Rethinking universal common ancestry

A few days ago, I posted a note about Koonin and Wolf's paper responding to Theobald's Nature paper on test common ancestry. I wrote it in haste after quickly reading over the paper. Now that I've had time to think it over, I'd like to make some clarifications to my original post.

First off, I noted that the paper was published in an online journal called Biology Direct. I think it's fair to note that the editor of Biology Direct is none other than Koonin himself. Why should that matter? Well, here's another point I made in my original post:
The result, they say, is statistically significant sequences with no true phylogenetic signal. In principle, this sounds like it would work, but they don't actually show that their random sequences are significantly similar and without phylogenetic signal. So I have that reservation at least. But again, in principle, this method should indeed generate significantly similar protein sequences without phylogenetic signal.
That's been nagging at me ever since I posted my note, because it seems like a really important issue that the authors didn't really bother with. The problem as I've come to see it is this notion of eliminating "phylogenetic signal." By scrambling the sequences the way they do, Koonin and Wolf eliminate the "signal" that supports a bifurcating tree. BUT that's not the only tree possible. If their sequences are truly randomized as they describe, then they are modeling a star phylogeny, which is still a phylogeny. On the other hand, I think it's entirely possible that we could reasonably expect that some bifurcating phylogenetic signal survived their randomization process (because randomization is never truly random), which would bias their results. So by not demonstrating that their sequences have no bifurcating "phylogenetic signal," their results become uninterpretable.

More to the point, though, a star phylogeny is still a phylogeny, which really undermines the whole strategy that Koonin and Wolf adopt. Consider this comment from their published response to the reviewers:
The hypotheses are stated quite explicitly by both Theobald and ourselves: the general null hypothesis of independent ancestry and the specific hypothesis of common ancestry.
That's only true if "independent ancestry" is identical to "star phylogeny," which it isn't. A star phylogeny is still a phylogeny, and the overarching concept of "common ancestry" cannot reasonably exclude a star phylogeny. So that's both "independent ancestry" and "common ancestry" that Koonin and Wolf have incorrectly conceived.

Given the deficiencies of this paper, it's not clear to me precisely what Koonin and Wolf have demonstrated other than their own confusion about what Theobald really did.

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