Complexity: A Guided Tour - Melanie Mitchell (2009)
Achacoso, T. B. and Yamamoto, W. S. AY’s Neuroanatomy of C. Elegans for Computation. Boca Raton, FL: CRC Press, 1991.
Adami, C. Introduction to Artificial Life, Springer, 1998.
Agutter P. S and Wheatley D. N. Metabolic scaling: Consensus or Controversy? Theoretical Biology and Medical Modeling, 18, 2004, pp. 283–289.
Albert, R. and Barabási, A-L. Statistical mechanics of complex networks. Reviews of Modern Physics, 74, pp. 48–97, 2002.
Ashby, H. R. Design for a Brain. New York: Wiley, 1954.
Aspray, W. John von Neumann and the Origins of Modern Computing. Cambridge, MA: MIT Press, 1990.
Aubin, D. and Dalmedico, A. D. Writing the history of dynamical systems and chaos: Longue Durée and revolution, disciplines, and cultures. Historia Mathematica 29, 2002, pp. 273–339.
Axelrod, R. The Evolution of Cooperation. New York: Basic Books, 1984.
Axelrod, R. An evolutionary approach to norms. American Political Science Review, 80 (4), 1986, pp. 1095–1111.
Axelrod R. Advancing the art of simulation in the social sciences. In Conte, R., Hegselmann, R., Terna, P. (editors). Simulating Social Phenomena. (Lecture Notes in Economics and Mathematical Systems 456). Berlin: Springer-Verlag, 1997.
Bak, P. How Nature Works: The Science of Self-Organized Criticality. New York: Springer, 1996.
Barabási, A.-L. Linked: The New Science of Networks. Cambridge, MA: Perseus, 2002.
Barabási, A.-L. and Albert, R. Emergence of scaling in random networks. Science, 286, 1999, pp. 509–512.
Barabási, A.-L. and Oltvai, Z. N. Network biology: Understanding the cell’s functional organization. Nature Reviews: Genetics, 5, 2004, pp. 101–113.
Barrett, P. (editor). Charles Darwin’s Notebooks, 1836-1844: Geology, Transmutaiton of Species, Metaphysical Enquiries. Ithaca, NY: Cornell University Press, 1987.
Bassett, D. S. and Bullmore, D. Small-world brain networks. The Neuroscientist, 12, 2006, pp. 512–523.
Bateson, G. H. Mind and Nature: A Necessary Unity. Skokie, IL: Hampton Press, 1979.
Beinhocker, E. D. The Origin of Wealth: Evolution, Complexity, and the Radical Remaking of Economics. Cambridge, MA: Harvard Business School Press, 2006.
Bennett, C. H. The thermodynamics of computation—a review. International Journal of Theoretical Physics, 21, 1982, pp. 905–940.
Bennett, C. H. Dissipation, information, computational complexity and the definition of organization. In Pines, D. (editor), Emerging Syntheses in Science. Redwood City, CA: Addison-Wesley, 1985, pp. 215–233.
Bennett, C. H. How to define complexity in physics, and why. In W. H. Zurek (editor), Complexity, Entropy, and the Physics of Information. Reading, MA: Addison-Wesley, 1990, pp. 137–148.
Berlekamp, E., Conway, J. H., and Guy, R. Winning Ways for Your Mathematical Plays, volume 2. San Diego, CA: Academic Press, 1982.
Bickhard, M. H. The biological foundations of cognitive science. In Mind 4: Proceedings of the 4th Annual Meeting of the Cognitive Science Society of Ireland. Dublin, Ireland: J. Benjamins, 1999.
Bolton, R. J. and Hand, D. J. Statistical fraud detection: A review. Statistical Science, 17(3), 2002, pp. 235–255.
Bonabeau, E. Control mechanisms for distributed autonomous systems: Insights from social insects. In L. A. Segel and I. R. Cohen (editors), Design Principles for the Immune System and Other Distributed Autonomous Systems. New York: Oxford University Press, 2001.
Bonabeau, E., Dorigo, M., and Theraulaz, G. Swarm Intelligence: From Natural to Artificial Systems. New York: Oxford University Press, 1999.
Borrell, B. Metabolic theory spat heats up. The Scientist (News), November 8, 2007. [http://www.the-scientist.com/news/display/53846/].
Bovill, C. Fractal Geometry in Architecture and Design. Boston: Birkhäuser. 1996.
Bowker, J. (editor). The Cambridge Illustrated History of Religions. Cambridge, UK: Cambridge University Press, 2002.
Bowlby, J. Charles Darwin: A New Life. New York: Norton, 1992.
Box, G. E. P. and Draper, N. R. Empirical Model Building and Response Surfaces. New York: Wiley, 1997.
Burgard, A. P., Nikolaev, E. V., Schilling, C. H., and Maranas, C. D. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Research, 14, 2004, pp. 301–312.
Burian, R. M. and Richardson, R. C. Form and order in evolutionary biology: Stuart Kauffman’s transformation of theoretical biology. In PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association, Vol. 2: Symposia and Invited Papers, 1990, 267–287.
Burkhardt, F. and Smith, S. (editors). The Correspondence of Charles Darwin, Volume 1. Cambridge, UK: Cambridge University Press, 1985.
