Courses: SYSC 557/657: Artificial Life: Spring 2005

"Artificial Life" (ALife) is a name given to theoretical, mathematical, and computationally "empirical" studies of phenomena commonly associated with "life," such as replication, metabolism, morphogenesis, learning, adaptation, and evolution. It focuses on the materiality-independent, i.e., abstract, bases of such phenomena. As such, it overlaps extensively with "theoretical biology" and, less extensively, with certain areas of physics and chemistry and the social sciences. It also raises important philosophical questions. It is part of a larger research program into "complex adaptive systems," one stream of contemporary systems theory.

In its intersection with computer science, ALife is the newest example of ¿the sciences of the artificial¿ (Herbert Simon). ALife is to life what AI is to intelligence. Christopher Langton writes that "Artificial Life ... complements the traditional biological sciences ... by attempting to synthesize life-like behaviors within computers and other artificial media." The purpose is twofold: to understand these phenomena better and to develop new computational technologies.

The course will sample the research literature in this field, and will be organized in a seminar format. Topics to be emphasized are: (1) discrete dynamics: cellular automata and random networks, (2) ecological & evolutionary dynamics, (3) genetic algorithm optimization and adaptation, (4) agent-based simulation. Other topics will include: artificial and real chemistry (metabolism, reproduction, & origin of life), ¿complex adaptive systems,¿ autonomous agents, and philosophical issues. For ALife research at PSU, see http://www.sysc.pdx.edu/res_alife.html

Texts

1. Christopher Langton, ed., Artificial Life: An Overview. MIT Press, Cambridge, 1997. (ISBN 0-262-62112-6 Paperback)

2. George Cowan, David Pines, David Meltzer, ed., Complexity: Metaphors, Models, and Reality, Santa Fe Institute Studies in the Sciences of Complexity. Addison-Wesley, New York, 1994. (ISBN 0-201-62606-3 Paperback)

3. Xeroxed articles (obtain packet at Smart Copy, 1915th SW 6th Ave, 227-6137)

Prerequisites

Graduate status or consent of instructor

Course Work

Term paper or project; class participation.

Course Outline

O = Overview, C = Complexity; X = xeroxed materials; beg. page in ( )

4/1 Introduction
O: Taylor C: Cowan (1), Anderson (7) X: Langtona,b

Main course areas:

4/3,8,10 Automata; dynamics & complexity; edge of chaos.
O: Prusinkiewicz C: Jen (473), Mitchell (497) X: Langtonc, Zwick

4/15,17 Evolutionary & ecological dynamics
O: Lindgren, Kaneko C: Hubler (343)
X: Sober, Fletcher [3 papers], Lindgren, Hillis

4/22,24 Agent-based simulation
O: Resnick, Maes C: Holland (309) X: Bonabeau

4/29, 5/1 Genetic algorithms (& neural nets); genetic programming
O:Dyer (ANN), Mitchell X: Holland, Goldberg, Koza, Ackley, Belew

Other important topics:

5/6 "Complex Adaptive Systems"
O: Steels C: Gell-Man (17), Arthur (65), Martin (263)

5/8 Computer Life (Tierra)
Project/paper mini-proposals due
O: Ray, Spafford C: Ray (161) X: Ray

5/13,15 Random nets & NK models; self-organized criticality
Project/paper declarations due

5/20 Artificial chemistry: autocatalytic networks, metabolism
O: Fontana C: Kauffman (83-100), Fontana (223) X: Bagley

5/22 Real chemistry & wet ALife
O: Schuster C: Frauenfelder, Schuster

5/27 HOLIDAY

5/29, 6/3 General discussion; philosophical issues
O:Dennett, Harnad, Bonabeau C: Crutchfield,Jen(553),Pines,Cowan (589-719)

6/3 PAPERS are DUE

6/5,10 Paper/project presentations

Xeroxed Articles

(in order of usage)

Distributed separately; not in packet

Langtona, C. G., Artificial Life, ALife I, 1989.

Langtonb, C. G., Introduction, ALife II, 1991.

Langtonc, C. G., Life at the Edge of Chaos, ALife II, 1991.

Zwick, M. and Shu, H., Set-Theoretic Reconstructability of Elementary Cellular Automata, Advances in Systems Science and Applications, 1996.

Papers in packet:

Sober, E., Altruism as a Biological Concept, Unto Others, 1998.

Fletcher, J.A., and Zwick, M., Simpson¿s Paradox Can Emerge from the N-Player¿s Prisoner¿s Dilemma: Implications for the Evolution of Altruistic Behavior, Proceedings of the World Congress of the Systems Sciences and 44th Annual Meeting of the International Society for the Systems Sciences, Toronto, 2000.

Fletcher, J.A., and Zwick, M., N-Player Prisoner¿s Dilemma in Multiple Groups: A Model of Multilevel Selection, Seventh International Conference on Aritificial Life, Workshop on Group Selection, Portland, 2000.

Fletcher, J.A., and Zwick, Altruism, The Prisoner¿s Dilemma, and the Components of Selection, Proceedings of the 2001 IEEE Systems, Man, and Cybernetics Conference, 2001.

Lindgren, K., Evolutionary Phenomena in Simple Dynamics, ALife II, 1991.

Hillis, W. D., Co-Evolving Parasites Improve Simulated Evolution as an Optimization Procedure. ALife II, 1991.

Holland, J. H., Genetic Algorithms, Scientific American, 1992.

Goldberg, D. E., Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-Wesley, 1989, Ch. 1-3.

Koza, J. R., Genetic Evolution and Co-Evolution of Computer Programs, ALife II, 1991.

Ackley, D. and Littman, M., Interaction between Learning and Evolution. ALife II, 1991.

Belew, R.K., McInerney, J., and Schraudolph, N.N., Evolving Networks: Using the Genetic Algorithm with Connectionist Learning. ALife II, 1991.

Ray, T. S., An Approach to the Synthesis of Life, ALife II, 1991.

Kauffman, S. and Johnsen, S., Coevolution to the Edge of Chaos: Coupled Fitness Landscapes, Poised States, and Co-Evolutionary Avalanches. ALife II, 1991.

Kauffman, S., Antichaos and Adaptation, Scientific American, Aug. 1991, pp. 78-84

Bak, P., and Chen, K., Self-Organized Criticality, Scientific American, Jan. 1991, pp. 46-53

Bagley, R. and Farmer, J.D. Spontaneous Emergence of a Metabolism. ALife II, 1991.