Evolving Intelligence (EI) Project

The EI project investigates the evolution of intelligence. Using evolving digital organisms in the Alife environment of Avida and other digital evolution systems, we explore patterns in the emergence of simple intelligent behavior and its components, including phenotypic plasticity, complexity, memory, inference, cooperation, and curiosity. I think of this as experimental epistemology.

Scan of page from Charles Darwin's notebook. His drawing of a hypothesized branching structure representing the evolution of lineages from a common ancestor. It is headed by his handwritten note "I think".
  • Robert T. Pennock. “Can Darwinian Mechanisms Make Novel Discoveries?: Learning from discoveries made by evolving neural networks.” Foundations of Science Vol. 5 no. 2, pp. 225-238, 2000.
  • Richard Lenski, Charles Ofria, Robert T. Pennock, Christoph Adami. “The Evolutionary Origin of Complex Features.” Nature. (2003, Vol. 423. 8 May, pp. 139-144)
  • Sherri Goings, Jeff Clune, Charles Ofria, Robert T. Pennock. “Kin-Selection: The Rise and Fall of Kin-Cheaters.” In Pollack, Jordan, M. Bedau, P. Husbands, T. Ikegami and R. Watson. (eds.) Artificial Life IX: Proceedings of the Ninth International Conference on the Simulation and Synthesis of Living Systems. (2004, pp. 303-308)
  • Robert T. Pennock. “Models, Simulations, Instantiations and Evidence: The Case of Digital Evolution” Journal of Experimental and Theoretical Artificial Intelligence (2007, Vol. 19, No. 1, pp. 29-42)
  • Jeff Clune, Charles Ofria, Robert T. Pennock. “Investigating the Emergence of Phenotypic Plasticity in Evolving Digital Organisms” In Almeida e Costa, F., Rocha, L.M., Costa, E., Harvey, I. and Coutinho, A., Advances in Artificial Life. Berlin: Springer. (2007, pp. 74-83).
  • Laura Grabowski, Wesley Elsberry, Charles Ofria and Robert T. Pennock. “On the Evolution of Motility and Intelligent Tactic Response.” Genetic and Evolutionary Computation Conference (GECCO ‘08) Proceedings. New York: Association for Computing Machinery (2008, pp. 209-216)
  • Jeff Clune, Charles Ofria and Robert T. Pennock. “How Generative Encodings Fare on Less Regular Problems.” Genetic and Evolutionary Computation Conference (GECCO ‘08) Proceedings. New York: Association for Computing Machinery (2008, pp. 867-868)
  • Jeff Clune, Charles Ofria and Robert T. Pennock. “How A Generative Encoding Fares as Problem-Regularity Decreases.” In G. Rudolph et al. (eds.). Parallel Problem Solving in Nature. Berlin: Springer-Verlag(2008, pp. 358-367).
  • Wesley R. Elsberry, Laura M. Grabowski, Charles Ofria, and Robert T. Pennock. “Cockroaches, Drunkards, and Climbers: Modeling the Evolution of Simple Movement Strategies Using Digital Organisms.” Proceedings of IEEE Symposium on Artificial Life (ALIFE 2009) Symposium Series on Computational Intelligence. (2009, pp. 92-99)
  • Jeff Clune, Benjamin E. Beckmann, Charles Ofria, and Robert T. Pennock. “Evolving coordinated quadruped gaits using the HyperNEAT generative encoding.” Proceedings of IEEE on Evolutionary Computing Special Section on Evolutionary Robotics. Trondheim, Norway. (2009, pp. 2764-2771) [GECCO best paper award winner]
  • Jeff Clune, Charles Ofria, and Robert T. Pennock. “The Sensitivity of HyperNEAT to Different Geometric Representations of a Problem.” Proceedings of the 2009 Genetic and Evolutionary Computation Conference (GECCO ‘09) Montreal, Canada. New York: Association for Computing Machinery (2009, pp. 675-682).
