemistry, biology, geology, oceanography, energy, climatology, and ecology, as well as the changes caused by human activity. He provides both the basics of the story and surprising asides illustrating critical but often neglected aspects of biospheric complexity."

  Vaclav Smil is Distinguished Professor at the University of Manitoba. In 2001 he was presented with the Award for Public Understanding of Science and Technology by the American Association for the Advancement of Science.

  John Maynard Smith and Eors Szathmary, The Major Transitions in Evolution, Oxford University Press, Oxford, UK, 1997. ISBN: 0-198-50294-X (Paperback, REPRINT EDITION).

  From the publisher: "This ambitious book provides the first unified discussion of the full range of evolutionary transitions. Engagingly written and filled with numerous illustrations, this book can be read with enjoyment by anyone with an undergraduate training in biology. It includes accessible discussions of a wide range of topics, from molecular biology and linguistics to insect societies."

  Ricard V. Solé and Brian Goodwin, Signs of Life: How Complexity Pervades Biology, Basic Books, 320 pp., January 2001. ISBN: 0-465-01927-7.

  From the publisher: "(This book) is an entirely new approach to the problems of understanding living systems. It applies the mathematics of order and disorder, of entropy, chance, and randomness, of chaos and nonlinear dynamics to the various mysteries of the living world at all levels. Less a set of answers than a guide to thinking about living systems, this book will help set the agenda for biology in the coming century."

  Ricard Solé is Associate Professor of physics and nuclear engineering at the Politechnic University of Barcelona and a Santa Fe Institute External Professor. Brian Goodwin is a Scholar in Residence at Schumacher College and a member of the Santa Fe Institute.

  Philip M. Tierno, Jr., The Secret Life of Germs: Observations of a Microbe Hunter, Pocket Books, New York, N.Y., 304 pp., January 2002. ISBN 0-743-42187-6

  From Publishers Weekly (Copyright 2001 Cahners Business Information, Inc.): "Germs are the seeds of life as well as disease, explains Tierno, the New York Medical Center doctor who helped solve the mystery of toxic shock syndrome. A germ hunter in the truest sense, Tierno spells out how to survive a world so rife with germs that `alien observers might conclude that they are the dominant life form on our planet.' His field samplings from high-trafficked New York City locations such as pay phones, taxicabs, public restrooms and even the engagement ring counter at Tiffany's will startle readers, but the author is not an alarmist: his aim is disease prevention, and his method is education. THe book opens with a quick history of germ evolution and of human understanding of germs, from biblical injunctions on cleanliness to the modern science of microbiology. It outlines the various ways illness-causing bacteria are transmitted and gives precise instructions for minimizing infection with a bulleted list of `protective response strategies' at the end of each chapter."

  F. J. Varela and P. Bourgine, eds., Towards a Practice of Autonomous Systems, MIT press, Cambridge, 1992.

  This is the proceedings volume from the first European conference on Alife.

  Edward O. Wilson, Consilience: The Unity of Knowledge, Random House, April 1999, 367 pp., ISBN: 0-679-76867-X.

  From an editorial review by Amazon.Com: "The biologist Edward O. Wilson is a rare scientist: having over a long career made signal contributions to population genetics, evolutionary biology, entomology, and ethology, he has also steeped himself in philosophy, the humanities, and the social sciences. The result of his lifelong, wide-ranging investigations is Consilience (the word means `a jumping together,' in this case of the many branches of human knowledge), a wonderfully broad study that encourages scholars to bridge the many gaps that yawn between and within the cultures of science and the arts. ... Wilson examines the ways (rightly and wrongly) in which science is done, puzzles over the postmodernist debates now sweeping academia, and proposes thought-provoking ideas about religion and human nature."

  Edward O. Wilson and Laura Simonds Southworth (Illustrator), Naturalist, Warner Books, 1995, 400 pp., $13.99 (paperback). ISBN 0-446-67199-1

  From Nature and Ecology, Editor's Recommended Book: "E. O. Wilson, among the most prominent biologists working today, has made signal contributions to the field both large and small. As an entomologist, and especially as a student of several kinds of ants, he is famed among a small audience. He is better known for his work in the controversial subdiscipine of sociobiology for his formulations of island-biogeographic theory, and for his catastrophic view of modern extinctions. His lucid memoir, Naturalist, treats all these matters and more, and it celebrates the sea change in our view of nature -- namely, that we now see that `we are bound to the rest of life in our ecology, our physiology, and even our spirit' -- that has come about in no small measure because of Wilson's distinguished career."

B. Game Theory Approaches to Biological Evolution

• W. G. Hines, "Evolutionary Stable Strategies: A Review of Basic Theory", Theoretical Population Biology 31 (1987), pp. 195-272.
  A survey of the biological literature focusing on evolutionarily stable strategies as possible attractors of "replicator dynamics," in which the rate of growth in the fraction of the population playing a particular strategy is equal to the deviation of that strategy's fitness or payoff from the average fitness or payoff.

  J. Hofbauer and Karl Sigmund, Evolutionary Games and Replicator Dynamics, Cambridge University Press, 1998, 0-521-62365-0.

  From the book blurb: "Evolutionary game theory replaces the static solutions of classical game theory by a dynamical approach centered not on the concept of rational players but on the population dynamics of behavioral programs. In this book the authors investigate the nonlinear dynamics of the self-regulation of social and economic behavior, and of the closely related interactions among species in ecological communities."

  John Maynard Smith, Evolution and the Theory of Games, Cambridge University Press, United Kingdom, 1982.

Copyright © 2005 Leigh Tesfatsion. All Rights Reserved.