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Research: Artificial Life and Theoretical Biology


Evolution of cooperation
(Fletcher, Zwick)

Structure and dynamics in cellular automata & random networks

Evolutionary simulations
(Bedau, Fletcher, Zwick)

Genetic algorithms
(Shervais, Zwick)

Random Boolean networks: reverse engineering, combinatorics, ensemble sampling


  • Yeates, J.A.M, Hilbe, C., Zwick, M., Nowak, M.A., & Lehman, N. (2016). "Dynamics of Prebiotic RNA Reproduction Illuminated by Chemical Game Theory." Proceedings of the National Academy of Sciences, (Abstract) (HTML).
  • Zwick, M. and Fletcher, J. (2014).  "Levels of Altruism." Biological Theory, March 2014, Volume 9, Issue 1, pp. 100-107: DOI 10.1007/s13752-013-0145-8.  (Abstract) (pdf) (journal format).  This paper is an updated and expanded version of the 2011 conference presentation below with the same title.
  • Zwick, M. and Fletcher, J. (2011) "Levels of Altruism." Presented at the Northwest Philosophy Conference, Lewis and Clark, Nov 4-5. (pdf)
  • Fletcher, J.A., and Zwick, M. (2007). "The Evolution of Altruism: Game Theory in Multilevel Selection and Inclusive Fitness." Journal of Theoretical Biology, 245:26-36. Abstract (HTML) (pdf)
  • Fletcher, J.A., Zwick, M., Doebeli, M., and Wilson, D.S. (2006). "What's Wrong with Inclusive Fitness?" TRENDS in Ecology and Evolution, vol. 21, no. 11, 597-598. (pdf)
  • Fletcher, J.A., and Zwick, M. (2006). "Unifying the Theories of Inclusive Fitness and Reciprocal Altruism." The American Naturalist, 168:252-262. Abstract (HTML) (pdf)
  • Fletcher, J.A., and Zwick, M. (2004). "Strong Altruism Can Evolve in Randomly Formed Groups". Journal of Theoretical Biology, 228:303-313. Abstract (HTML) (pdf)
  • Fletcher, J.A., and Zwick, M. (2004). "Hamilton's Rule Applied to Reciprocal Altruism". In Proceedings of the 2004 IEEE Congress on Evolutionary Computation, Portland, Oregon, June. Abstract (HTML) (pdf)
  • Aviles, L., Fletcher, J. A., and Cutter, A. (2004). "The Kin Composition of Social Groups: Trading Group Size for Degree of Altruism". The American Naturalist,164:132-144. Abstract (HTML) (pdf)
  • Shervais, S. and Zwick, M. (2003). "Ordering Genetic Algorithm Genomes With Reconstructability Analysis", International Journal of General Systems: accepted, in press." Abstract (HTML) (pdf)
  • Zwick, M., and Shervais, S. (2002). "Reconstructability Analysis Detection of Optimal Gene Order in Genetic Algorithms", 12th International World Organization of Systems and Cybernetics Congress and 4th International Institute of General Systems Studies Workshop. Abstract (HTML)
  • Fletcher, J.A., and Zwick, M. (2001). "Altruism, the Prisoner's Dilemma, and the Components of Selection". In Proceedings of the 2001 IEEE Systems, Man, and Cybernetics Conference, Tucson, Arizona, Oct. Abstract (HTML) (pdf)
  • Fletcher, J.A., and Zwick, M. (2000). "N-Player Prisoner's Dilemma in Multiple Groups: A Model of Multilevel Selection". In Proceedings of the Artificial Life VII Workshops, Portland, Oregon, Eilis Boudreau and Carlo Maley, eds. Abstract (HTML) (pdf) (postscript)
  • Fletcher, J.A., and Zwick, M. (2000). "Simpson's Paradox Can Emerge from the N-Player Prisoner's Dilemma: Implications for the Evolution of Altruistic Behavior". In Proceedings of The WorldCongress of the Systems Sciences and ISSS 2000, Allen, J.K. and Wilby, J.M. eds., Toronto, Canada: International Society for the Systems Sciences. Abstract (HTML) (pdf) (postscript)
  • Myers, John E. (2000). "Avoiding Bias in Boolean Network Statistical Studies". (pdf)
  • Myers, John E. (1999). "Two Reverse Engineering Algorithms for Boolean Genetic Networks". (pdf)
  • Rechtsteiner, A., and Bedau, M. A. (1999). "A Generic Neutral Model for Measuring Excess Evolutionary Activity of Genotypes". In D. Floreano, J.-D. Nicoud, F. Mondada, eds., Fifth European Conference on Artificial Life (pp. 109-118). Heidelberg: Springer-Verlag. Abstract (HTML) (pdf) (postscript)
