BACKGROUND INFORMATION
• To find out about some of the pedagogical goals of the project and the thinking that shaped the design and development of Avida-ED see:
Robert T. Pennock. “Learning Evolution and the Nature of Science using Evolutionary Computing and Artificial Life” McGill Journal of Education (Vol. 42, No. 2, pp. 211-224, 2007)
• Publications about curricular materials using Avida-ED:
James J Smith; Wendy R Johnson; Amy M Lark; Louise S Mead; Michael J Wiser, Robert T. Pennock “An Avida-ED digital evolution curriculum for undergraduate biology“ Evolution: Education and Outreach (2016, 9(1), 1-11; DOI 10.1186/s12052-016-0060-0)
Amy Lark, Gail Richmond, Robert T. Pennock. “Modeling Evolution in the Classroom: The Case of the Fukushima Butterflies.” American Biology Teacher (2014, 76(7):450-454)
Elena B. Speth, Tammy Long, Robert T. Pennock and Diane Ebert-May. “Using Avida-ED for teaching and learning about evolution in undergraduate introductory biology courses.” Evolution Education & Outreach. (Vol. 2, No. 3, pp. 415-428, 2009)
• Avida-ED is meant to be used not only to help teach about evolution, but also the nature of science. Evolution is one of the best examples for helping students understand how science works.
Robert T. Pennock. “On Teaching Evolution and the Nature of Science” In Cracraft, J. and R. Bybee (eds.). Evolutionary Science and Society: Educating a New Generation. Biological Sciences Curriculum Study, Colorado Springs, CO. (pp. 1-12, 2005)
• Avida-ED is not a simulation of evolution, but an instance of it. For a philosophical treatment of scientific models and the difference between a simulation and an instance as these concepts relate to evolutionary computation see:
Robert T. Pennock. “Models, Simulations, Instantiations and Evidence: The Case of Digital Evolution.” Journal of Experimental and Theoretical Artificial Intelligence (Vol. 19, No. 1, 2007)
• To learn more about the power of evolutionary computation see:
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)
• The research platform that Avida-ED is built upon is a well-established model system that has been used to test a wide range of evolutionary hypotheses. Some of the research done by our Digital Evolution Lab at Michigan State University was written up in a cover story “Testing Darwin” in Discover magazine. Following are a few of the scientific publications that have resulted from this exciting research:
Richard E. Lenski, Charles Ofria, Robert T. Pennock, Christoph Adami. “The Evolutionary Origin of Complex Features” Nature (2003, Vol. 423, pp. 139-145)
Sherry 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)
Clune J, Ofria C, and Pennock RT. ” Investigating the Emergence of Phenotypic Plasticity in Evolving Digital Organisms“, Lecture Notes in Computer Science: Proceedings of the 2007 European Conference on Artificial Life, (2007. 4648:74-83.)
Grabowski LM, Elsberry WR, Pennock RT, and Ofria C.”On the Evolution of Motility and Intelligent Tactic Response“, Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta GA, (July 2008, Pages 209-216. http://doi.acm.org/10.1145/1389095.1389129)
Elsberry W, Grabowski L, Ofria C, and Pennock R “Cockroaches, Drunkards, and Climbers: Evolving Simple Movement Strategies Using Digital Organisms“, Proceedings of the IEEE Symposium on Artificial Life.(2009)
Grabowski LM, Bryson DM, Dyer F, Pennock RT, Ofria C “Early Evolution of Memory Usage in Digital Organisms“, The Proceedings of the 12th International Conference on Artificial Life, Odense, Denmark. (2010)
Clune J, Goldsby HJ, Ofria C, and Pennock RT “Selective Pressures for Accurate Altruism Targeting: Empirical Support for Difficult-to-Test Aspects of Inclusive Fitness Theory“, Proceedings of the Royal Society of London, (2011. 278(1706):666-674).
Grabowski LM, Bryson DM, Dyer FC, Pennock RT, and Ofria C “Clever Creatures: Case Studies of Evolved Digital Organisms“, Proceedings of the Proceedings of the 2011 European Conference on Artificial Life. (2011)
Clune J, Pennock RT, Ofria C, and Lenski RE “Ontogeny Tends to Recapitulate Phylogeny in Digital Organisms“, The American Naturalist, (2012. 180:E54-E63).
Grabowski LA, Bryson DM, Dyer FC, Pennock RT, and Ofria C “A Case Study of the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms“, PLoS ONE (2013)
Covert AW, Lenski RE, Wilke CO, and Ofria C Experiments on the role of deleterious mutations as stepping stones in adaptive evolution, Proceedings of the National Academy of Sciences, (2013, 110(34), E3171-E3178)
Zaman L, Meyer JR, Devengam S, Bryson DM, Lenski RE, and Ofria C. Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability, PLoS Biology, (2014. 12.12: e1002023)
Ostrowski EA, Ofria C, Lenski RE Genetically integrated traits and rugged adaptive landscapes in digital organisms, BMC Evolutionary Biology, (2015. 15(1):83)
Rosangela Canino-Koning, M Wiser, Charles Ofria. The evolution of evolvability: Changing environments promote rapid adaptation in digital organisms, Proceedings of the Artificial Life Conference. (2016)
Miguel A Fortuna, Luis Zaman, Charles Ofria, Andreas Wagner. The genotype-phenotype map of an evolving digital organism , PLoS computational biology. (2017. 13(2):e1005414)
© Robert T. Pennock
