DIMACS Workshop on Evolution as Computation

January 11 - 12, 1999
Princeton University

Organizers:

Laura Landweber, Princeton University, lfl@princeton.edu

Erik Winfree, Caltech, winfree@hope.caltech.edu

Richard Lipton, Princeton University, rjl@cs.princeton.edu

Stephen Freeland, Cambridge University, sjf23@cam.ac.uk

Workshop Program:

Monday, January 11, 1999

8:15  Continental breakfast

      Session I:  The comparison between computers and biology
                           Erik Winfree, chair

9 am  Jim Shapiro,  University of Chicago
       "Genome System Architecture and Natural Genetic Engineering"

9:45  John Koza,  Stanford University
       "Genetic Programming:  Biologically Inspired Computation
        that Creatively Solves Non-Trivial Problems"

10:30 - 11  coffee break

11     Pim Stemmer,  Maxygen, Inc.
       "Molecular breeding of sequences by DNA shuffling"

11:45  Junghuei Chen, Eugene Antipov, Bertrand Lemieux, Walter Cedeno,
                and David Harlan Wood, University of Delaware
       "Programming a Genetic Algorithm on a DNA Computer"

12 noon lunch

      Session II:  Complex Genomes
          Laura Landweber, chair

2 pm  David Prescott and Grzegorz Rozenberg
           University of Colorado & Leiden University
       "Computational Aspects of Gene Scrambling in Ciliates"

3 pm  Laura Landweber and Lila Kari
           Princeton University & University of Western Ontario
       "Universal Molecular Computation in Ciliates"

3:45  Brief poster Introductions

4 - 4:30    coffee break / poster session

4:30  Jim Crutchfield,  Santa Fe Institute
       "The Evolutionary Unfolding of Complexity"

5:15 - 6 pm    poster session

6 pm  Reception - Prospect House
6:30  Banquet   - Prospect House
        (registration by January 6, 1999 required to attend)


Tuesday, January 12, 1999

8:15  Continental breakfast

      Session III:  Systems
        Erik Winfree, chair

9 am  Thomas Baeck, Joost Kok, and Grzegorz Rozenberg, Leiden University
       "Evolutionary Computation as a Paradigm for DNA-Based Computing"

9:25  Theodore and Patricia Theodosopoulos
       "Evolution at the Edge of Chaos: A Paradigm for the
        Maturation of the Humoral Immune Response"

9:50  Charles Ofria and Christoph Adami, Caltech
       "Evolution of Genetic Organization in Digital Organisms"

10:15 Eric Baum and Igor Durdanovic, NEC Research Institute
       "Toward Code Evolution by Artificial Economies"

10:40 - 11  coffee break

      Session IV:  The Genetic Code
         Stephen Freeland, chair

11    Robin Knight, Princeton University
       "Genetic Code Evolution in the RNA World and Beyond"

11:20 Stephen Freeland, Cambridge University
       "Is Ours the Best of All Possible Codes?"

11:40 David Ardell and Guy Sella, Stanford University
       "Code-Message Coevolution Generates an Error-Correcting Genetic Code"

12:00 Discussion

12:15 Lunch

      Session V:  Switches and Networks
           Laura Landweber, chair

2:00  Mark Ptashne,  Memorial Sloan Kettering Cancer Center
       "Regulation by Localization: Mechanisms and Evolvability"

2:45  Drew Endy,  Molecular Sciences Institute
       "Exploration and Characterization of the Bacteriophage T7 Genome Space"

3:15  Roger Brent,  Molecular Sciences Institute
       "Might functional genomic analysis, and simulation, of cellular
        genetic networks, teach us anything about evolution and computation?"

3:45  Ron Weiss, George Homsy, and Tom Knight,  M.I.T.
        "Toward in vivo Digital Circuits"

4:30  close of workshop

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