I posted this on the original book blog back in the summer of 2008. Since then, the book blog was hacked and lost. So let me repost it again. A current update is appended at the end.
For the past several years, I have been focused on how one might facilitate the evolution of metazoa. But because of recent scientific discoveries, I should pause and comment on an old topic – the bacterial flagellum.
Five years ago, I wrote an essay that raised many questions and expressed skepticism about Nick Matzke’s hypothesis of homology between the bacterial flagellum and the F ATPase. At the time I wrote this, the skepticism was justified. But since then, new data have come in that have served to significantly strengthen Matzke’s hypothesis and undercut my skepticism.
Since 2003, Matzke hooked up with Mark Pallen, a researcher who studies the flagellum/TTSS and who uncovered sequence evidence that indicated the flagellar gene FliH is a fusion of domains that are homologous to the b subunit and the delta subunit of the F-ATPase. This was a significant piece of support for Matzke’s hypothesis. And in 2006, Matzke and Palin published a paper in Nat Rev Microbiol.and I congratulated Nick.
And it now appears as if the structure of another flagellar gene, FliJ, further supports his hypothesis:
Namba and colleagues have now solved the structure of FliJ, another protein that interacts with FliI and FliH. And what they found was clear evidence of homology with yet another protein from the F-type ATPase–the gamma subunit!
Looking back, I would say my skepticism was justified in a trivial sense. Matzke argued that FliH was homologous to the b subunit, FliJ was homologous to the delta subunit, and FliP was homologous to the gamma subunit. At the time, the data did not exist to justify such claims and as it turns out FliH is homologous to both b and delta, while FliJ is homologous to gamma. These specific predictions did not bear out.
But in a far more important and global sense, it does indeed look like Matzke’s hypothesis is correct and that the TTSS machinery is homologous to the F-ATPase.
In The Design Matrix, I explore how the concept of IC interfaces with cooption and intelligent design and offer the following as part of my approach:
Instead, independent evidence is needed to support such a hypothesis of cooption cobbling a machine together. This does not mean we need something that amounts to a proof. Nor does it mean that an exhaustive Darwinian explanation is needed. On the contrary, the evidence we need is extremely modest and lacking in detail……First, if an irreducibly complex machine did evolve into existence through cooption, then the parts must have predated the machine. They must have been doing something else prior to being recruited into the machine. Thus, some evidence of this pre-machine activity is needed. Since we cannot travel back in time, we will have to settle for traditional evidence of common descent. Do the various parts of the machine have homologs that are in turn part of a system that is more ancient than the machine?
Multiple points of homology between the components of the F-ATPase and flagellum/TTSS would clearly qualify as “various parts of the machine” having “homologs that are in turn part of a system that is more ancient than the machine.” Thus, if I were to assign a Discontinuity Score to the flagellum, it would reside within the negative realm of the continuum.
And it becomes more interesting when we realize that the themes of cooption, modularity, and subfunctionalization have apparently played critical roles in the evolution of the bacterial flagellum. This is something to dig into at a later date.
As you can see, I am trying to approach these issues in an open-minded and open-ended fashion, while, given the abundant evidence that evolution is in play, setting the bar quite high for any discontinuity score. In fact, the essay I wrote above follows seamlessly from something I posted to the ARN forum back in the Spring of 2001:
Now, when I infer ID behind the bacterial flagellum, I am focused on the core aspects that are shared by all bacterial flagella (I have previously explained how core IC modular systems are under functional constraint and surveying 3.5 billion years of evolutionary tinkering is a good way to detect such constraint). This core aspect of the bacterial flagellum is thus hypothesized to be essential to basic flagellar function in all bacteria while more peripheral elements, while important/essential in the context of individual species, can be tweaked in accord with the needs of the organism. And it’s when one focuses on the core constituents of “the bacterial flagellum” that we still find a hefty IC system that is not convincingly explained by cooption ,as (for one reason) there are no apparent precursors for all components of this core (remember we are talking about what happened and not about what could have happened). However, some have proposed such things as the type III secretory system and the F-ATP synthases. I simply don’t find such explanations convincing (the former probably post-dates flagella and the latter doesn’t look like a precursor). And it is not bias behind my skepticism, as both precursor states would nicely fit into a front-loading hypothesis (in fact, if anything, I’d love to fit the flagella into a front-loading hypothesis).
What has been the sole change? In 2001, “the latter doesn’t look like a precursor” while in 2008 it is shaping up like one. BTW, the type III secretory system still looks like it was derived from the flagellum.