What is Universal Common Descent?

Well your arguments and examples aren’t doing much to demonstrate your expertise, save for your human-chimp example, but that one suffers from being circular. Sorry, but you can’t assume the truth of evolution when attempting to argue that it works just fine.

Oh, gosh no. Unless you know of some ID folks that I don’t know. ID arguments do not preclude the immune system antibodies. For these vertebrate immune system antibodies, a relatively few residues are substituted, differently across a large number of antibodies, and essentially immediately tested against targets, in a continuous procedure. This is light years away from the hypothetical, glacial, evolutionary process. Your continued appeal to the antibody search problem is not helping your case.

Well you are really fighting the science here. You are heroically fighting the tide. Axe’s paper is far from the only work showing these results. This is by no means an ID conspiracy (I wasn’t even aware of Axe’s work for quite sometime). If Axe’s estimates are “wildly off,” then so are several others. Also, the “all or none” phrase comes from the paper, and is specifically directed at the protein-protein binding problem. My point was simply that the paper’s finding of such an “all or none” is no surprise.

Well now you’ve gone beyond fighting the tide. The notion that protein sequence space is that densely packed with function is, frankly, [pick some outrageous word to go here]. The problem here is that you are zooming in on the tactical, narrow, view, and then extrapolating that to a strategic, wide view. Your result is “wildly off” to use your phraseology.

Protein functionality is not limited to a single canonical sequence. There generally is a large number of tightly clustered sequences that will provide the functionality. And most proteins have multiple functions. What you are focusing in on here is even more tactical: you are looking at the few residues that influence the binding interface. With a few mutations, you can bind to a similar membrane protein (which a similar phage is known to bind to). So you have switched from one membrane protein to another, both sharing the same fold and tertiary structure. And the protein J is providing the same overall functionality, just with a different membrane protein. This in no way extrapolates to the different question of the density of protein function across the entire, astronomical, sequence space.

So back to our topic, your article incorrectly casts [Meyer, et. al., 2012, Science] as rebuking Behe, and I would still like to hear ideas on why Meyer, et. al. found zero synonymous mutations in all their protein J alleles.