Unclear on the concept

As you know, the book Why Intelligent Design Fails:A Scientific Critique of the New Creationism edited by our own Matt Young and Taner Edis http://www2.truman.edu/~edis/books/id/ has just been published. I am one of the authors, with a chapter on the evolution of bacterial flagella. So I feel particularly honoured that one of the first responses to the book is to my chapter.

Unfortunately, the response shows the author is somewhat unclear on the concepts involved.

In the chapter “Evolution of the Bacterial Flagellum” I try, amongst other things, to show a motility system can be built up by cooption of the components of a secretory system to motility functions, it also helps to know that that there are multiple bacterial motility systems, some simple (but now out of date) background can be found at my Evolution of the Bacterial Flagellum page, and an excellent and more exhaustive work is Nic Matzke’s Evolution in (Brownian) space.

For the purposes of this blog though, it is enough to point out that while Dembski and Behe characterize the eubacterial flagella, a swimming motility system, as an “outboard motor”, it is also a secretory system. The secretory system is a key part of flagella function. The flagellar secretory system is also the structure that rotates, and the flagellar secretory system is homologous to the type III secretion system (TTSS) that pathogenic bacteria use to secrete proteins necessary to invade eukaryotic cells. Indeed, place flagella side by side with TTSS and it is hard to tell them apart. In many ways, a TTSS is a flagellum without a motor. Phylogenetic analysis show that TTSS and flagella share a common ancestor, and most workers in the field think that flagella evolved from a primitive secretory system.

One of these is a secretory TTSS, one is a flaellum, but which one?

The question is why would a motor be added to a TTSS that is secreting without it? It turns out that the motor of the flagellum, MotAB, is a proton pump and is part of a family of proton pumps (TolPQ) that drive secretion in a number of systems. Interestingly, the advential gliding motility system of Myxococcus xanthus (where bacteria glide along surfaces rather than swim freely), is a secretory system driven by a TolPQ family proton pump. It is also of interest that flagella are required for a form of gliding motility called swarming. This suggests a pathway for evolving a swimming motility system from a secretion system via functionally intermediate steps.

Secretion system -> secretion system + proton pump -> gliding motility (via secretion) -> swimming motility

This is in clear contrast to the “flagella poofed in one go” model used by Dembski in his calculations. But back to the question, “why would a motor be added to a TTSS that is secreting without it”? Because the proton motor increases secretion efficiency. If you knock out the flagella motor then the flagella is paralysed and flagellar secretion continues, but at reduced rate. This suggests that adding a proton pump to a proto-flagellar TTSS-like secretion system would increases secretion, so that association of a proton pump with the proto-flagella secretion system would be beneficial (and result in a system that could be co-opted for motility).

Now in this paper Wilharm G, et al., Yersinia enterocolitica type III secretion depends on the proton motive force but not on the flagellar motor components MotA and MotB. Infect Immun. 2004 Jul;72(7):4004-9. a non-flagellar TTSS has been described which also uses a proton-pump to help drive secretion. This is completely consistent with the scenario above, where a proton motor is not essential for secretion, but addition of a proton motor is beneficial as it increases secretion.

Also consistent with my model is the distribution of functional motility systems, which show the functional intermediates postulated by my model.

E. Coli TTSS- ATP pump drives secretion Y. enterocolitica TTSS - ATP pump and proton pump drives secretion, proton pump not essential for secretion Myxococcus TolPQ related transporter proteins and proton gradient necessary for adventital gliding motility, not clear if secretion is reduced or abolished by deletion of TolPQ proteins. Cytophaga - ATP pump and proton pump, proton gradient essential for gliding motility via rotatory structure. Not clear if secretion is reduced or abolished by deletion of proton pump. E. coli flagella. ATP dependent transporter and proton pump, proton pump not essential for secretion but essential for swimming motility.

Hmmm, can you see a pattern here?

The Yersina non-flagella TTSS doesn’t use MotAB (and wouldn’t it be cool if it did), but I am willing to bet a copy of Gould’s brick that the proton pump turns out to be a TolPQ related protein (heck what if it turns out to be a homolog of MotAB, wouldn’t that be cool).

Now, over to our friends at ARN

The abstract of the paper is quoted and then they say that it

. . … shows that, protein secretion by the flagellar system of Yersinia is not affected by a mutation in motAB. This indicates that motility and protein secretion are not linked as they appear to be in bacteria that exhibit gliding motility.

Now, this shows they don’t grasp the model (or indeed what the paper says). The paper confirms an expectation from the flagellar secretion system that addition of a proton motor to a TTSS increases, but is not essential for, secretion. Thus addition of a proton pump to a primitive TTSS would be beneficial, and provide a pre-adaptation which later could be co-opted to provide motility.

The key mistake made is not reading the paper (or abstract) carefully. The secretion is via a non-flagella TTSS, not the flagella, as the ARN author says. The experiment was to find out if non-flagella TTSS co-opted flagella MotAB to help drive secretion. The non-flagella TTSS doesn’t use MotAB, rather some other proton pump. As I said, I’ll bet a copy of Gould’s brick they use a TolPQ derived system. Again, this finding is entirely consistent with my model.

So the entire objection arises because the ARN author didn’t understand the difference between a flagellar TTSS and the non-flagella Ysc TTSS. Lets hope further comments on the book don’t make such basic mistakes.

Note also the discover of proton pump involvement was driven by the hypothesis that flagella non-flagella TTSS share a common ancestor. This is a fruitful hypothesis, and several discoveries have come form investigations based on it (see Blocker A, Komoriya K, Aizawa S. Type III secretion systems and bacterial flagella: insights into their function from structural similarities.Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3027-30). Compare this to the sterility of the Paleyist hypothesis, which has given us no insights to TTSS structure of function at all.