If you have not checked out the Panda's Thumb, I recommend starting with this post by Ian Musgrave. It is a devestating critique of an article by Discovery Institute fellow Jonathan Witt. Ian is an Australian biochemist and he simply shreds Witt's arguments against the argument from jury-rigged design. It is an appropriate venue for such an article, since the "panda's thumb" is a textbook example of how evolution cobbles together useful structures out of existing ones, as would be expected. If an omnipotent designer had started from scratch, it would certainly have done a better job of it because, unlike evolution, such a designer would not be constrained. The human eye is another great example of jury-rigged design. At any rate, go read the entire article, as the work by Ian is excellent from beginning to end.