Burks, A. W. Von Neumann’s self-reproducing automata. In A. W. Burks (editor), Essays on Cellular Automata. Urbana: University of Illinois Press, 1970.
Calvino, I. Invisible Cities. New York: Harcourt Brace Jovanovich, 1974. (Translated by W. Weaver.)
Carlson, J. M. and Doyle, J. Complexity and robustness. Proceedings of the National Academy of Science, USA 99, 2002, pp. 2538–2545.
Carroll, S. B. Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom. New York: Norton, 2005.
Caruso, D. A challenge to gene theory, a tougher look at biotech. New York Times, July 1, 2007.
Churchland, P. S., Koch, C., and Sejnowski, T. J. What is computational neuroscience? In E. L. Schwartz (editor), Computational Neuroscience. Cambridge, MA: MIT Press, 1994, pp. 46–55.
Clauset, A., Shalizi, C. R., and Newman, M. E. J. Power-law distributions in empirical data. Preprint, 2007, [http://arxiv.org/abs/0706.1062].
Coale, K. Darwin in a box. Wired, June 14, 1997.
Cochrane, E. Viva Lamarck: A brief history of the inheritance of acquired characteristics. Aeon 2(2), 1997, 5–39.
Cohen, I. Informational landscapes in art, science, and evolution. Bulletin of Mathematical Biology, 68, 2006, pp. 1213–1229.
Cohen, I. Immune system computation and the immunological homunculus. In O. Niestrasz, J. Whittle, D. Harel, and G. Reggio (editors), MoDELS 2006, Lecture Notes in Computer Science, 4199, 2006, pp. 499–512. Berlin: Springer-Verlag.
Cohen, R., ben-Avraham, D., and Havlin, S. Efficient immunization strategies for computer networks and populations. Physics Review Letters, 91(24), 2003, p. 247901.
Connell, J. H. Minimalist Mobile Robotics: A Colony-Style Architecture for an Artificial Creature. San Diego, CA: Academic Press, 1990.
Cook, M. Universality in elementary cellular automata. Complex Systems 15(1), 2004, pp. 1–40.
Coullet, P. and Tresser, C. Itérations d’endomorphismes et groupe de renormalization. Comptes Rendues de Académie des Sciences, Paris A, 287, 1978, pp. 577–580.
Coy, P., Woolley, S., Spiro, L. N., and Glasgall, W. Failed wizards of Wall Street. Business Week, September 21, 1998.
Crutchfield, J. P. The calculi of emergence. Physica D, 75, 1994, 11–54.
Crutchfield, J. P., Farmer, J. D., Packard, N. H., and Shaw, R. S. Chaos. Scientific American, 255, December 1986.
Crutchfield, J. P., and Hanson, J. E. Turbulent pattern bases for cellular automata. Physica D 69, 1993, pp. 279–301.
Crutchfield, J. P., Mitchell, M., and Das, R. Evolutionary design of collective computation in cellular automata. In J. P. Crutchfield and P. K. Schuster (editors), Evolutionary Dynamics—Exploring the Interplay of Selection, Neutrality, Accident, and Function. New York: Oxford University Press, 2003, pp. 361–411.
Crutchfield, J. P. and Shalizi, C. R. Thermodynamic depth of causal states: When paddling around in Occam’s pool shallowness is a virtue. Physical Review E, 59 (1), 1999, pp. 275–283.
Crutchfield, J. P. and Young, K. Inferring statistical complexity. Physical Review Letters 63, 1989, pp. 105–108.
Cupitt, R. T. Target rogue behavior, not rogue states. The Nonproliferation Review, 3, 1996, pp. 46–54.
Cupitt, R. T. and Grillot, S. R. COCOM is dead, long live COCOM: Persistence and change in multilateral security institutions. British Journal of Political Science 27, 1997, pp. 361–389.
Darwin, C. The Autobiography of Charles Darwin. Lanham, MD: Barnes & Noble Publishing, 2005. Originally published 1887.
Darwin, C. and Barlow, N. D. The Autobiography of Charles Darwin (Reissue edition). New York: Norton, 1993. [Originally published 1958.]
Darwin, E. The Temple of Nature; or, The Origin of Society: A Poem with Philosophical Notes. London: J. Johnson, 1803.
Dawkins, R. The Extended Phenotype (Reprint edition). New York: Oxford University Press, 1989. (Originally published 1982.)
Dean, W., Santos, F., Stojkovic, M., Zakhartchenko, V., Walter, J., Wolf, E., and Reik, W. Conservation of methylation reprogramming in mammalian development: Aberrant reprogramming in cloned embryos. Proceedings of the National Academy of Science, USA, 98(24), 2001, pp. 13734–13738.
Dennett, D. R. Elbow Room: The Varieties of Free Will Worth Wanting. Cambridge, MA: MIT Press, 1984.
Dennett, D. R. Consciousness Explained. Boston: Little, Brown & Co, 1991.
Dennett, D. R. Darwin’s Dangerous Idea. New York: Simon & Schuster, 1995.
Descartes, R. A Discourse on the Method. Translated by Ian Maclean. London: Oxford World’s Classics, Oxford University Press, 2006 .
