Lance - The process of Natural Selection states only mutations which are advantageous for survival are preserved.

Lance - However the flagellar motor does not function unless all parts are present...

If we assume for the moment that both statements are true (I'm skeptical), that still wouldn't logically rule out natural selection. Notice that your 2nd sentence doesn't quite match up with the first (motor function v.s. advantageous for survival). You would need to at least repair those premises to come to the conclusion I think you want to come to.

@Talyyn: Sickle cell anemia is inherited in an autosomal recessive pattern. People who have it are immune to malaria. Just one of those things I have picked up over the years.

@Talyyn

"There is a population in Africa which is at risk from a recessive disease BUT it enables them to be resistant from a disease I forgot what the name was.

The point is that there are advantageous, neutral and "bad" mutations but even the "badness" on one can be offset by external factors"

You might be referring to sickle cell anemia. Sickle cell anemia protects one against malaria.

Even though sickle cell anemia can be a debilitating condition, it is better, from an evolutionary standpoint, than malaria since it assures survival until reproductive age.

@lance
First you have to prove there is an intelligent designer. So you are going to need some objective evidence that can be tested by anyone, and get the same results.

Oh, someone has brought up the bacterial flagellum. Whoopee. Time for this ...

THE BACTERIAL FLAGELLUM REVISITED

The bacterial flagellum was erected, wholly wrongly it has to be added, by Michael Behe, as the supposed "poster child" for "irreducible complexity". Unfortunately for Behe, his attempt to erect "irreducible complexity" as a purported "problem" for evolution merely demonstrated that he hadn't done his homework. First of all, the concept wasn't his to begin with - it was, in fact, alighted upon way back in 1918 by an evolutionary biologist, and was erected not as a "problem" for evolutionary biology, but as a natural outcome of evolutionary processes. The biologist in question was Hermann Joseph Müller, and the paper in which he first expounded upon the concept was this:

Genetic Variability, Twin Hybrids and Constant Hybrids in a Case of Balanced Lethal Factors by Hermann Joseph Müller, Genetics, 3(5): 422-499 (1918)

The requisite quote can be found starting near the bottom of page 464 of that paper, and moving on to page 465, where it reads as follows:

[quote="Hermann Joseph Müller, 1918"]Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect upon which it produced upon the 'reaction system' that had been brought into being by the many previously formed factors in cooperation; thus, a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent upon the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery.[/quote]

So, Müller alighted upon so-called "irreducibly complex" systems in 1918. He and other evolutionary biologists placed this on a rigorous footing by the 1930s, before Behe was even born. Behe's canard has been KNOWN to be a canard for over six decades. The mechanism by which so-called "irreducibly complex" structures arise is known as the Müllerian Two Step, which is described succinctly as follows:

[1] Add a component;

[2] Make it necessary.

Müller and other contemporaries placed this on a rigorous footing by the 1930s. Therefore Behe's "irreducible complexity" nonsense was known to be a canard by actual biologists the moment he aired it in public.

Of course, Behe's failure to perform the requisite literature search, and realise that this problem had, in essence, been solved back in 1918, merely set a precedent that he was to revisit during the Dover Trial, where he asserted that evolutionary biology not only had no answer to the "problems" purportedly posed by the vertebrate blood clotting cascade, but that evolutionary biology never would find any answers. His rashness in uttering this was sharply exposed, when the cross examining counsel presented Behe with no less than fifty-eight peer reviewed scientific papers, and nine university textbooks, containing the very material Behe had claimed would never exist.

Likewise, his arguments with respect to the bacterial flagellum revealed that he had not bothered performing even the most perfunctory of literature searches. Not least because scientists were publishing papers containing research unravelling the secrets of the bacterial flagellum several years before it was erected as a purported "poster child" for "intelligent design". However, it appears that the situation is now even worse for the "cdesign proponentsists" with regard to the bacterial flagellum.

Those nice people over at TalkRational pointed me to a very interesting blog. Namely the blog of Mark Pallen, who was co-author with Nick Matzke of at least one peer reviewed paper in Nature on the bacterial flagellum (and indeed probably wrote more - I just happen to be aware of the one I have saved to my hard drive). That paper is the following one:

From The Origin Of Species To The Origin Of Bacterial Flagella by Mark J. Pallen & Nicholas J. Matzke, Nature Reviews Microbiology, 4(10): 784-790 (October 2006).

I shall return to this paper shortly, but first, a little preamble is needed.

