Thanks to those people who have commented - positive and negative - it's great to have some thought-provoking debate stirred up following what I have written.
Tim posted a link to this paper, by Nick Matzke, relating to a proposed evolutionary pathway for the bacterial flagellum. I read this - it took some time, it runs to 58 pages (including lots of references), and my biochemistry isn't brilliantly up-to-speed - but I got there. My initial thoughts are that William Dembski has given an appropriate response to the paper. He highlights the fact that Matzke has in fact failed to achieve what he set out to achieve - a testable, verifiable model for flagellar evolution - but he has gone some way further than has been achieved by previous writers.
However, there was one particular aspect I wanted to comment on, and this was the issue of co-option. The idea of co-option is that a biochemical system (one or more proteins), used in one context, finds a use in another context following a minor modification. It is widely assumed to be a "Get out of jail free" for darwinist evolution - a means of avoiding the improbability barriers of coming up with new proteins from random sequences of DNA. For example, Matzke writes:
The hypothesis that the entirety of a primitive F1F0-ATP synthetase may have been coopted in toto into a primitive gated pore (proto-FliF and proto-FlhA/B) is certainly provocative; it would explain at a stroke the origin of most of the type III export apparatus and provide a phylogenetically basal precursor to the flagellum even though clearly basal type III secretion systems remain undiscovered.My comment is: how improbable is this sort of event? Because it is certainly a specified event - in this case, it is necessary for an existing biochemical system (F1F0-ATP synthetase) to be co-opted to an entirely new role (proto-FliF and proto-FlhA/B). Of course, it isn't necessary that a specific protein is suitable for doing this, but it is necessary that a protein is available to do this. So there has to be a protein somewhere in the cell that will provide the primitive functionality that is required, that is the right shape to "fit" where it is needed, and that is expressed at the right time.
These probabilities could be estimated - what proportion of proteins are the right shape to fit on the gated pore? What proportion of proteins in the organism would provide the desired functionality? Is it possible to estimate the proportion of proteins that have ATP-synthetase activity that would also have the shape and size appropriate to provide this functionality. It would be possible to compare these probabilities with the number of opportunities available to bacteria, to determine whether this co-option event is feasible.
The probability is significant. Dawkins pointed out in (I think) "The Blind Watchmaker" that you couldn't have too much improbability, and Dembski's work on the Universal Probability Boundary effectively extended this. You can't rely over and over again on highly improbable events as an engine of evolution. What I am getting at, I guess, is that if co-option events turn out to be pretty improbable, then rather than being a handy tool that would allow evolution to progress, they would actually turn out to be evidence of prior design - design would be a more reasonable explanation of them than "lucky old evolution".
There are proponents of "front-loading" over at Telic Thoughts. They argue that one of the mechanisms by which evolution* proceeds is by information included in organisms at the start of the evolutionary process. If co-option is an improbable event (as it seems quite likely to be) then it would be the sort of event that would be likely to mark out front-loading, rather than a purely darwinian process. If it turns out that proto-F1F0-ATP synthetase is incredibly well specified for its role in the proto-bacterial flagellum, that wouldn't be evidence for darwinism at all.
Whilst I'm writing, and since my last post was on abiogenesis, I wanted to take the opportunity to draw readers' attention to the fact that (doubtless influenced by my post!!) David Berlinski has written an essay for Commentary on abiogenesis - which gives some idea of the problems associated with this field that is apparently completely unrelated to evolution.
* Please note the distinction here between evolution and darwinism. There are many proponents of ID who are happy with the idea of evolution but who don't accept darwinism.