Complexity - A Guided Tour Part 22

"Jim Crutchfield had earlier invented": See, e.g., Crutchfield, J. P., and Hanson, J. E., Turbulent pattern bases for cellular automata. Physica D 69, 1993, pp. 279301.

"Twenty Problems in the Theory of Cellular Automata": Wolfram, S., Twenty problems in the theory of cellular automata. Physica Scripta, T9, 1985, pp. 170183.

"Botanist Keith Mott, physicist David Peak": See 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. 918922.

Chapter 12.

"Information Processing in Living Systems": Parts of this chapter were adapted from Mitch.e.l.l, M., Complex systems: Network thinking. Artificial Intelligence, 170 (18), 2006, pp. 11941212.

"we need to answer the following": My questions are related to the three levels of description of information processing proposed by David Marr, described in his book Vision: Marr, D. Vision. San Francisco, Freeman, 1982. Questions similar to mine were formulated by Ron McClamrock; see McClamrock, R., Marr's three levels: A re-evaluation. Minds and Machines, 1 (2), 1991, pp. 185196.

"The Immune System": Two excellent, readable overviews of the immune system are Sompayrac, L. M., How the Immune System Works, 2nd edition, Blackwell Publis.h.i.+ng, 1991; and 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.

"A third mechanism has been hypothesized": For more details, see Lesley, R. Xu, Y., Kalled, S. L., Hess, D. M., Schwab, S. R., Shu, H.-B., and Cyster, J. G., Reduced compet.i.tiveness of autoantigen-engaged B cells due to increased dependence on BAFF. Immunity, 20 (4), 2004, pp. 441453.

"foraging for food works roughly as follows": For more detailed descriptions of ant foraging, see Bonabeau, E., Dorigo, M., and Theraulaz, G., Swarm Intelligence: From Natural to Artificial Systems. New York: Oxford University Press, 1999.

"The ecologist Deborah Gordon has studied task allocation": See, e.g., 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.

"construction of bridges or shelters": e.g., see Lioni, A., Sauwens, C., Theraulaz, G., and Deneubourg, J.-L., Chain formation in OEcophylla longinoda. Journal of Insect Behavior, 14 (5), 2001, pp. 679696.

"All three systems described above use randomness": The role of randomness in complex adaptive systems is also explored in Millonas, M. M., The importance of being noisy. Bulletin of the Santa Fe Inst.i.tute, Summer, 1994.

"Eventually, the ants will have established a detailed map": Ziff, E. and Rosenfield, I., Evolving evolution. The New York Review of Books, 53, 8, May 11, 2006.

"'parallel terraced scan' ": Hofstadter D., Fluid Concepts and Creative a.n.a.logies. New York: Basic Books, 1995, p. 92.

"Maintaining a correct balance": This is discussed in Holland, J. H., Adaptation in Natural and Artificial Systems. Cambridge, MA: MIT Press, 1992 (first edition, 1975); and Hofstadter, D. R. and Mitch.e.l.l, M., The Copycat project: A model of mental fluidity and a.n.a.logy-making. In K. Holyoak and J. Barnden (editors), Advances in Connectionist and Neural Computation Theory, Volume 2: a.n.a.logical Connections, 1994, pp. 31112.

" who or what actually perceives the meaning": Some of the many books and articles addressing these issues from a philosophical standpoint are the following: Hofstadter, D. R., G.o.del, Escher, Bach: an Eternal Golden Braid. New York: Basic Books, 1979; Dennett, D. R., Consciousness Explained. Boston: Little, Brown, 1991; 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; Floridi, L., Open problems in the philosophy of information. Metaphilosophy, 35 (4), 2004, pp. 554582; and Hofstadter, D., I am a Strange Loop. New York: Basic Books, 2007.

"artificial immune systems": See, e.g., Hofmeyr, S. A. and Forrest, S., Architecture for an artificial immune system. Evolutionary Computation, 8 (4), 2000, pp. 443473.

"ant colony optimization algorithms": See, e.g., Dorigo, M. and Stutzle, T., Ant Colony Optimization, MIT Press, 2004.

Chapter 13.

"How to Make a.n.a.logies": Parts of this chapter were adapted from Mitch.e.l.l, M., a.n.a.logy-Making as Perception, MIT Press, 1993; and Mitch.e.l.l, M., a.n.a.logy-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.

