This chapter describes the behavior of the immune system from an informationprocessing perspective. It reviews a series of projects conducted at the University of New Mexico and the Santa Fe Institute, which have developed and explored the theme "immunology as information processing." The projects cover the spectrum from serious modeling of real immunological phenomena, such as crossreactive responses in animals and the generation of diversity, to computer science applications, especially the attempt to develop an immune system for computers to protect them against viruses, intrusions, and other malicious activities. In each project, we have used an approach with the following steps: (1) Identify a specific mechanism that appears to be interesting computationally, (2) write a computer program that implements or models the mechanism, (3) study its properties through simulation and mathematical analysis, and (4) demonstrate its capabilities, either by applying the ...

The immune system uses many strategies to generate its enormous repertoire of diverse antibodies, but their relative importance is not understood. Here we address the contribution of antibody gene libraries to the antibody repertoire. We introduce a general framework, in which we can study many antibody-pathogen matching rules, including the widely-used shape-space model (Perelson and Oster, 1979). We use the genetic algorithm as a model of evolution to investigate the type of antibody repertoires that might evolve in relation to a given pathogenic environment. For the antibody/pathogen matching rules that we studied, the scaling relation between fitness and the size of the evolved antibody library is only a shifted variant of the scaling relation that we obtain with random libraries of the same size. We discuss how our results compare to the antibodies that are expressed in newborns, and we discuss the implications of our results for recent experiments with phage a...

This dissertation is approved, and it is acceptable in quality and form for publication on microfilm: Approved by the Dissertation Committee: Accepted: