To explain ID, *don't* look up the homologies

William Dembski has just blogged about a short comment I made this morning on The Thumb answering someone’s question about whether or not a detailed evolutionary model for the bacterial flagellum would deserve a Nobel Prize. In that comment, I pointed to this long web article I wrote on the evolution of the bacterial flagellum (which is already badly in need of an update), but I said that, no, such a model would clearly not deserve a Nobel, because it would be entirely routine and conventional – simply the application of the current paradigm (modern evolutionary theory) to fill in one more little gap in our knowledge of evolutionary history. Although creationists don’t realize it, discoveries showing how complex system evolved come out all the time in the scientific literature. (A number of examples are linked from my comment here.)

Dembski’s post in reply is entitled “To Explain the Flagellum � Just Look Up All the Homologies.” There are numerous dubious assertions in Dembski’s short post that would take all day to write up, but I just want to focus on one limited point for the moment. Will the ID advocates admit that they made a mistake in asserting that, except for the 10 proteins of the Type III secretion system, they other 30-40 parts of the flagellum were “unique”?

Dembski first mischaracterizes the evolutionary argument for a complex system like the flagellum as merely looking up related (homologous) proteins.

This is wrong: Taking my flagellum evolution essay as an example, in addition to reviewing the homologies (something no IDist has ever done – they regularly show their ignorance of the literature on flagellum homologies, see below), it also includes a review of relevant biological analogies, a quantitative analysis of passive and active bacterial dispersal, a step-by-step analysis of function at each stage and the transitions between the stages, and a review of the literature on the types of molecular steps that would be involved in the transitions – origin of new genes with new functions, origin of new protein-protein binding sites, origin of multiple-proteins-required systems, etc. By showing that all of these micro-processes have been observed to occur in the lab and/or in the wild, and showing that the origin of the flagellum can be broken down into a series of such micro-processes, and showing that function is continuously maintained throughout, I showed that a reasonably detailed model for the evolutionary origin of the bacterial flagellum was perfectly plausible.

I invite readers to check out Dembski’s hilarious 2003 reply to my essay – he mostly does a page-count analysis, and then chokes out the latest last-ditch, if-all-else-fails ID argument, “Not…detailed…enough!” (This is often soon followed by, “And we’re not going to give you any detail at all about our ID hypothesis, either!”)

Dembski also concludes today’s post with the emergency backup IC argument:

The problem is not a matter of identifying similar parts, but of coordinating them into novel, functional wholes. No literature search of preexisting components will resolve this problem.

Dembski, “To Explain the Flagellum � Just Look Up All the Homologies

This is yet another instance of IDists making an unacknowledged retreat (here is another recent example, from Behe) from the original irreducible complexity argument.

IDists originally claimed that IC systems that were missing parts would have no function, and therefore partial systems would be unselectable by natural selection, and therefore gradual evolution couldn�t produce such systems. This is precisely why Dembski himself, just back in 2003, highlighted what he thought was a great argument against Ken Miller’s essay on evolution of the bacterial flagellum:

It follows that the TTSS does not explain the evolution of the flagellum (despite the handwaving of Aizawa 2001). Nor, for that matter, does the bacterial flagellum explain in any meaningful sense the evolution of the TTSS. The TTSS is after all much simpler than the flagellum. The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique.

Dembski (2003), “The Flagellum Unspun

Dembski is not the only one to make this argument. In 2004, DI Fellows Scott Minnich and Stephen C. Meyer wrote in an allegedly peer-reviewed article (see my analysis) for a conference proceedings volume,

Natural selection can preserve the motor once it has been assembled, but it cannot detect anything to preserve until the motor has been assembled and performs a function. If there is no function, there is nothing to select. Given that the flagellum requires ca. 50 genes to function, how did these arise?


Additionally, the other thirty proteins in the flagellar motor (that are not present in the TTSS) are unique to the motor and are not found in any other living system. From whence, then, were these protein parts co-opted?

Minnich & Meyer

Both of these essays are late enough in the history of ID that they have included backup arguments just in case those protein parts are found (many of the homologies are documented in the big flagellum essay, and although I’m pretty well convinced that most of the IDists never read the essay in any detail, perhaps the general idea reached Minnich and Meyer). Regardless of the emergency backup argument, both Dembski and Minnich and Meyer thought that “look at all those unique parts” was a pretty spiffy argument.

Behe (1997) shows an example of the original IC argument, in bold form, and shorn of emergency backup arguments:

Without any one of a number of parts, the flagellum does not merely work less efficiently; it does not work at all. Like a mousetrap it is irreducibly complex and therefore cannot have arisen gradually.

Behe (1997)

It is clear that IDists have tacitly given up on this simple version of the IC argument for the intelligent design of the bacterial flagellum. They have not, however, ever admitted that they were wrong about the original argument, “flagellum = multiple-required-parts = subset of parts can’t function = no selection = can’t evolve.” Questions like, “do subsets of flagellar parts have other functions, or not?” are the kinds of simple factual questions that are easily checked, and IDist errors on these questions are common, widely copied, and easily explained. On the flagellum, the ID people should have found the homologies out for themselves years ago, before the ID critics got around to doing it for them, forcing the ID advocates to drag the goalposts further back. This kind of basic, endlessly copied mistake, easily explained to anyone willing to pay close attention, is why ID has no chance in science, with well-informed science teachers, or in a real courtroom (the Kansas Kangaroo Court was, of course, something entirely different).

To conclude, I would just like to get the answer to one simple question from Dembski. Dr. Dembski: do you now concede that your 2003 statement, “The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique” was incorrect, and that, in fact, systems homologous to flagellum subsystems (in addition to the T3SS) are known which do have selectable function?