Eric - Originally I had an idea for "chromosomes" behaving like simoltaneous threads, each with their own instsance of the 1000 memory array. (Or you could think of it as the chromosomes "filter" reading through their past actions, if that makes any sense ).
The problem that I could never find a satisfactory solution for was how to resolve conflicting commands. -1 .up store and 1 .up store. There are some obvious solutions, but they all have various conceptual problems depending on the sysvar.
Elite - I haven't thought about viruses except that viruses should be codule based and conspec specific (to a limited degree). ie: pass codule 2 to another bot, which happens to have code to pass itself on to other bots. Bots that don't execute codule 2 will have nothing to worry about (non-conspecs). These transfered codules replace whatever was there before them.
Anyway, that's as far as I've gotten.