Dietrich, M. R. The origins of the neutral theory of molecular evolution. Journal of the History of Biology, 27(1), 1994, pp. 21–59.
Dorigo, M. and Stützle, T. Ant Colony Optimization, MIT Press, 2004.
Dover, G. A. On the edge. Nature, 365, 1993, pp. 704–706.
Dukas, H. and Hoffmann B. (editors). Albert Einstein, The Human Side: New Glimpses from His Archives. Princeton University Press, 1979.
Dunne, J. A. The network structure of food webs. In M. Pascual and J. A. Dunne (editors). Ecological Networks: Linking Structure to Dynamics in Food Webs. New York: Oxford University Press, 2006, pp. 27–86.
Dunne, J. A. Williams, R. J. and Martinez, N. D. Food-web structure and network theory: The role of connectance and size. Proceedings of the National Academy of Science, USA, 99(20), 2002, pp. 12917–12922.
Eddington, A. E. The Nature of the Physical World. New York: Macmillan, 1928.
Eigen, M. How does information originate? Principles of biological self-organization. In S. A. Rice (editor), For Ilya Prigogine. New York: Wiley 1978, pp. 211–262.
Eigen, M. Steps Towards Life. Oxford: Oxford University Press, 1992.
Einstein, A. Out of My Later Years (revised edition). Castle Books, 2005 [originally published 1950, New York: Philosophical Books.]
Eldredge, N. and Tattersall, I. The Myths of Human Evolution. New York: Columbia University Press, 1982.
Erwin, D. H. The developmental origins of animal bodyplans. In S. Xiao and A. J. Kaufman (editors), Neoproterozoic Geobiology and Paleobiology. New York: Springer, 2006, pp. 159–197.
Everdell, W. R. The First Moderns: Profiles in the Origins of Twentieth-Century Thought. Chicago, IL: University of Chicago Press, 1998.
Feigenbaum, M. J. Universal behavior in nonlinear systems. Los Alamos Science, 1(1), 1980, pp. 4–27.
Fell, D. A. and Wagner, A. The small world of metabolism. Nature Biotechnology, 18, 2000, pp. 1121–1122.
Felton, M. J. Survival of the fittest in drug design. Modern Drug Discovery, 3(9), 2000, pp. 49–50.
Floridi, L., Open problems in the philosophy of information. Metaphilosophy, 35(4), 2004, pp. 554–582.
Fogel, D. B. Evolutionary Computation: The Fossil Record. New York: Wiley-IEEE Press, 1998.
Forrest, S. Emergent Computation. Cambridge, MA: MIT Press, 1991.
Franks, N. R. Army ants: A collective intelligence. American Scientist, 77(2), 1989, pp. 138–145.
Freud, S. Moses and Monotheism. New York: Vintage Books, 1939.
Friedheim, R. L. Ocean governance at the millennium: Where we have been, where we should go: Cooperation and discord in the world economy. Ocean and Coastal Management, 42(9), pp. 747–765, 1999.
Fry, I. The Emergence of Life on Earth: A Historical and Scientific Overview. Piscataway, NJ: Rutgers University Press, 2000.
Galan, J. M. and Izquierdo, L. R. Appearances can be deceiving: Lessons learned re-implementing Axelrod’s ‘Evolutionary Approaches to Norms.’ Journal of Artificial Societies and Social Simulation, 8(3), 2005, [http://jasss.soc.surrey.ac.uk/8/3/2.html].
Garber, D. Descartes, mechanics, and the mechanical philosophy. Midwest Studies in Philosophy 26 (1), 2002, pp. 185–204.
Gell-Mann, M. The Quark and the Jaguar. New York: Freeman, 1994.
Gell-Mann, M. What is complexity? Complexity, 1(1), 1995, pp. 16–19.
Gide, A. The Counterfeiters. Translated by D. Bussy. New York: Vintage, 1973, p. 353. Original: Journal des Faux-Monnayeurs, Librairie Gallimard, Paris, 1927.
Gladwell, M. The Tipping Point: How Little Things Can Make a Big Difference. Boston: Little, Brown, 2000.
Gleick, J. Chaos: Making a New Science. New York: Viking, 1987.
Gleick, J. Isaac Newton, New York: Pantheon Books, 2003.
Goldstine, H. H. The Computer, from Pascal to von Neumann. Princeton, NJ: Princeton University Press, 1993. First edition, 1972.
Goodrich, C. S. and Matache, M. T. The stabilizing effect of noise on the dynamics of a Boolean network, Physica A, 379(1), 2007, pp. 334–356.
Gordon, D. M. Task allocation in ant colonies. In L. A. Segel and I. R. Cohen (editors), Design Principles for the Immune System and Other Distributed Autonomous Systems. New York: Oxford University Press, 2001.
Gordon, D. M. Control without hierarchy. Nature, 446(7132), 2007, p. 143.
Gould, S. J. Is a new and general theory of evolution emerging? Paleobiology, 6, 1980, pp. 119–130.
Gould, S. J. Sociobiology and the theory of natural selection. In G.W. Barlow and J. Silverberg (editors), Sociobiology: Beyond Nature/Nurture?, pp. 257–269. Boulder, CO: Westview Press Inc., 1980.
