Nums, this is something I would love to be a part of. I am actually considerring going back to school and finishing my doctorate in Alife. Yea, I have a long way to go.... Haven't made that decision yet, but it's on the table.
Here's some thinking off the top:
When I think about the unique attributes of DB relative to Avida or Tierra, one thing that comes to mind is competition. Most of the ALife papers I've read (I actually have the proceedings from Artifical Life IX on my desk at the moment) and most of the research done in these other systems utilize an external fitness routine, selecting for sorting ability or some such. I think there's a general paper just on the topic of using competition as a fitness criteria which could discuss limiting energy in the sim, mutation rates, etc.
Another half formed idea is the seperation of genotype and phenotype. Other systems often have organisms interacting directly on each others DNA, kind of Core Wars on steriods. DB has a pretty sophisticed phenotype encironemnt where most interaction is between phenotypes and the environment they inhabit via ties, shots and other artifacts withdirect interaction with the genome playing a background role. This strikes me as paper worthy.
And lest I forget to sneak my broken record pitch in, I think that if we added in-genome locale-relative mutation probabilites, then there is a paper on Genotypic Plastisity (as opposed to phenotypic Plastisity) - the importance of this mechanism for increasing the probability of varation in places in the genome where doing so is advantageous and vice versa...
-E
