Thursday, June 22, 2006

Salvador's Redundancy II

[Update: The saga continues.]

Salvador has chosen an strange venue to reply to my recent posts about him. I tried adding another comment there, but it was becoming too long, so I moved it here. I'll focus on three points.

"Junk" DNA

After his comments it's no longer clear (if it ever was) what Salvador is actually arguing on "junk" DNA. The point is that deleting a piece of DNA that we suspect to be "junk" (e.g., because it is a pseudogene) is a scientific test of whether the DNA is "junk". If the deletion doesn't have any detectable effect, then the "junk" hypothesis is supported. That does not mean that we have proven that the DNA is "junk" (we cannot accept a null hypothesis); any number of alternative hypotheses may, conceivably, turn out to be correct in the end. However, it does mean that one cannot simply assert an alternative hypothesis (e.g., unknown interacting regions) and expect everyone to just accept them without further scientific test. Incidentally, many researchers (only a handful of which are connected to ID creationism) have proposed hypothetical functions for "junk" DNA, so Salvador isn't even right in his claim that ID is particularly well suited for thinking outside the 'evolutionary box'. I for one find the ideas of John Mattick on "junk" DNA much more interesting than anything ID supporters have ever said. However, his ideas will have to be tested in the laboratory or the computer -- something he is actively engaged in. I would love to hear about the research efforts of the ID scientists. In other words, we are still waiting for a good example of the supposed superiority of ID as a "framework for scientific investigation".


Salvador writes:
The premise that systems with survival value are sufficiently visible to natural selection for them to be maintained and evolved is a false one. Those issues are theoretically pursued in Cornell Geneticist, John Sanford's book [...]
Salvador is simply hallucinating here. Is this the same John Sanford who declared in the Kansas Evolution Hearings that the earth was probably between 5,000 and 100,000 years old? Is this the Courtesy Associate Professor at the Department of Horticultural Sciences who has never published a peer-reviewed article on evolutionary biology? You'll forgive me if I continue to walk down the corridor (toward Dan Graur's office and lab) for my genome evolution.

C. elegans vulva

Salvador: when will you retract that nonsense about the "independently successful redundant developmental pathways" for making a vulva? Knocking out either the EGF receptor / RAS / RAF / MAPK inductive signaling pathway or the LIN-12 / Notch lateral signalling pathway results in the development of an abnormal vulva (often, no vulva at all). It would appear that your ID colleagues' "never apologize, never explain" attitude is contagious.