Government Accounting Office. Long-Term Capital Management: Regulators Need to Focus Greater Attention on Systemic Risk. Report to Congressional Request, 1999 [http://www.gao.gov/cgi-bin/getrpt?GGD-00-3].
Grant, B. The powers that be. The Scientist, 21(3), 2007.
Grene, M. and Depew, D., The Philosophy of Biology: An Episodic History. Cambridge, U.K.: Cambridge University Press, 2004.
Grinnell, G. J. The rise and fall of Darwin’s second theory. Journal of the History of Biology, 18(1), 1985, pp. 51–70.
Grosshans, H. and Filipowicz, W. The expanding world of small RNAs. Nature, 451, 2008, pp. 414–416.
Hales, D. and Arteconi, S. SLACER: A Self-Organizing Protocol for Coordination in Peer-to-Peer Networks. IEEE Intelligent Systems, 21(2), 2006, pp. 29–35.
Hardin, G. The tragedy of the commons. Science, 162, 1968, pp. 1243–1248.
Heims, S. The Cybernetics Group. Cambridge, MA: MIT Press, 1991.
Heims, S. J. John von Neumann and Norbert Wiener: From Mathematics to the Technologies of Life and Death. Cambridge: MIT Press, 1980.
Hobbes, T. Leviathan. Cambridge, U.K.: Cambridge University Press, (1651/1991).
Hodges, A. Alan Turing: The Enigma. New York: Simon & Schuster, 1983.
Hoelzer, G. A. Smith, E., and Pepper, J. W., On the logical relationship between natural selection and self-organization. Journal of Evolutionary Biology, 19(6), 2007, pp. 1785–1794.
Hofmeyr, S. A. An interpretive introduction to the immune system. In L. A. Segel and I. R. Cohen (editors), Design Principles for the Immune System and Other Distributed Autonomous Systems. New York: Oxford University Press, 2001.
Hofmeyr, S. A. and Forrest, S. Architecture for an artificial immune system. Evolutionary Computation, 8(4), 2000, pp. 443–473.
Hofstadter, D. R. Gödel, Escher, Bach: an Eternal Golden Braid. New York: Basic Books, 1979.
Hofstadter, D. R. Mathematical chaos and strange attractors. Chapter 16 in Metamagical Themas. New York: Basic Books, 1985.
Hofstadter, D. R. The Genetic Code: Arbitrary? Chapter 27 in Metamagical Themas. Basic Books, 1985.
Hofstadter D. Fluid Concepts and Creative Analogies. New York: Basic Books, 1995.
Hofstadter, D. I am a Strange Loop. New York: Basic Books, 2007.
Hofstadter, D. R. and Mitchell, M. The Copycat project: A model of mental fluidity and analogy-making. In K. Holyoak and J. Barnden (editors), Advances in Connectionist and Neural Computation Theory, Volume 2: Analogical Connections, 1994, pp. 31–112.
Holland, J. H. Adaptation in Natural and Artificial Systems. Cambridge, MA: MIT Press, 1992. (First edition, 1975.)
Holland, J. H. Emergence: From Chaos to Order. Perseus Books, 1998.
Hölldobler, B. and Wilson, E. O. The Ants. Cambridge, MA: Belknap Press, 1990.
Holtham, C. Fear and opportunity. Information Age, July 11, 2007. [http://www.information-age.com/article/2006/february/fear_and_opportunity].
Horgan, J. From complexity to perplexity. Scientific American, 272, June 1995, pp. 74–79.
Horgan, J. The End of Science: Facing the Limits of Knowledge in the Twilight of the Scientific Age. Reading, MA: Addison-Wesley, 1996.
Huberman, B. A. and Glance, N. S. Evolutionary games and computer simulations. Proceedings of the National Academy of Science, USA, 90, 1993, pp. 7716–7718.
Hüttenhofer, A., Scattner, P., and Polacek, N. Non-coding RNAs: Hope or Hype? Trends in Genetics, 21 (5), 2005, pp. 289–297.
Huxley, J. Evolution: The Modern Synthesis. New York, London: Harper & Brothers, 1942.
Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., and Barbási, A.-L. The large-scale organization of metabolic networks. Nature, 407, 2000, pp. 651–654.
Joy, B. Why the future doesn’t need us. Wired, April 2000.
Kadanoff, Leo P. Chaos: A view of complexity in the physical sciences. In From Order to Chaos: Essays: Critical, Chaotic, and Otherwise. Singapore: World Scientific, 1993.
Kauffman, S. A. The Origins of Order. New York: Oxford University Press, 1993.
Kauffman, S. A. At Home in the Universe. New York: Oxford University Press, 1995.
Kauffman, S. A. Investigations. New York: Oxford University Press, 2002.
Keller, E. F. Revisiting ‘scale-free’ networks. BioEssays, 27, 2005, pp. 1060–1068.
Kleinfeld, J. S. Could it be a big world after all? The “six degrees of separation” myth. Society, 39, 2002.
Kleinfeld, J. S. Six degrees: Urban myth? Psychology Today, 74, March/April 2002.
Kollock, P. The production of trust in online markets. In E. J. Lawler, M. Macy, S. Thyne, and H. A. Walker (editors), Advances in Group Processes, 16. Greenwich, CT: JAI Press, 1999.
