Now, since this topic is once again two years old, and since it is relevant to the development of DB3, I would like to revive this long dead discussion with a little bit of my own thinking.
After reading how many of you view the different kinds of specialization, I have decided to try and make a more finite distinction between them.
1. The DNA for the "Brain" of the bot is what exists in DB2, and works quite well for its purpose. I believe this should remain mostly unchanged.
2. What I think would work best is to introduce and entirely separate DNA for the "Body" of the bot. This DNA would specify how it grows, depending on its conditions of course, and would determine things like energy use efficiency, poison/venom type, waste disposal, ect. The problem I envision with this is that it is so flexible that the slightest error in tuning could create a horribly imbalanced simulation. If even the slightest amount of favor was given to one characteristic, evolution might refuse to take any other path, and the purpose of such a DNA would become non-existent.
I am curious as to what solutions there might be to the second DNA I am proposing here. Certainly using co-existing physics environments in a simulation is one approach, but other than that, nothing really comes to mind.