Sorry milady, but I don't really know anything about it. I've never really been very interested in Alife -- while it may be entertaining, I don't think it is a particularly useful pursuit. My expertise is generally in computational theory and information theory at large. I have a background in chemistry, but even that isn't something I keep up with.
What would be the Avida parameter setup for bootstrap abiogenesis - genome length of zero?
Genes are very coarse functional units; you would actually bootstrap from much finer functional units than genes. For real-world simulation purposes, you might be able to start with amino acids using precomputed phase spaces and then do as-needed computation beyond that (taking advantage of the fact that higher-order combinations aren't as common as lower order combinations).
I think the Avida software is an engine for modeling the system dynamics, not real biological systems. This is plenty useful though. The real argument about evolution is whether or not that particular mathematical model of system dynamics leads to interesting results, which can be demonstrated in painstaking detail using this modeling system. If the system dynamics model works, then so does biological evolution (ignoring whether or not evolution is actually responsible for speciation).
My personal theory is actually a bit different than conventional doctrines. I'm more inclined to say that variation and complexification is caused by automata mechanisms, with a fair bit of selection pruning the automata process. To my own mathematical mind, this is the fastest and simplest bootstrap pathway to very high-order complex biologies, NOT textbook evolution. My apparent defense of evolution is primarily that the mechanism is definitely valid, not because I think that is best theory for speciation mechanisms. It irritates me that people constantly argue that it is an invalid mechanism (which is an argument from ignorance), and yet choose to ignore the fact that it is a weak argument from a systems dynamics theory standpoint. To me it says that most of the detractors are not educated on the topic enough to formulate a reasonable and coherent argument.
I'm not defending evolution per se, I'm attacking the egregiously poor arguments against it (though most people apparently have a hard time seeing the difference).
There are some people around here who are not "purist" evolutionist or anti-evolutionist. betty boop posted the Wolfram article (a view like yours) which was very informative and it was refreshing to see a positive response!
Thank you for your response on Avida! I'll keep looking for the particulars of the software, because a declaration that "the program worked" is meaningless to me until I know something of its structure.