Kozlowski, J. and Konarzweski, M. Is West, Brown and Enquist’s model of allometric scaling mathematically correct and biologically relevant? Functional Ecology, 18, 2004, pp. 283–289.
Kubrin, D. Newton and the cyclical cosmos: Providence and the mechanical philosophy. Journal of the History of Ideas, 28(3), 1967.
Kurzweil, R. The Age of Spiritual Machines: When Computers Exceed Human Intelligence. New York: Viking, 1999.
Langton, C. G. Artificial Life: An Overview. Cambridge, MA: MIT Press, 1997.
Laplace, P. S. Essai Philosophique Sur Les Probabilites. Paris: Courcier, 1814.
Lee, B. and Ajjarapu, V. Period-doubling route to chaos in an electrical power system. IEE Proceedings, Part C, 140, 1993, pp. 490–496.
Leff, H. S. and Rex, A. F. Maxwell’s Demon: Entropy, Information, Computing. Princeton, NJ: Princeton University Press. Second edition 2003, Institute of Physics Pub., 1990.
Leibniz, G. In C. Gerhardt (Ed.), Die Philosophischen Schriften von Gottfried Wilhelm Leibniz. Volume vii. Berlin: Olms, 1890.
Lesley, R. Xu, Y., Kalled, S. L., Hess, D. M., Schwab, S. R., Shu, H.-B., and Cyster, J. G. Reduced competitiveness of autoantigen-engaged B cells due to increased dependence on BAFF. Immunity, 20(4), 2004, pp. 441–453.
Levy, S. The man who cracked the code to everything. Wired, Issue 10.06, June 2002.
Lewin, R. Complexity: Life at the Edge of Chaos. New York: Macmillan, 1992.
Li, M. and Vitanyi, P. An Introduction to Kolmogorov Complexity and Its Applications. 2nd Edition. New York: Springer-Verlag, 1997.
Li, T. Y. and Yorke, J. A. Period three implies chaos. American Mathematical Monthly 82, 1975, p. 985.
Liebreich, M. How to Save the Planet: Be Nice, Retaliatory, Forgiving, & Clear. White Paper, New Energy Finance, Ltd., 2007 [http://www.newenergyfinance.com/docs/Press/
Liljeros, F., Edling, C. R., Nunes Amaral, L. A., Stanely, H. E., and Aberg, Y. The web of human sexual contacts. Nature, 441, 2001, pp. 907–908.
Lioni, A., Sauwens, C., Theraulaz, G., and Deneubourg, J.-L. Chain formation in OEcophylla longinoda. Journal of Insect Behavior, 14(5), 2001, pp. 679–696.
Liu, H. A brief history of the concept of chaos, 1999 [http://members.tripod.com/~huajie/Paper/chaos.htm].
Lloyd, S. The calculus of intricacy. The Sciences, 30, 1990, pp. 38–44.
Lloyd, S. Measures of complexity: A non-exhaustive list. IEEE Control Systems Magazine, August 2001.
Lloyd, S. and Pagels, H. Complexity as thermodynamic depth. Annals of Physics, 188, 1988, pp. 186–213.
Locke, J. An Essay concerning Human Understanding. Edited by P. H. Nidditch. Oxford: Clarendon Press, 1690/1975.
Lohr, S. This boring headline is written for Google. New York Times, April 9, 2006.
Lorenz, E. N. Deterministic nonperiodic flow. Journal of Atmospheric Science, 357, 1963, pp. 130–141.
Lovelock, J. E. The Ages of Gaia. New York: Norton, 1988.
Luisi, P. L. The Emergence of Life: from Chemical Origins to Synthetic Biology. Cambridge, U.K.: Cambridge University Press, 2006.
Mackenzie, D. Biophysics: New clues to why size equals destiny. Science, 284(5420), 1999, pp. 1607–1609.
Macrae, N. John von Neumann. New York: Pantheon Books, 1992.
Maddox, J. Slamming the door. Nature, 417, 2007, p. 903.
Malone, M. S. God, Stephen Wolfram, and everything else. Forbes ASAP, November 27, 2000. [http://members.forbes.com/asap/2000/1127/162.html].
Mandelbrot. B. An informational theory of the statistical structure of languages. In W. Jackson (editor), Communication Theory, Woburn, MA: Butterworth, 1953, pp. 486–502.
Mandelbrot, B. B. The Fractal Geometry of Nature. New York: W. H. Freeman, 1977.
Markoff, J. Brainy robots start stepping into daily life, New York Times, July 18, 2006.
Marr, D. Vision. San Francisco: Freeman, 1982.
Mattick, J. S. RNA regulation: A new genetics? Nature Reviews: Genetics, 5, 2004, pp. 316–323.
Maturana, H. R. and Varela, F. J. Autopoiesis and Cognition: The Realization of the Living, Boston: D. Reidel Publishing Co., 1980.
Maxwell, J. C. Theory of Heat. London: Longmans, Green and Co, 1871.
May, R. M. Simple mathematical models with very complicated dynamics. Nature, 261, 459–467, 1976.
Mayr, E. An overview of current evolutionary biology. In New Perspectives on Evolution, 1991, pp. 1–14.
