Teh digital life laboratory at California Institute of Technology has produced a software application called Avida that is an auto-adaptive genetic system designed primarily for use as a platform in Digital or Artificial Life research.
By studying this system, one can examine evolutionary adaptation, general traits of living systems (such as self-organization), and other issues pertaining to theoretical or evolutionary biology and dynamic systems. The power of Avida is that it gives us a controllable digital system in which to study the theories of evolutionary biology. Often, we can study elements of evolutionary theory that are difficult or impossible in biological systems.
Avida can be downloaded from here. Of course, to truely appreciate the power of this tool, one must be a Linux geek.