"About a year ago, the Sacramento Bee ": Lohr, S., This boring headline is written for Google. New York Times, April 9, 2006.

"At conferences you are hearing the phrase 'human-level AI' ": Eric Horvitz, quoted in Markoff, J., Brainy robots start stepping into daily life. New York Times, July 18, 2006.

"Easy things are hard": Minsky, M., The Society of Mind. New York: Simon & Schuster, 1987, p. 29.

"All perception of truth is the detection of an a.n.a.logy": Th.o.r.eau, H. D. (with L. D. Walls, editor). Material Faith: Th.o.r.eau on Science. New York: Mariner Books, 1999, p. 28.

"a relatively new book written by a Computer Science professor": Hofstadter, D. R., G.o.del, Escher, Bach: an Eternal Golden Braid. New York: Basic Books, 1979.

"an even more impressive array of successor programs": For descriptions of several of these programs, including Copycat, see Hofstadter D., Fluid Concepts and Creative a.n.a.logies. New York: Basic Books, 1995.

"the barrier of meaning": Rota, G.-C., In memoriam of Stan Ulam-The barrier of meaning. Physica D, 2 (13), 1986, pp. 13.

Chapter 14.

"necessary and sufficient components of all models in physics": Garber, D., Descartes, mechanics, and the mechanical philosophy. Midwest Studies in Philosophy 26 (1), 2002, pp. 185204.

"he pictured the Earth like a sponge": Kubrin, D., Newton and the cyclical cosmos: Providence and the mechanical philosophy. Journal of the History of Ideas, 28 (3), 1967.

"intuition pumps": Dennett, D. R., Elbow Room: The Varieties of Free Will Worth Wanting. Cambridge, MA: MIT Press, 1984, p. 12.

"Merrill Flood and Melvin Drescher, invented the Prisoner's Dilemma": For an entertaining and enlightening discussion of the Prisoner's Dilemma, and, more generally, game theory and its history and applications, see Poundstone, W., Prisoner's Dilemma. New York: Doubleday, 1992.

"the pursuit of self-interest for each": Axelrod, R., The Evolution of Cooperation. New York: Basic Books, 1984, p. 7.

"the tragedy of the commons": Hardin, G., The tragedy of the commons. Science, 162, 1968, pp. 12431248.

"Under what conditions will cooperation emerge": Axelrod, R., The Evolution of Cooperation. New York: Basic Books, 1984, p. 3.

"Thomas Hobbes, who concluded that cooperation could develop": Hobbes' arguments about centralized governments can be found in Hobbes, T., Leviathan. First published in 1651; 1991 edition edited by R. Tuck. Cambridge University Press, 1991.

"Albert Einstein similarly proposed": Einstein's thoughts about world government and many other issues can be found in a collection of his writings, Einstein, A., Out of My Later Years. First published in 1950; revised edition published in 2005 by Castle Books.

"Axelrod experimented with adding norms": Axelrod, R., An evolutionary approach to norms. American Political Science Review, 80 (4), 1986, pp. 10951111.

"Meta-norms can promote and sustain cooperation": Axelrod, R., An evolutionary approach to norms. American Political Science Review, 80 (4), 1986, pp. 10951111.

"Nowak performed computer simulations": Nowak, M. A. and May, R. M., Evolutionary games and spatial chaos. Nature, 359 (6398), 1992, pp. 826829.

"We believe that deterministically generated spatial structure": Ibid.

"chaotically changing": Ibid.

"That territoriality favours cooperation": Sigmund, K., On prisoners and cells, Nature, 359 (6398), 1992, p. 774.

"John Holland has likened such models to 'flight simulators'": Holland, J. H., Emergence: From Chaos to Order. Perseus Books, 1998, p. 243.

"proposals for improving peer-to-peer networks": e.g., Hales, D. and Arteconi, S., SLACER: A Self-Organizing Protocol for Coordination in Peer-to-Peer Networks. IEEE Intelligent Systems, 21 (2), 2006, pp. 2935.

"preventing fraud in electronic commerce": e.g., see 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, Vol. 16. Greenwich, CT: JAI Press, 1999.

" ... work by Martin Nowak": Nowak, M. A., Five rules for the evolution of cooperation. Science, 314 (5805), 2006, pp. 15601563.