McAllister, J. W. Effective complexity as a measure of information content. Philosophy of Science 70, 2003, pp. 302–307.
McClamrock, R. Marr’s three leves: A re-evaluation. Minds and Machines, 1(2), 1991, pp. 185–196.
McCulloch, W. and Pitts, W. A logical calculus of ideas immanent in nervous activity. Bulletin of Mathematical Biophysics 5, 1942, pp. 115–133.
McShea, D. W. The hierarchical structure of organisms: A scale and documentation of a trend in the maximum. Paleobiology, 27(2), 2001, pp. 405–423.
Metropolis, N., Stein, M. L., and Stein, P. R. On finite limit sets for transformations on the unit interval. Journal of Combinatorial Theory, 15(A), 1973, pp. 25–44.
Milgram, S. The small-world problem. Psychology Today 1, 1967, pp. 61–67.
Millay, E. St. Vincent. Mine the Harvest: A Collection of New Poems. New York: Harper, 1949.
Miller, G. A. Some effects of intermittent silence. The American Journal of Psychology, 70, 1957, pp. 311–314.
Millonas, M. M. The importance of being noisy. Bulletin of the Santa Fe Institute, Summer, 1994.
Minsky, M. The Society of Mind, Simon & Schuster, 1987.
Mitchell, M. Computation in cellular automata: A selected review. In T. Gramss et al. (editors), Nonstandard Computation. Weinheim, Germany: Wiley-VCH, 1998, pp. 95–140.
Mitchell, M. Analogy-Making as Perception, MIT Press, 1993.
Mitchell, M. Analogy-making as a complex adaptive system. In L. Segel and I. Cohen (editors), Design Principles for the Immune System and Other Distributed Autonomous Systems. New York: Oxford University Press, 2001.
Mitchell, M. Life and evolution in computers. History and Philosophy of the Life Sciences, 23, 2001, pp. 361–383.
Mitchell, M. Complex systems: Network thinking. Artificial Intelligence, 170(18), 2006, pp. 1194–1212.
Mitchell, M. Crutchfield, J. P., and Das, R. Evolving cellular automata to perform computations: A review of recent work. In Proceedings of the First International Conference on Evolutionary Computation and its Applications (EvCA ’96). Moscow: Russian Academy of Sciences, 1996, pp. 42–55.
Mitzenmacher, M. A brief history of generative models for power law and lognormal distributions. Internet Mathematics, 1(2), 2003, pp. 226–251.
Montoya, J. M. and Solé, R. V. Small world patterns in food webs. Journal of Theoretical Biology, 214(3), 2002, pp. 405–412.
Moore, C. Recursion theory on the reals and continuous-time computation. Theoretical Computer Science, 162, 1996, pp. 23–44.
Moravec, H. Robot: Mere Machine to Transcendent Mind. New York: Oxford University Press, 1999.
Morton, O. Attack of the stuntbots. Wired, 12.01.2004.
Mukherji, A., Rajan, V., and Slagle, J. R. Robustness of cooperation. Nature, 379, 1996, pp. 125–126.
Muotri, A. R., Chu, V. T., Marchetto, M. C. N., Deng, W., Moran, J. V. and Gage, F. H. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature, 435, 2005, pp. 903–910.
Nagel, E. and Newman, J. R. Gödel’s Proof. New York: New York University Press, 1958.
Newman, M.E.J. Power laws, Pareto distributions and Zipf’s law. Contemporary Physics, 46, 2005, pp. 323–351.
Newman, M.E.J., Moore, C., and Watts, D. J. Mean-field solution of the small-world network model. Physical Review Letters, 84, 1999, pp. 3201–3204.
Newman, M.E.J., Forrest, S., and Balthrop, J. Email networks and the spread of computer viruses. Physical Review E, 66, 2002, p. 035101.
Nicolis, G. and Progogine, I. Exploring Complexity. New York: W.H. Freeman, 1989.
Niklas, K. J. Size matters! Trends in Ecology and Evolution 16(8), 2001, p. 468.
Nowak, M. A. Five rules for the evolution of cooperation. Science, 314(5805), 2006, pp. 1560–1563.
Nowak, M. A., Bonhoeffer, S., and May, R. M. Spatial games and the maintenance of cooperation. Proceedings of the National Academy of Sciences, USA, 91, 1994, pp. 4877–4881.
Nowak, M. A., Bonhoeffer, S., and May, R. M. Reply to Mukherji et al. Nature, 379, 1996, p. 126.
Nowak, M. A. and May, R. M. Evolutionary games and spatial chaos. Nature, 359(6398), 1992, pp. 826–829.
Nowak, M. A. and Sigmund, K. Biodiversity: Bacterial game dynamics. Nature, 418, 2002, pp. 138–139.
Packard, N. H. Adaptation toward the edge of chaos. In J.A.S. Kelso, A. J. Mandell, M. F. Shlesinger (editors), Dynamic Patterns in Complex Systems, pp. 293–301. Singapore: World Scientific, 1988.
Pagels, H. The Dreams of Reason. New York: Simon & Schuster, 1988.
Paton, R., Bolouri, H., Holcombe, M., Parish, J. H., and Tateson, R. (editors). Computation in Cells and Tissues: Perspectives and Tools of Thought. Berlin: Springer-Verlag, 2004.
