Blogging and common ancestry in Nature

This week's Nature has some interesting stuff. There's a very blunt editorial on the recent arsenic-using proteobacterium and criticisms published on blogs. The authors of the original study (so far) refuse to respond to the blog criticisms, instead insisting that critics must go through the normal peer reviewed channels. Says Nature:
Purists who hold peer review as the casting vote in such debates will read her words with approval. But the problem is that Wolfe-Simon's reticence is the polar opposite of the fanfare with which NASA trailed her discovery to the public.
As a peer review purist, I admit that I am sympathetic to the desire to hash this out in the peer review press, but I agree that NASA started the whole mess with their overhyped press conference. Doesn't seem fair to dodge criticism now. Also from the editorial:
Bloggers and online commentators have an important part to play in the assessment of research findings, and many researchers' blogs, in particular, contain better analyses of the true significance of a scientific finding or debate than is seen in much of the mainstream media.
Mainstream media don't handle scientific reporting very well? Scientists ought not publish by press release or overhype their results? Where have I heard these things before? Here, here, and here. Read the Nature editorial here: Response required

In other news, Theobald responded to another criticism of his common ancestry paper, this time from Yonezawa and Hasegawa. I was a little confused by the brevity of their argument, but basically they showed that the likelihood test Theobald used could be used to show that two unrelated proteins were in fact related. The problem was that they used DNA sequences to do this, which will be artificially similar due to the limited nucleotide alphabet. Protein sequences have a bigger alphabet (20 amino acids), and we can infer sophisticated models of amino acid substitution from very similar sequences. Theobald responded that when you do their test with the protein sequences, independent ancestry of the two sequences is actually preferred. Also, he said,
I have not tested all possible competing hypotheses, and my analysis will not be the "last word on common ancestry." I emphasize that I have in no sense provided an absolute 'proof’ of universal common ancestry. One of the great advantages of the model selection framework that I presented is that if a novel model is proposed with a well-defined likelihood function, then we can easily compare it to the common ancestry models and see how it fares.
He's right about that. The burden is indeed on his critics to come up with an alternative model that can be compared, and not one that mistakes a different kind of phylogeny for no phylogeny at all.

Yonezawa and Hasegawa. 2010. Was the universal common ancestry proved? Nature 468:E9.
Theobald. 2010. Theobald reply. Nature 468:E10.

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