For those unfamiliar with the background, Nick Matzke was the author of an interesting article, namely this one, which hypothesised that the various proteins that are found in the bacterial flagellum would be found to be homologous with other proteins belonging to other metabolic systems, and that as a consequence, the bacterial flagellum would eventually be found to be the result of co-opting existing, earlier systems and re-using them for another purpose - a classic evolutionary process. Needless to say, a lot of noise was emitted by the ID brigade to the effect that Matzke's ideas were "speculation", and the rest of it, but, the point here is that Matzke made testable predictions in his article, and in doing so provided evolutionary biologists with real substance that they could pursue in the laboratory. The following quote from the abstract of Matzke's original paper is apposite:

A new model is proposed based on two major arguments. First, analysis of dispersal at low Reynolds numbers indicates that even very crude motility can be beneficial for large bacteria. Second, homologies between flagellar and nonflagellar proteins suggest ancestral systems with functions other than motility. The model consists of six major stages: export apparatus, secretion system, adhesion system, pilus, undirected motility, and taxis-enabled motility. The selectability of each stage is documented using analogies with present-day systems. Conclusions include: (1) There is a strong possibility, previously unrecognized, of further homologies between the type III export apparatus and F1F0-ATP synthetase. (2) Much of the flagellum’s complexity evolved after crude motility was in place, via internal gene duplications and subfunctionalization. (3) Only one major system-level change of function, and four minor shifts of function, need be invoked to explain the origin of the flagellum; this involves five subsystem-level cooption events. (4) The transition between each stage is bridgeable by the evolution of a single new binding site, coupling two pre-existing subsystems, followed by coevolutionary optimization of components. Therefore, like the eye contemplated by Darwin, careful analysis shows that there are no major obstacles to gradual evolution of the flagellum.

Now, note that specific predictions were made with respect to the homologies involved, namely that homologies would be found between flagellar proteins and those of the Type 3 Secretory System, plus an enzyme called F1F0-ATP synthetase. I'll leave the latter enzyme aside for a moment, but return to it because this one turns out to play an important role. Stay tuned for the fun revelations!

Now, first of all, the paper from Nature Reviews Microbiology I cited above by Matzke & Pallen itself dispenses wholesale with the idea of the bacterial flagellum being "irreducibly complex", because, lo and behold, there are bacteria with flagella that are missing numerous components. From that paper, I copy the following details with respect to the presence or absence of specific flagellar proteins in various bacteria possessing flagella:

FlgA (P ring) - Absent from Gram-Positive bacteria
FlgBCFG (Rod) - universal
FlgD (Hook) - universal
FlgE (Hook) - universal
FlgH (L Ring) - Absent from Gram-Positive bacteria
FlgI (P Ring) - Absent from Gram-Positive bacteria
FlgJ (Rod) - FlgJ Rod N-terminal domain absent from some systems
FlgK (Hook-Filament Junction) - universal
FlgL (Hook-Filament Junction) - universal
FlgM (Cytoplasm & Exterior) - Absent from Caulobacter
FlgN (Cytoplasm) - Undetectable in some systems
FlhA (T3SS apparatus) - universal
FlhB (T3SS apparatus) - universal
FlhDC (Cytoplasm) - Absent from many systems
FlhE (Unknown) - Mutant retains full motility
FliA (Cytoplasm) - Absent from Caulobacter
FliB (Cytoplasm) - Absent from Escherichia coli
FliC (Filament) - universal
FliD (Filament) - Absent from Caulobacter
FliE (Rod/Basal Body) - universal
FliF (T3SS apparatus) - universal
FliG (Peripheral) - universal
FliH (T3SS apparatus) - Mutant retains some motility
FliI (T3SS apparatus) - universal
FliJ (Cytoplasm) - Undetectable in some systems
FliK (Hook/Basal Body) - universal
FliL (Basal body) - Mutant retains full motility
FliM (T3SS apparatus) - universal
FliN (T3SS apparatus) - universal
FliO (T3SS apparatus) - Undetectable in some systems
FliP (T3SS apparatus) - universal
FliQ (T3SS apparatus) - universal
FliR (T3SS apparatus) - universal
FliS (Cytoplasm) - Absent from Caulobacter
FliT (Cytoplasm) - Absent from many systems
FliZ (Cytoplasm) - Absent from many systems
MotA (Inner membrane) - universal
MotB (Inner membrane) - universal

