CSE 891, Section 002

Digital Evolution and Biocomplexity

Spring 2009

Instructor: Dr. Charles A. Ofria
Office: 2140 Engineering
Phone: 355-8389
E-mail: ofria@cse.msu.edu (best way to reach me)

Consulting instructor: Mike Wiser (Evolutionary Biology)
Phone: 884-5378
E-mail: mwiser@msu.edu

Textbook: none (all reading will be made available on the web or as handouts in class.)
Meeting time & Room: M/W 3-4:20pm, 2320 Engineering
Pre-reqs: Knowledge of at least one major programming language.
Web page: http://www.cse.msu.edu/~ofria/cse891/

Description: An introduction to evolution in simple systems of self-replicating computer programs, with a special emphasis on the two way flow of ideas between evolutionary biology and computer science. Topics will include the basic principles of biological evolution, experimental evolution techniques, information theory and evolution, the evolutionary origin of complexity, the emergence of complex digital ecosystems, and more. All students will be expected to do a semester project involving digital evolution.

You can find the course Wiki here.

Handouts

  • Basic Info
  • Schedule
  • Project proposal guidelines
  • Project report guidelines

    • Homework

  • HW1: "Definitions of Life" and "An Introduction to Avida"
  • HW2: Evolvable Virtual Hardware
  • HW3: Implmenting a Virtual Machine
  • HW4: "Information Theory" and "Implementing am Evolving Population of Virtual Machines"
  • HW5: Tracking Evolvable Populations

    • Avida Software

  • The Avida Software is available at http://sourceforge.net/projects/avida/
  • Documentation for Avida can be found in the documentation/ directory when you download it or here.
  • An introductory paper on Avida can be found here

    • Papers

      Avida and Complexity Topics
  • Lenki RE, Twice as natural, Nature, 414:255 (2001).
  • Lenski RE, Ofria C, Pennock RT, and Adami C, The Evolutionary Origin of Complex Features, Nature, 423:139-144 (2003).
    •   Virtual CPU Design
  • Optimizing Avida Instruction Sets: Ofria C, Adami C, and Collier TC Design of Evolvable Computer Languages, IEEE Transactions in Evolutionary Computation 17:528-532 (2002)
  • Virtual CPU Design in Tierra: Ray TS, Evolution, Complexity, Entropy, and Artificial Reality, Physica D 75:239-263 (1994)
  • A blog entry: The black art of evolvable instruction sets by Adam Ierymenko.
    •   Other
  • Bedau MA, McCaskil JS, Packard NS, Rasmussen S, Adami C, Green DG, Ikegami T, KanekoT and Ray TS Open Problems in Artificial Life Artificial Life 6:363-376 (2000).
  • Adami C, Ofria C, Collier TC, Evolution of Biological Complexity, Proc. Natl. Acad. Sci., 97:4463-4468 (2000).
  • Ofria C, Adami C and Collier TC, Selective Pressures on Genomes in Molecular Evolution, J. Theor. Biol., 222:477-483 (2003).

  • Lenski RE, Evolutionary Rate, Pp. 671-672 in S. Brenner and J. Miller, editors-in-chief. Encyclopedia of Genetics. Academic Press, San Diego.
  • Ray TS, Evolution, Ecology and Optimization of Digital Organisms, Santa Fe Institute working paper 92-08-042 (1992).
  • Ray TS, Evolution, Complexity, Entropy, and Artificial Reality, Physica D, 75:239-263 (1994).
  • Sims K, Evolving Virtual Creatures, SigGraph, (1994).
  • Ray TS, Aesthetically Evolved Virtual Pets, Proceedings of the Seventh Artificial Life Conference. Pp. 158--161.
  • Astor JC and Adami C, A Developmental Model for the Evolution of Artificial Neural Networks, Artificial Life 6 189-218 (2000).
  • Shannon C, A Mathematical Theory of Communication, The Bell System Technical Journal, 27:379-423,623-656 (1948).
  • Lenski RE and Travisano M, Dynamics of adaptation and diversification: A 10,000-generation experiment with bacterial populations, Proc. Natl. Acad. Sci. 91:6808-6814 (1994).
  • Cooper T and Ofria C, Evolution of stable ecosystems in populations of digital organisms, Artificial Life 8 (2002) pp. 227-232, Standish RK, Bedau MA and Abbass HA (eds.)
  • Ofria C, Adami C, Collier TC, Hsu GK, Evolution of differentiated expression patterns in digital organisms Lect. Notes Artif. Intell. 1674:129-138 (1999).
  • Ofria C and Adami C, Evolution of genetic organization in digital organisms DIMACS Workshop, Princeton, January 1999, L. F. Landweber and E. Winfree, eds., Springer-Verlag, N.Y. (2002) pp. 296-313.
  • Wilke CO, Wang J, Ofria C, Adami C, and Lenski RE, Evolution of Digital Organisms at High Mutation Rate Leads To Survival of the Flattest, Nature, 412:331-333 (2001).
  • Lenski RE, Come Fly, and Leave the Baggage Behind, Science, 294:533-534 (2001).

    • Links

  • Evolution Education Site (by PBS).
  • Conway's Game of Life (in Java).
  • www.alife.org: International Society for Artificial Life.
  • Core War home page
  • Core War FAQ
  • Core Wars Genetics: The Evolution of Predation by John Perry