DIMACS Working Group on Evolution of Gene Regulatory Logic

January 6 - 8, 2006
Santa Fe Institute, Santa Fe, New Mexico

Tanya Berger-Wolf, University of New Mexico, tanyabw@unm.edu
David Krakauer, Santa Fe Institute, krakauer@ias.edu
Presented under the auspices of the DIMACS/BioMaPS/MB Center Special Focus on Information Processing in Biology.

This special focus is jointly sponsored by the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), the Biological, Mathematical, and Physical Sciences Interfaces Institute for Quantitative Biology (BioMaPS), and the Rutgers Center for Molecular Biophysics and Biophysical Chemistry (MB Center).

The Evolution of Gene Regulatory Logic workshop is being convened to discuss that the discovery of the near "universal" or canonical character of the genetic code in 1953 by Watson and Crick, demonstrated that beneath the extensive diversity of forms in nature, there are conserved regularities that have made possible the development of a general science of genetics and molecular biology. The elucidation of the mechanism of action of the prokaryotic operon by Jacob and Monod, extended the investigation of regular features of genetic control to include a simple form of logic based on feedback principles. The discovery of the highly conserved homeogenes in eukaryotes, revived interest in general principles of morphology, extending the notion of the Bauplan into that of the Zootype, and establishing a connection between development and gene regulation.

Current work on genetic regulatory networks and cis-regulatory logic extends the operon concept to include complex networks of feedback, Boolean logic, and regular sequence motifs or codes, collectively correlated with regular patterns of gene expression. The history of studies of gene regulation and phenotypic development have repeatedly uncovered fundamental mechanisms shared by distantly related lineages, and observed essentially similar modes of control. In this workshop we wish to step back from an exclusively sequence level study of the evolution of gene regulation, and ask what forms of logic are instantiated in regulatory networks and how these vary among species. We interpret logic as some set of mechanisms for encoding computations which perform adaptive functions within and between cells. Another way to think about logic is as the set of rules and memory stores the cell uses to process information about its local environment.

Is there as Jacob suggested a single "Logic of Life" or multiple logics and if so how can we best characterize these logics in order to uncover the transformation series by which they come about throughout evolutionary history?

In this meeting we shall review our current understanding of prokaryotic and eukaryotic gene regulation and establish similarities based on common modes of operation. We shall explore the value of regulatory architectures conceived in the engineering and computational realms when applied to biology, and explore the possibility of new hybrid forms of logic derived from biology which often possess fascinating robustness and evolveability properties. The meeting will bring together biologists and computer scientists who seek to understand the logic underpinning the construction of complex adaptive functions.

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Document last modified on December 19, 2005.