The Evolution of Secondary Organization

in Immune System Gene Libraries 1

January 4, 1993

Ron Hightower
Dept. of Comp. Sci.
University of New Mexico
Albuquerque, NM 87131 USA
[email protected]

Stephanie Forrest
Dept. of Comp. Sci.
University of New Mexico
Albuquerque, NM 87131 USA
[email protected]

Alan S. Perelson
Theoretical Division
Los Alamos Nat. Lab.
Los Alamos, NM 87545 USA
[email protected]

Abstract

A binary model of the immune system is used to study the effects of evolution on the genetic encoding for antibody molecules. We report experiments which show that the evolution of immune system genes, simulated by the genetic algorithm, can induce a high degree of genetic organization even though that organization is not explicitly required by the fitness function. This secondary organization is related to the true fitness of an individual, in contrast to the sampled fitness which is the explicit fitness measure used to drive the process of evolution.

Keywords: immune system, genetic algorithm, V-region gene libraries

1 Introduction

The interplay between concrete actions at a local level and emergent behaviors at the global level is one of the major themes of artificial life. In the context of evolution, an important question is how selection pressures operating only at the global, phenotypic level can produce appropriate low-level, genetic structures. This question is most interesting when the connection between phenotype and genotype is more than a simple, direct mapping. The immune system provides a good subject for experimentation from this point of view|the phenotype is not a direct mapping from the genotype but the connection is simple enough that it can be studied.

In order to defend against foreign cells and molecules, called antigens, an immune system must first be able to recognize them. Antibody molecules are one of the agents responsible for antigen recognition. Recognition is achieved when an antibody physically binds to an antigen molecule. Molecular binding requires that the two molecules, antibody and antigen, have complementary shapes. Because the two molecules must match" in order to bind, it would seem that every antigen requires a corresponding antibody molecule in order to be

1Submitted to the European Conference on Artificial Life, January 4, 1993.