So, the mere fact that there are in existence bacteria with missing proteins from the above list whose flagella still function rather makes a mockery of the "irreducible complexity" assertion to begin with. But, this is only part of the story. The same paper continues with the following:

Many paths to motility

Although the evolution by random mutation and natural selection of something as complex as a contemporary bacterial flagellum might, in retrospect, seem highly improbable, it is important to appreciate that probabilities should be assessed by looking forward not back [2]. For example, from studies on protein design it is clear that creating proteins from scratch that, like flagellin, self-assemble into filaments is not very difficult [39,40]. Furthermore, it is clear that there are many other filamentous surface structures in bacteria that show no apparent evolutionary relationship to bacterial flagella [41,42]. In other words, there are plenty of potential starting points for the evolution of a molecular propeller. Evolution of something like the flagellar filament is therefore far less surprising than it might at first seem. In fact, microorganisms have adopted other routes to motility besides the bacterial flagellum [43]. Most strikingly, although archaeal flagella superficially resemble bacterial flagella, in that they too are rotary structures driven by a proton gradient, they are fundamentally distinct from their bacterial counterparts in terms of protein composition and assembly.

Intermediate forms

What about intermediate forms between bacterial flagella and other biological entities? Darwin encountered a similar argument about gaps in the fossil record, and in response he pointed out how improbable fossilization was, so that little of any extinct biosphere could ever be expected to appear in the fossil record [14]. Although fossils are of no use in reconstructing flagellar evolution, similar arguments might be made at the molecular level. Despite a decade of bacterial genome sequencing, we have scarcely begun to sample the molecular diversity of the biosphere. Yet even with the scant coverage of genome sequence data to date, several curiosities have already been revealed. For example, there is growing evidence that flagellin and the flagellar filament are homologous to the NF T3SS protein EspA and the EspA filament, respectively [35,44–48]. The EspA filament therefore provides a model for how the ancestral flagellar filament might have functioned for purposes other than locomotion (adhesion or targeted protein secretion). Furthermore, the EspA protein from E. coli initially seemed to be one of a kind. However, thanks to genome sequencing, related proteins have been identified in several bacteria occupying diverse niches, including: S. typhimurium, Edwardsiella ictaluri, Shewanella baltica, Chromobacterium violaceum, Yersinia frederiksenii, Yersinia bercovieri and Sodalis glossinidius. In addition, proteins that resemble flagellar components but that are encoded in the genomes of bacteria that do not engage in flagellar motility have also been identified. The first example of these potential ‘missing links’ came from the chlamydias [49]. More recently, flagellar-related genes have been detected in the genome of the soil bacterium Myxococcus xanthus, which uses gliding rather than flagellar motility [35]. It seems likely that other examples of potential evolutionary intermediaries will be found as we sequence an increasing proportion of the biosphere.

The paper continues with:

Towards a plausible evolutionary model

From the above discussions of sequence homologies and modularity, it is clear that designing an evolutionary model to account for the origin of the ancestral flagellum requires no great conceptual leap. Instead, one can envisage the ur-flagellum arising from mergers between several modular subsystems: a secretion system built from proteins accreted around an ancient ATPase, a filament built from variants of two initial proteins, a motor built from an ion channel and a chemotaxis apparatus built from pre-existing regulatory domains (FIG. 1). As we have seen, each of these function in a modular fashion and share ancestry with simpler systems — thereby answering the question ‘what use is half a flagellum?’ Furthermore, it is not hard to envisage how an ancestral crude and inefficient flagellum, if it conferred any motility at all, could function as the starting material for natural selection to fashion today’s slicker flagellar apparatus.

However, one could still question how, from such bricolage, natural selection could lock on to an evolutionary trajectory leading to an organelle of motility in the first place, when none of the components alone confer the organism with a selective advantage relevant to motility. The key missing concept here is that of exaptation, in which the function currently performed by a biological system is different from the function performed while the adaptation evolved under earlier pressures of natural selection [50]. For example, a bird’s feathers might have originally arisen in the context of selection for, say, heat control, and only later have been used to assist with flight [51,52]. Under this argument, a number of slight but decisive functional shifts occurred in the evolution of the flagellum, the most recent of which was probably a shift from an organelle of adhesion or targeted secretion, such as the EspA filament, to a curved structure capable of generating a propulsive force.