  • Jeff Clune, Benjamin E. Beckmann, Robert T. Pennock and Charles Ofria. “HybrID: A Hybridization of Indirect and Direct Encodings for Evolutionary Computation.” Proceedings of the 2009 Evolutionary Conference of Artificial Life (ECAL). Springer. (2010)
  • Laura M. Grabowski, David M. Bryson, Fred C. Dyer, Charles Ofria, Robert T. Pennock. “Early Evolution of Memory Usage in Digital Organisms.” Proceedings of the International Conference on Artificial Life (ALife XII) (August 2010)
  • Jeff Clune, Heather Goldsby, Charles Ofria, Robert T. Pennock. “Selective pressures for accurate altruism targeting: Evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory.” Proceedings of the Royal Society B (Vol. 278, pp. 666-674, doi:10.1098/rspb.2010.1557. Published online: 15 September, 2010)
  • Jeff Clune, Kenneth O. Stanley, Robert T. Pennock, and Charles Ofria. “On the Performance of Indirect Encoding Across the Continuum of Regularity.” IEEE Transactions on Evolutionary Computation, Vol. 15, No. 3, pp. 346-367. (June 2011)
  • Laura M. Grabowski, David M. Bryson, Fred C. Dyer, Robert T. Pennock and Charles Ofria. “Clever Creatures: Case Studies of Evolved Digital Organisms.” Proceedings of the European Conference on Artificial Life 11 (August 2011)
  • Jeff Clune, Robert T. Pennock, Charles Ofria and Richard Lenski. “Ontogeny tends to recapitulate phylogeny in digital organisms.” The American Naturalist, Vol. 180, No. 3 (July 2012, E54-E63)
  • Laura M. Grabowski, David M. Bryson, Fred C. Dyer, Robert T. Pennock and Charles Ofria. “A Case Study in the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms.” PLoS ONE (2013; 8(4):e60466)
  • Robert T. Pennock. “Evolution and Computing.” In Jonathan B. Losos & Richard E. Lenski (eds.) How Evolution Shapes Our Lives: Essays on Biology and Society. Princeton: Princeton University Press. (2016, pp. 206-219)
  • Lehman, J., J. Clune, D. Misevic, C. Adami, L. Altenberg, J. Beaulieu, P. J. Bentley, S. Bernard, G. Beslon, D. M. Bryson, P. Chrabaszca, N. Cheney, A. Cully, S. Doncieux, F. C. Dyer, K. O. Ellefsen, R. Felt, S. Fischer, S. Forrest, A. Frenoy, C. Cagné, L L. Goff, L. M. Grabowski, B. Hodjak, F. Hutter, L. Keller, C. Knibbe, P. Krcah, R. E. Lenski, H. Lipson, R. MacCurdy, C. Maestre, R. Miikkulainen, S. Mitri, D. E. Moriarty, J. Morret, A. Nguyen, C. Ofria, M. Parizeau, D. Parsons, R. T. Pennock, W. F. Punch, T. S. Ray, M. Schoenauer, E. Schulte, K. Sims, K. O. Stanley, F. Taddei, D. Tarapore, S. Thibault, W. Weimer, R. Watson, J. Yosinsky.  “The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities.” Artificial Life. (2020, Vol. 26, pp. 274-306), DOI: 10.1162/artl_a_00319)
A small population of digital organisms in the Avida virtual Petri dish.
A small population of digital organisms in the Avida virtual Petri dish has begun to evolve.
A small population of digital organisms in the Avida virtual Petri dish has evolved with several visible sub-populations.
  • Former Lab Group Students and Postdocs
    • Jory Schossau (Postdoc, Integrative Biology)
    • Jake Cosineau (Undergraduate Professorial Assistant)
    • Leigh Sheneman (PhD Student, Computer Science)
    • Arend Hintze (Postdoc)
    • Mike Weiser (Master’s Student)
    • Robin Miller (Undergraduate Professorial Assistant)
    • Frank Bartlett (Postdoc, Zoology)
    • Aaron Wagner (Postdoc, Zoology & Computer Science)
    • David Bryson (PhD Student, Computer Science)
    • Jason Walker (Undergraduate Student, Computer Science)
    • Jesus Rivera (Master’s Student, Computer Science)
    • Wesley R. Elsberry (Postdoc)
    • Jeff Clune (PhD Student, Computer Science / Philosophy)
    • Laura Grabowski (PhD Student, Computer Science)
  • Faculty Collaborators
    • Kay Holekamp (University Distinguished Professor; Director of the Ecology, Evolutionary Biology and Behavior Program, Integrative Biology)
    • Arend Hintze (Assistant Professor, Integrative Biology)
    • Richard Lenski (Hannah Distinguised Professor of Microbial Ecology)
    • Risto Mikkulainen (Professor, Computer Science, Univ. of Texas – Austin)
    • Charles Ofria (Professor, Computer Science and Engineering)
    • Fred C. Dyer (Professor, Dept. of Zoology)
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