It appears that Dembski and Marks (and a student of Marks by the name of Winston Ewert) have a third paper [pdf] which Dembski describes as “a thorough deconstruction” of the AVIDA program. Unsurprisingly, it was presented at an engineering conference, the 2009 IEEE International Conference on Systems, Man, and Cybernetics. I’m unsure as to how much peer review was involved for this one and I’m unqualified to comment on the content, so I’ll leave that to others.
Update (12/14): See here for further comments on the IEEE International Conference on Systems, Man, and Cybernetics.
stranger fruit 
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The main point of this paper appears to be that Avida had difficulty producing an EQU function without a bunch of transitional functions, the presence of which is, apparently, a form of active information.
Mutation, fitness and selection are also, apparently, “active information”. I guess Dembski is eventually planning on defining the entirety of evolutionary theory (the bits he’s heard of, anyway) as active information.
Moth Eyes – he already has. By definition of active information, as evolution increases the probability of finding a target, it has active information. Tornadoes in junkyards don’t have any.