Now, as a slight tangential diversion, which along the way provides yet more evidence for evolutionary hypotheses, one avenue of attack being considered with respect to the development of the bacterial flagellum is the reconstruction of earlier, more ancient versions of the proteins responsible for the construction of this structure. Precedents already exist with respect to the reconstruction of ancient genes, and the following four papers are examples thereof:

Crystal Structure Of An Ancient Protein: Evolution By Conformational Epistasis by Eric A. Ortlund, Jamie T. Bridgham, Matthew R. Redinbo and Joseph W. Thornton, Science, 317: 1544-1548 (14 September 2007)

Resurrecting Ancient Genes: Experimental Analysis Of Extinct Molecules by Joseph W. Thornton, Nature Reviews: Genetics, 5: 366-375 (5 May 2004)

Resurrection Of DNA Function In Vivo From An Extinct Genome by Andrew J. Pask, Richard R. Behringer and Marilyn B. Renfree, PLoS One, 3(5): e2240 (online version, May 2008)

The Past As The Key To The Present: Resurrection Of Ancient Proteins From Eosinophils by Steven A. Benner, Proc. Natl. Acad. Sci. USA., 99(8): 4760-4761 (16 April 2002)

From the paper by Pask et al above, we have:

There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine), obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.

So scientists are already resurrecting ancient proteins and testing their functionality in model organisms. Indeed, one of the results in the scientific literature comes courtesy of this paper:

Resurrecting The Ancestral Steroid Receptor: Ancient Origin Of Oestrogen Signalling by J.W. Thornton, E. Need and D. Crews, Science, 301: 1714-1717 (2003)

in which the scientists determined that the modern receptors for steroid hormones in modern organisms are traceable to an ancestral receptor dating back 600 million years, and reconstructed the ancestral steroid receptor in the laboratory to determine that it worked.

So, given that precedents already exist for the successful reconstruction of ancient proteins and the genes coding for them, this avenue of attack is likely to prove highly instructive with respect to the bacterial flagellum. Indeed, Pallen & Matzke make this very observation in their paper:

But obviously, one cannot model millions of years of evolution in a few weeks or months. So how might such studies be conducted? One option might be to look back in time. It is feasible to use phylogenetic analyses to reconstruct plausible ancestral sequences of modern-day proteins, and then synthesize and investigate these ancestral proteins. Proof of principle for this approach has already been demonstrated on several NF proteins [69–75]. Similar studies could recreate plausible ancestors for various flagellar components (for example, the common ancestor of flagellins and HAP3 proteins). These proteins could then be reproduced in the laboratory in order to examine their properties (for example, how well they self-assemble into filaments and what those filaments look like). An alternative, more radical, option would be to model flagellar evolution prospectively, for example, by creating random or minimally constrained libraries and then iteratively selecting proteins that assemble into ever more sophisticated artificial analogues of the flagellar filament. Another experimental option might be to investigate the environmental conditions that favour or disfavour bacterial motility. The fundamental physics involved (diffusion due to Brownian motion) is mathematically tractable, and has already been used to predict, for example, that powered motility is useless in very small bacteria [76,77].

However, let us move on to the more recent developments.

Now, back in 2006, Pallen & Matzke listed some known homologies, and once again, I reproduce their results from the table in the paper:

FlgA (P ring) - CpaB
FlgBCFG (Rod) - FlgBCEFGK
FlgD (Hook) - none specified
FlgE (Hook) - FlgBCEFGK
FlgH (L Ring) - none yet known
FlgI (P Ring) - none yet known
FlgJ (Rod) - none yet known
FlgK (Hook-Filament Junction) - FlgBCEFGK
FlgL (Hook-Filament Junction) - FliC
FlgM (Cytoplasm & Exterior) - none yet known
FlgN (Cytoplasm) - none yet known
FlhA (T3SS apparatus) - LcrD/YscV
FlhB (T3SS apparatus) - YscU
FlhDC (Cytoplasm) - Other activators
FlhE (Unknown) - none specified
FliA (Cytoplasm) - RpoD, RpoH, RpoS
FliB (Cytoplasm) - none specified
FliC (Filament) - FlgL, EspA
FliD (Filament) - none yet known
FliE (Rod/Basal Body) - none yet known
FliF (T3SS apparatus) - YscJ
FliG (Peripheral) - MgtE
FliH (T3SS apparatus) - YscL, AtpFH
FliI (T3SS apparatus) - YscN, AtpD, Rho
FliJ (Cytoplasm) - YscO
FliK (Hook/Basal Body) - YscI
FliL (Basal body) - none yet known
FliM (T3SS apparatus) - FliN, YscQ
FliN (T3SS apparatus) - FliM, YscQ
FliO (T3SS apparatus) - none
FliP (T3SS apparatus) - YscR
FliQ (T3SS apparatus) - YscS
FliR (T3SS apparatus) - YscT
FliS (Cytoplasm) - none yet known
FliT (Cytoplasm) - none yet known
FliZ (Cytoplasm) - none yet known
MotA (Inner membrane) - ExbB, TolQ
MotB (Inner membrane) - ExbD, TolR, OmpA

