Evolutionary Computation in Gene Regulatory Network Research

CHAPTER 10USING EVOLUTIONARY ALGORITHMS TO STUDY THE EVOLUTION OF GENE REGULATORY NETWORKS CONTROLLING BIOLOGICAL DEVELOPMENT

Alexander Spirov

Computer Science and CEWIT, SUNY Stony Brook, Stony Brook, NY, USA; and theSechenov Institute of Evolutionary Physiology and Biochemistry, St.-Petersburg, Russia

David Holloway

Mathematics Department, British Columbia Institute of Technology,Burnaby, B.C., Canada

10.1 INTRODUCTION

Developmental biologists approach the embryological formation of organisms in terms of the temporal and spatial regulation of gene expression. How does gene regulation precisely specify in what cells and at what time a gene is expressed (to a given level)? Much of the work in the field is on the gene–gene interactions, frequently in extended regulatory networks, which control given events in development.

Computational work on developmental gene regulatory networks (GRNs), to construct the “wiring diagrams” of gene connections and characterize network dynamics, has been going for many decades. More recently, there has been increasing focus on the evolutionary dynamics of how these GRNs arose. Since developmental GRNs are fundamental to creating the body plan of a species (and the functions associated with the form), understanding the evolution of GRNs is fundamental to understanding the dynamics of speciation: how is an organism’s form (phenotype) maintained, despite environmental variation and genetic mutation, and how is such stability balanced against evolvability, ...