  • Bedau, M. A. (1999). "Quantifying the Extent and Intensity of Adaptive Evolution." In A. Wu, ed., Proceedings of 1999 Genetic and Evolutionary Computation ConferenceWorkshop Program (pp. 34-37). Abstract (HTML) (pdf) (postscript)
  • Fletcher, J., Bedau, M., and Zwick, M. (1998). "Effect of Environmental Structure on Evolutionary Adaptation", in Proc. of Artificial Life VI, Los Angeles, June 26-29; C. Adami, R. Belew, H. Kitano, and C. Taylor, eds., pp.189-198, MIT Press Abstract (HTML) Entire paper (postscript) (pdf)
  • Shannon, T. (1998). "Generic Behavior in the Lindgren Non-Spatial Model of Iterated Two Player Games", in Proc. of Artificial Life VI, Los Angeles, June 26-29; C. Adami, R. Belew, H. Kitano, and C. Taylor, eds., MIT Press Abstract (HTML)
  • Smith, R., and Bedau, M. (1997). "Measuring Evolutionary Activity in Echo", presented at the International Conference on Complex Systems, Nashua, NH, Sept. 21-26. Entire paper (postscript)
  • Zwick, M., and Shu, H. (1997). "Structure and Dynamics of Cellular Automata", presented at the International Institute for General Systems Studies, 2nd Workshop, Southwest Texas St. Univ., San Marcos, TX, Jan.9-11 Abstract (HTML)
  • Fletcher, J., Zwick, M., and Bedau, M. (1997). "Dependence of Adaptability on Environmental Structure in a Simple Evolutionary Model", Adaptive Behavior, 4, #3/4, pp. 275-307, MIT Press. Abstract (HTML), Entire paper (pdf with figures at end) (postscript without figures) (zip file of postscript figures)
  • Zwick, M., Lovell, B., and Marsh, J. (1996). "Global Optimization Studies On The 1-D Phase Problem", Int. J. of General Systems, 25, #1, pp.47-59. Abstract (HTML), (postscript) (pdf )
  • Zwick, M., and Shu, H. (1995). "Set-Theoretic Reconstructability of Elementary Cellular Automata", Advances in Systems Science and Applications, 1, pp.31-36. Abstract (HTML), (postscript) (pdf)
  • Bedau, M., Zwick, M., and Bahm, A. (1995). "Variance and Uncertainty Measures of Population Diversity Dynamics", Advances in Systems Science and Applications, SP 1, pp.7-13. Abstract (HTML) (postscript)) (pdf)
  • Bedau, M., Giger, M., and Zwick, M. (1995). "Diversity Dynamics in Static Resource Models", Advances in Systems Science and Applications, SP 1, pp.1-7. Abstract (HTML) (postscript) (pdf)
  • Bedau, M.A., Ronneburg, F., and Zwick, M. (1992). "Dynamics of Diversity in an Evolving Population", Parallel Problem Solving from Nature,2, pp 94-104, Elsevier Science Publishers B.V. (pdf)
  • Lovell, B., and Zwick, M. (1992). "Application of the Genetic Algorithm to Simplified Form of the Phase Problem", Cybernetics and Systems Research, pp.261-268. Abstract (HTML) (pdf)
  • Podjarny, A. D., Bhat, T. N., and Zwick, M. (1987). "Improving Crystallographic Macromolecular Images: the Real-Space Approach", Ann. Rev. Biophys. Chem. 16:351-73. Abstract (HTML) (pdf)

Relevant Courses

SYSC 557/657 Artificial Life

SYSC 552/652 Game Theory

ECE 559 Genetic Algorithms (also discusses Evolutionary Computation)

CS 410/510 NonStandard Computation

CS 441/541 Artificial Intelligence



Martin Zwick
Jeff Fletcher

Other Faculty

(collaborating or with related interests)

Mark Bedau (adjunct)
Garrison Greenwood ECE
Niles Lehman Chemistry
Melanie Mitchell, CS
Marek Perkowski, ECE
Radu Popa, Biology


John Myers
Steve Shervais , Ph.D SySc (PSU)

Meetings & Events

Artificial Life VIII: The 8th International Conference on the Simulation and Synthesis of Living Systems


ALife's Role in the Group Selection Debate Workshop, ALife VII Conference, Portland, Oregon 2000

ALife VII Conference

International Society For Artificial Life

ALife VI Conference

NovaGenetica The GA source

Reed ALife Project

CalTech:Avida Group

Genetic Algorithms and Artificial Life Resources

Artificial Life Syllabus

Yahoo - Science:Artificial Life