I recently wrote an article discussing IC and cooption:
I did not have a chance to nuance all of my points, so I will expand on one of them here. One key issue is the rarity of functional proteins, and this article describes how the tolerance of proteins to mutations drops off exponentially, or more quickly, with increasing numbers of mutations:
https://www.researchgate.net/publication/6674932_Robustness-epistasis_link_shapes_the_fitness_landscape_of_a_randomly_drifting_protein
The study demonstrates that after 1 to 2 mutations to a protein, about 2/3 of the following possible non-synonymous mutations could be “tolerated”. However, after a few more mutations (around 5-6), the likelihood of the following non-synonymous mutation being tolerated is roughly 1/3. This result closely matches Axe’s result for the rarity of functional sequences in the vicinity of a functional beta-lactamase: (1/3)^150 is around 1E-77.
In addition, the Chatterjee et al. paper I cite analyzed targets which represent half (c=0.5) of a sequence matching the target (e.g. 500 out of 1000 nucleotides in a gene). In contrast, the Tokuriki and Tawfik results suggest that a protein becomes nonfunctional after considerably less than 30 mutations, none of which individually would necessarily disable a gene, and that number corresponds to c=0.2. In other words, Chatterjee et al. demonstrate the impossibility for a random search finding a target which is vastly larger than that represented by actual proteins.
After you read my article and the referenced articles, all of my comments should make sense. I will try to respond to comments and questions over the holidays. However, I will only have time to respond to those who have made a sincere effort to thoroughly understand my arguments and the content of the research I cite.
As a side note, I mentioned to Mike Behe the following comment related to the upcoming responses to his new book
Let the 23rd annual Behe games begin.
May the odds ever be in your favor.
And to all, have a wonderful holiday season.