Peak, D., West, J. D., Messinger, S. M., and Mott, K. A. Evidence for complex, collective dynamics and emergent, distributed computation in plants. Proceedings of the National Academy of Sciences, USA, 101(4), 2004, pp. 918–922.
Pearson, H. What is a gene? Nature, 441, 2006, pp. 399–401.
Pierce, J. R. An Introduction to Information Theory: Symbols, Signals, and Noise. New York: Dover, 1980. (First edition, 1961.)
Pines, D. (editor). Emerging Syntheses in Science. Reading, MA: Addison-Wesley, 1988.
Poincaré, H. Science and Method. Translated by Francis Maitland. London: Nelson and Sons, 1914.
Poundstone, W. The Recursive Universe. William Morrow, 1984.
Poundstone, W. Prisoner’s Dilemma. New York: Doubleday, 1992.
Price, D. J. Networks of scientific papers. Science 149, 1965, pp. 510–515.
Provine, W. B. The Origins of Theoretical Population Genetics. University of Chicago Press, 1971.
Rapoport, A. General System Theory: Essential Concepts and Applications, Cambridge, MA: Abacus Press, 1986.
Redner, S. How popular is your paper? An empirical study of the citation distribution. European Physical Journal B, 4(2), 1998, pp. 131–134.
Regis, E. Who Got Einstein’s Office? Eccentricity and genius at the Institute for Advanced Study. Menlo Park, CA: Addison-Wesley, 1987.
Rendell, P. Turing universality of the game of Life. In A. Adamatzky (editor), Collision-Based Computing. London: Springer-Verlag, 2001, pp. 513–539.
Robbins, K. E., Lemey, P., Pybus, O. G., Jaffe, H. W., Youngpairoj, A. S., Brown, T. M., Salemi, M., Vandamme, A. M. and Kalish, M. L., U.S. human immunodeficiency virus type 1 epidemic: Date of origin, population history, and characterization of early strains. Journal of Virology, 77(11), 2003, pp. 6359–6366.
Rota, G-C, In memoriam of Stan Ulam—The barrier of meaning. Physica D, 2, 1986, pp. 1–3.
Rothman, T. The evolution of entropy. Chapter 4 in Science à la Mode. Princeton, NJ: Princeton University Press, 1989.
Russell, B. A History of Western Philosophy, Touchstone, 1967 (First edition, 1901.)
Schlossberg, D. LAX Computer Crash Strands International Passengers. ConsumerAffairs.com, August 13, 2007. [http://www.consumeraffairs.com/news04/2007/08/lax_computers.html].
Schneeberger, A. Mercer, C. H., Gregson, S. A., Ferguson, N. M., Nyamukapa, C. A., Anderson, R. M., Johnson, A. M., and Garnett, G. P. Scale-free networks and sexually transmitted diseases: A description of observed patterns of sexual contacts in Britain and Zimbabwe. Sexually Transmitted Diseases, 31(6), 2004, pp. 380–387.
Schwartz, J. Who needs hackers? New York Times, September 12, 2007.
Selvam, A. M. The dynamics of deterministic chaos in numerical weather prediction models. Proceedings of the American Meteorological Society, 8th Conference on Numerical Weather Prediction, Baltimore, MD, 1988.
Shalizi, C. Networks and Netwars, 2005. Essay at [http://www.cscs.umich.edu/~crshalizi/weblog/347.html].
Shalizi, C. Power Law Distributions, 1/f noise, Long-Memory Time Series, 2007. Essay at [http://cscs.umich.edu/~crshalizi/notebooks/power-laws.html].
Shannon, C. A mathematical theory of communication. The Bell System Technical Journal, 27, 1948, pp. 379–423, 623–656.
Shaw, G. B. Annajanska, the Bolshevik Empress. Whitefish, MT: Kessinger Publishing, 2004. (Originally published 1919.)
Shouse, B. Getting the behavior of social insects to compute. Science, 295(5564), 2002, p. 2357.
Sigmund, K. On prisoners and cells. Nature, 359(6398), 1992, p. 774.
Simon, H. A. On a class of skew distribution functions. Biometrika 42(3–4), 1955, p. 425.
Simon, H. A. The architecture of complexity. Proceedings of the American Philosophical Society, 106(6), 1962, pp. 467–482.
Sompayrac, L. M. How the Immune System Works, 2nd edition, Blackwell Publishing, 1991.
Stam, C. J. and Reijneveld, J. C. Graph theoretical analysis of complex networks in the brain. Nonlinear Biomedical Physics, 1(1), 2007, p. 3.
Stoppard, T. Arcadia. New York: Faber & Faber, 1993.
Strogatz, S. Nonlinear Dynamics and Chaos. Reading, MA: Addison-Wesley, 1994.
Strogatz, S. Sync: How Order Emerges from Chaos in the Universe, Nature, and Daily Life. New York: Hyperion, 2004, p. 287.
Szilard, L. On the decrease of entropy in a thermodynamic system by the intervention of intelligent beings. Zeitschrift fuer Physik, 53, 1929, pp. 840–856.
