AAAARRRRGGGGGHHHHH!!!!!!!!!!!!!!!!!!
At best, A-Girl, what you've got there is a list of interesting research projects for PhD candidates to work on. I don't see anything that even remotely contradicts evolution. But this thread is way too long, and no one is likely to jump in at this stage, so we should save it for another thread. Perhaps after this Bush/Frist/ID mess calms down, if it ever does. I'm not up to getting into anything serious at the present.
Items on the "laundry list" are offered as comparables to the deficiency of the standard model to explain matter. Supersymmetry and geometric physics don't replace the standard model, they subsume it.
For Lurkers: the point of the sidebar is the difference in how the two disciplines prioritize and deal with problematic evidence. Physics revisits the theory, biology follows the evidence.