1 Avida: Evolution Experiments with Self-Replicating Computer Programs
Charles Ofria and Claus O. Wilke
Avida is a software platform for experiments with self-replicating and evolv- ing computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated meth- ods to analyze and postprocess experimental data. This chapter explains the general principles on which Avida is built, its main components and their interactions, and gives an overview of some prior research with Avida.
1.1 Introduction to Avida
When studying biological evolution, we have to overcome a large obstacle: Evolution happens extremely slowly. Traditionally, evolution has therefore been a field dominated by observation and theory, even though some regard the domestication of plants and animals as early, unwitting evolution exper- iments. Realistically, we can carry out controlled evolution experiments only with organisms that have very short generation times, so that populations can undergo hundreds of generations within a timeframe of months to a few years. With the advances in microbiology, such experiments in evolution have become feasible with bacteria and viruses [14, 39]. However, even with mi- croorganisms, evolution experiments still take a lot of time to complete and are often cumbersome to carry out. In particular, certain data can be diffi- cult or impossible to obtain, and it is often impractical to carry out enough replicas for high statistical accuracy. According to Daniel Dennett, “evolution will occur whenever and wher- ever three conditions are met: replication, variation (mutation), and differen- tial fitness (competition)” [9]. It seems to be an obvious idea to set up these conditions in a computer and to study evolution in silico rather than in vitro.