Saturday, May 12, 2007
JCVI Evolutionary Genomics Journal Club on Liu-Ochman
This week I was the presenter for our "Evolutionary Genomics" journal club at JCVI and I chose to present the Liu-Ochman paper on the the stepwise formation of the bacterial flagellum and its reception (part two, three) in the blogosphere. The basic claim of the article is that the 24 core proteins are homologous to each other and this explains how the flagellum evolved through repeated gene duplication events.
Nick Matzke doesn't buy the argument for several reasons: 1) It doesn't seem to be congruent with previous studies 2) At least two of the structures of the presumed homologous proteins don't "look" homologous. and 3) The authors seem to be using the Bl2Seq tool incorrectly. It's odd that Nick focuses so much effort on points 1) and 2) because it is really 3) that is the issue. Personally, I've never been convinced that protein structure is of much use in inferring homology or the lack of it; systematists have been burned so many times by incorrectly assumed (non)homology of gross morphological traits in light of convergent and divergent evolution; why should morphology at the protein level be any different? The beauty of molecular systematics is that it's freed us from having to deal with morphology at all.
At the journal club, we were split on the value of structure for inferring homology, but we all agreed that eyeballing structures, particularly structures that seem to have drawn with different programs and rotated differently. was not a very convincing argument.
We were much more convinced, however, by Nick's demonstration that the authors seem to have performed their BLAST matches incorrectly. As Nick showed, the authors did not have sequence filters enabled, which means that matches to low-complexity regions can artificially inflate BLAST significance, and perhaps more damning, the authors used multiple pairwise BL2Seq runs without correcting for the true size of the search space. And these weren't just assumed to be the problem; Nick demonstrated on a subset of the data that using the correct parameters caused several "significant" BLAST matches to disappear.
This was the introduction to scientific blogging for many of the attendees of the journal club, and they also had some interesting comments about the phenomenon after preparing for the club.
1) While the paper was much mentioned in scientific blogs, generally the mentions were just "Nick Matzke has shown that the Liu-Ochman paper is flawed; here's the link", and not independent analyses of the paper. Yes, this is true of blogs in general, not just scientific ones. But this sort of laziness is very common in traditional media too. Take a look at your newspaper and see how many articles are from news services like AP or Reuters rather than being independent reporting.
2) Why did discussion suddenly fall off after Nick's articles? Does the blogosphere really have such a short attention span?
3) Why haven't we seen a response from Liu and Ochman? Are they not aware of the discussion, or do they simply see criticism on blogs as not being worth responding to?