To summarize the recent Open Letters series, some time ago a student of HIV, Ms Smith posted a list of binding sites found in the HIV-1 protein Vpu that contradicted Dr. Behe’s assertion that HIV has evolved no new protein-protein binding sites. Central to this was the demonstration that HIV-1 Vpu had evolved into an ion channel, a viroporin. Over two months later, Dr. Behe wrote a response, which did a disservice to Ms Smith on many levels, most especially by ignoring the key argument about Vpu viroporin. I remonstrated with Dr. Behe about this in an Open Letter. Dr. Behe publishing a series of responses to this open letter, which I responded to post by post as they were published.
As you may realize, Dr. Behe has finally conceded that he was wrong, and Vpu viroporin represents a real example of protein-protein binding. I have suggested that he issue an erratum to this effect, thanking Ms Smith for bringing this example to his attention (and the HIV Vpx duplication, which he also claimed didn’t exist). This is the very stuff of science, we all at some stage support ideas that were wrong, but when we realize they are wrong, we give them up. I thank Dr. Behe for acknowledging his mistake.
Along the way we have also learned that Dr. Behe’s citations don’t actually support his statements in “edge of Evolution”, his estimation of HIV mutation rates and effective population numbers is off by orders of magnitude, and his rationale for excluding viral protein-cellular protein binding has no biological basis (and is inconsistent).
For ease of perusal, I have put the links for all the Open Letters into this one post.
The Original Open Letter, where I protest at Dr. Behe’s treatment of Ms Smith.
An Open Letter Part 2, where I detail Vpu viroporin and point out that Dr. Behe’s references do not support his assertions.
An Open Letter Part 3, where I chide Dr. Behe for his continuing poor treatment of Ms Smith.
An Open Letter Part 4, where I go into more detail about why Dr. Behe’s attempt to exclude certain binding sites is not valid.
An Open Letter Part 5, where I dig even deeper into binding sites, and show why Dr. Behe’s attempt to exclude certain binding sites is not valid in even more detail.
An Open Letter Part 6, where I point out that Dr. Behe’s population and mutation rate estimates for HIV are wrong by orders of magnitude.
An Open Letter Part 7, where I thank Dr. Behe for admitting he was wrong, point out that “impresessedness” is not a biologically valid standpoint, and show that yet another reason for excluding viral protein-cell protein interactions is invalid.