"New Energy Finance ... recently put out a report": 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/

NEF_WP_Carbon-Game-Theory_05.pdf]

"impact on policy-making research regarding government response to terrorism, arms control, and environmental governance policies": For example, see Cupitt, R. T., Target rogue behavior, not rogue states. The Nonproliferation Review, 3, 1996, pp. 4654; Cupitt, R. T. and Grillot, S. R., COCOM is dead, long live COCOM: Persistence and change in multilateral security inst.i.tutions. British Journal of Political Science 27, 7, pp. 36189; and 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), 1999, pp. 747765.

"areas ranging from the maintenance of biodiversity to the effectiveness of bacteria in producing new antibiotics": E.g., Nowak, M. A. and Sigmund, K., Biodiversity: Bacterial game dynamics. Nature, 418, 2002, pp. 138139; Wiener, P., Antibiotic production in a spatially structured environment. Ecology Letters, 3(2), 2000, pp. 122130.

"All models are wrong": Box, G.E.P. and Draper, N. R., Empirical Model Building and Response Surfaces. New York: Wiley 1997, p. 424.

"Replication is one of the hallmarks": 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.

"Bernardo Huberman and Natalie Glance re-implemented": Huberman, B. A. and Glance, N. S., Evolutionary games and computer simulations. Proceedings of the National Academy of Science, USA, 90, 1993, pp. 77167718.

"A similar result was obtained independently by Arijit Mukherji, Vijay Rajan, and James Slagle": Mukherji, A., Rajan, V., and Slagle, J. R., Robustness of cooperation. Nature, 379, 1996, pp. 125126.

"Nowak, May, and their collaborator Sebastian Bonhoeffer replied": 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. 48774881; Nowak, M. A., Bonhoeffer, S., and May, R. M., Reply to Mukherji et al. Nature, 379, 1996, p. 126.

"Jose Manuel Galan and Luis Izquierdo published results": 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://ja.s.ss.soc.surrey.ac.uk/8/3/2.html].

"The art of model building": Anderson, n.o.bel Prize acceptance speech, 1977.

Part IV

"In Ersilia": From Calvino, I. Invisible Cities. New York: Harcourt Brace Jovanovich, 1974, p. 76. (Translated by W. Weaver.)

Chapter 15.

"The Science of Networks": Parts of this chapter were adapted from Mitch.e.l.l, M., Complex systems: Network thinking. Artificial Intelligence, 170 (18), 2006, pp. 11941212.

"Milgram wrote of one example": From Milgram, S., The small-world problem. Psychology Today 1, 1967, pp. 6167.

"Later work by psychologist Judith Kleinfeld": see Kleinfeld, Could it be a big world after all? Society, 39, 2002.

228. an "urban myth": Kleinfeld, J. S., Six degrees: Urban myth? Psychology Today, 74, March/April 2002.

"When people experience an unexpected social connection": Kleinfeld, J. S., Could it be a big world after all? The "six degrees of separation" myth. Society, 39, 2002.

"the 'new science of networks'": E.g., Barabasi, A.-L., Linked: The New Science of Networks. Cambridge, MA: Perseus, 2002.

"the publication of two important papers": Watts, D. J. and Strogatz, S. H., Collective dynamics of 'small world' networks. Nature 393, 1998, pp. 440442; Barabasi, A.-L. and Albert, R., Emergence of scaling in random networks, Science, 286, 1999, pp. 509512.

"No one descends with such fury": Watts, D. J., Six Degrees: The Science of a Connected Age. New York: W. W. Norton & Co, 2003, p. 32.

"network thinking is poised": Barabasi, A.-L. Linked: The New Science of Networks. Cambridge, MA: Perseus, 2002, p. 222.

"123 incoming links": All the in-link counts in this chapter were obtained from [http://www.microsoft-watch.org/cgi-bin/ranking.htm]. The count includes only in-links from outside the Web page's domain.

"mathematically define the concept of 'small-world network'": See Watts, D. J. and Strogatz, S. H., Collective dynamics of 'small world' networks. Nature, 393, 1998, pp. 440442.

"The average path length of the regular network of figure 15.4 turns out to be 15": This value was calculated using the formula l = N/2k. Here l is the average path length, N is the number of nodes, and k is the degree of each node (here 2). See Albert, R. and Barabasi, A-L., Statistical mechanics of complex networks. Reviews of Modern Physics, 74, 2002, pp. 4897.