Tattersall, I. Becoming Human: Evolution and Human Uniqueness. New York: Harvest Books, 1999.
Travis, J. Eye-opening gene. Science News Online, May 10, 1997.
Turing, A. M. On computable numbers, with an application to the Entscheidungsproblem. Proceedings of the London Mathematical Society, 2(42), 1936, pp. 230–265.
Ulam, S. M. and von Neumann, J. On combination of stochastic and deterministic processes (abstract). Bulletin of the American Mathematical Society, 53, 1947, 1120.
Varn, D. P., Canright, G. S., and Crutchfield, J. P. Discovering planar disorder in close-packed structures from X-ray diffraction: Beyond the fault model. Physical Review B, 66, 2002, pp. 174110-1–174110-4.
Verhulst, P.-F. Recherches mathematiques sur la loi d’accroissement de la population. Nouv. mem. de l’Academie Royale des Sci. et Belles-Lettres de Bruxelles 18, 1845, pp. 1–41.
Von Bertalanffy, L. An outline of general system theory. The British Journal for the Philosophy of Science, 1(92), 1950, 134–165.
Von Bertalanffy, L. General System Theory: Foundations, Development, Applications, New York: G. Braziller, 1969.
Von Neumann, J. Theory of Self-Reproducing Automata (edited and completed by A. W. Burks). Urbana: University of Illinois Press, 1966.
Wagner, N. R. The logistic equation in random number generation. Proceedings of the Thirtieth Annual Allerton Conference on Communications, Control, and Computing, University of Illinois at Urbana-Champaign, 1993, pp. 922–931.
Wang, H. Reflections on Kurt Gödel. Cambridge, MA: MIT Press, 1987.
Watts, D. J. Six Degrees: The Science of a Connected Age. New York: Norton, 2003.
Watts, D. J. and Strogatz, S. H. Collective dynamics of ‘small world’ networks. Nature, 393, 1998, pp. 440–442.
Weiner, J. The Beak of the Finch: A Story of Evolution in Our Time. New York: Knopf, 1994.
Wiener, N. The Human Use of Human Beings. Boston: Houghton Mifflin, 1950.
Wiener, N. Cybernetics: Or the Control and Communication in the Animal and the Machine. Cambridge, MA: MIT Press, 1948.
Wiener, P. Antibiotic production in a spatially structured environment. Ecology Letters, 3(2), 2000, pp. 122–130.
West, G. B., Brown, J. H., and Enquist, B. J. The fourth dimension of life: Fractal geometry and allometric scaling of organisms. Science, 284, 1999, pp. 1677–1679.
West, G. B. and Brown, J. H. Life’s universal scaling laws. Physics Today, 57(9), 2004, p. 36.
West, G. B. and Brown, J. H. The origin of allometric scaling laws in biology from genomes to ecosystems: Towards a quantitative unifying theory of biological structure and organization. Journal of Experimental Biology 208, 2005, pp. 1575–1592.
West, G. B., Brown, J. H., and Enquist, B. J. Yes, West, Brown and Enquist’s model of allometric scaling is both mathematically correct and biologically relevant. (Reply to Kozlowski and Konarzweski, 2004.) Functional Ecology, 19, 2005, pp. 735–738.
Westfall, R. S. Never at Rest: A Biography of Isaac Newton. Cambridge, U.K.: Cambridge University Press, 1983.
Whitfield, J. All creatures great and small. Nature, 413, 2001, pp. 342–344.
Williams, F. Artificial intelligence has a small but loyal following. Pensions and Investments, May 14, 2001.
Williams, S. Unnatural selection. Technology Review, March 2, 2005.
Willinger, W., Alderson, D., Doyle, J. C., and Li, L. More ’normal’ than normal: Scaling distributions and complex systems. In R. G. Ingalls et al., Proceedings of the 2004 Winter Simulation Conference, pp. 130–141. Piscataway, NJ: IEEE Press, 2004.
Wolfram, S. Universality and complexity in cellular automata. Physica D, 10, 1984, pp. 1–35.
Wolfram, S. Twenty problems in the theory of cellular automata. Physica Scripta, T9, 1985, pp. 170–183.
Wolfram, S. A New Kind of Science. Champaign, IL: Wolfram Media, 2002.
Wright, R. Did the universe just happen? Atlantic Monthly, April 1988, pp. 29–44.
Yoon, C. K. From a few genes, life’s myriad shapes. New York Times, June 26, 2007.
Yule, G. U. A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis. Philosophical Transactions of the Royal Society of London, Ser. B, 213, 1924, pp. 21–87.
Ziff, E. and Rosenfield, I. Evolving evolution. The New York Review of Books, 53(8), May 11, 2006.
Zipf, G. K. Selected Studies of the Principle of Relative Frequency in Language. Cambridge, MA: Harvard University Press, 1932.
Zuse, K. Rechnender Raum. Braunschweig: Friedrich Vieweg & Sohn, 1969. English translation: Calculating Space. Cambridge, MA: MIT Technical Translation AZT-70-164-GEMIT, Massachusetts Institute of Technology (Project MAC), 02139, February 1970.
Zykov, V. Mytilinaios, E., Adams, B., and Lipson, H. Self-reproducing machines. Nature, 435, 2005, pp. 163–164.