design

The January 2009 issue of Trends in Microbiology contains an article entitled “Bacterial flagellar diversity and evolution: seek simplicity and distrust it?”  Unfortunately, like many people, the authors have a mistaken view of irreducible complexity, as well as a very shallow idea of what a Darwinian “precursor” to an irreducibly complex system might be. I wrote a letter to the editor of the journal to point out these difficulties. Alas, they said they had no room to publish it. Below is the letter that I sent. To the editor: In their recent article “Bacterial flagellar diversity and evolution: seek simplicity and distrust it?” Snyder et al. (2009) [1] attribute to me a view of irreducible complexity concerning the flagellum that I do Read More ›

This is the fifth of five posts in which I reply to Dr. Ian Musgrave’s “Open Letter to Dr. Michael Behe” on the Panda’s Thumb blog. Finally, Dr. Musgrave objects to my placing viral protein – cellular protein interactions in a separate category from cellular protein-cellular protein interactions. In Chapter 8 of The Edge of Evolution I had written: Another, more important point to note is that I’m considering just cellular proteins binding to other cellular proteins, not to foreign proteins. Foreign proteins injected into a cell by an invading virus or bacterium make up a different category. The foreign proteins of pathogens almost always are intended to cripple a cell in any way possible. Since there are so many more ways Read More ›

This is the fourth of five posts in which I reply to Dr. Ian Musgrave’s “Open Letter to Dr. Michael Behe” on the Panda’s Thumb blog. And now let’s talk about Dr. Musgrave’s “core argument,” that subsequent to the virus leaping to humans from chimps Vpu developed the ability to act as a viroporin, allowing the leakage of cations which helps release the virus from the cell membrane. Yes, I’m perfectly willing to concede that this does appear to be the development of a new viral protein-viral protein binding site, one which I overlooked when writing about HIV. So the square point in Figure 7.4 representing HIV should be placed on the Y axis at a value of one, instead Read More ›

This is the third of five posts in which I reply to Dr. Ian Musgrave’s “Open Letter to Dr. Michael Behe” on the Panda’s Thumb blog. In my reply to Smith I quoted from a review (3) which asked the question why, with so much genetic variation, do we just see “interesting variations” in biological properties. Smith, replying to me on her blog in high dudgeon, quotes the next paragraph of the review which details some of those interesting variations: The long terminal repeat region (LTR) of the HIV genome regulates transcription and viral replication, acting as a promoter responsive to the viral Tat protein. Although all subtypes share the same LTR function, they differ with respect to LTR sequence Read More ›

This is the second of five posts in which I reply to Dr. Ian Musgrave’s “Open Letter to Dr. Michael Behe” on the Panda’s Thumb blog. Musgrave: But by far the worst, you ignored her core argument. That in the space of a decade HIV-1 Vpu developed a series of binding sites that made it a viroporin, a multisubunit structure with a function previously absent from HIV-1. Behe: It is not clear to me why you call that Smith’s “core argument.” In her post, her writing meanders quite a bit; it’s hard for me to glean what she thinks is most important. After sneering a bit at me, Smith began her post by asserting that vpu is a “new” gene (even though Read More ›

This is the first of five posts in which I reply to Professor Ian Musgrave’s “Open Letter to Dr. Michael Behe” on the Panda’s Thumb blog. Musgrave: Dear Dr. Behe I have recently read your response to Abbie Smith’s article on the HIV-1 protein VPU. Ms Smith showed how Vpu’s recently evolved viroporin activity directly contradicts your statement that HIV has evolved no new biding sites since it entered humans (Edge of Evolution, page 143 and figure 7.4, page 144 ). I was greatly disappointed in your response. I must admit to having a special involvement in this case. Firstly, I drew the illustrations for Ms Smith’s article, and its follow up. But secondly, as a member of my professional Read More ›