Now, as Pallen states in his blog entry as linked above, out of this list of proteins, only two were listed as being both essential to all bacterial flagella AND possessing no known homologues in 2006. Those proteins were FliE and FlgD. From the 2006 update of Matzke's original 2003 paper, we read:

Many of the homologous and/or inessential proteins found in Table 1 of Pallen and Matzke 2006 were cited in the 2003 paper, but the 2006 table is an authoritative update and supercedes what is said here. The important overall point, as discussed in my blog post, is that of the 42 proteins in Table 1 of Pallen and Matzke, only two proteins, FliE and FlgD, are both essential and have no identified homologous proteins. This is substantially more impressive than the situation in 2003, and means that the evidence for the evolutionary origin of the flagellum by standard gene duplication and cooption processes is even stronger than in 2003. Important specific updates include: a homolog of FlgA has been confirmed (along the lines that I suggested in 2003); FliG has no homolog in NF-T3SS or the Exb/Tol systems, rather it may be homologous to the magnesium transporter MgtE; and the flagellar filament protein FliC (and its sister FlgL) is probably homologous to EspA and other pilus proteins found in NF-T3SS. I still suspect that all of the axial proteins (including FliE and FlgD) are homologous to each other and therefore to pilus proteins in NF-T3SS, but only the confirmed homologies are reported in Pallen and Matzke 2006.

At least, this was the situation back in 2006. However, science moves on!

First, take a look at this site, which is the site devoted to ATP synthase. Now, one of the homologies that Matzke originally hypothesised was that at least one of the flagellar proteins would prove to be homologous to proteins in the ATP synthase group, in particular the awkwardly named F1F0-ATP synthetase. Now it turns out that ATP synthases are themselves complex entities, and indeed F1-ATPase rotates on an axis as it performs its synthesis! However, as this paper:

Axle-Less F1-ATPase Rotates In The Correct Direction by Shou Furuike, Mohammad Delawar Hossain, Yasushi Maki, Kengo Adachi, Toshiharu Suzuki, Ayako Kohori, Hiroyasu Itoh, Masasuke Yoshida and Kazuhiko Kinosita, Jr., Science, 319: 955-958 (No. 5865, 15 February 2008)

reveals very succinctly, dismantling this structure so that it no longer has an axle to rotate about does not stop it from functioning! Here's the abstract:

F1–adenosine triphosphatase (ATPase) is an ATP-driven rotary molecular motor in which the central γ subunit rotates inside a cylinder made of three α and three β subunits alternately arranged. The rotor shaft, an antiparallel α-helical coiled coil of the amino and carboxyl termini of the γ subunit, deeply penetrates the central cavity of the stator cylinder. We truncated the shaft step by step until the remaining rotor head would be outside the cavity and simply sat on the concave entrance of the stator orifice. All truncation mutants rotated in the correct direction, implying torque generation, although the average rotary speeds were low and short mutants exhibited moments of irregular motion. Neither a fixed pivot nor a rigid axle was needed for rotation of F1-ATPase.

Another blow to "irreducible complexity" (Hermann Müller would doubtless have smiled wryly over this!), but this isn't all. Returning to Pallen's blog, we find this:

Since the early 1990s, it has been known, from sequence comparisons, that the flagellar ATPase (FliI) is homologous to the alpha and beta subunits of the F-type ATPase, a transmembrane protein complex (see figure) found in bacteria, mitochondria and chloroplasts (see http://www.atpsynthase.info).

In 2003, Nick Matzke (then at the NCSE and so a couple of years later science adviser to the plaintiffs in the Dover trial) wrote an essay summarising plausible evolutionary scenarios for the origin of the bacterial flagellum. He noted a couple of previous suggestions that the proto-flagellum might have originated from the F-type ATPase. Crucially, he predicted that additional homologies would be found between components of the F-type ATPase and the flagellar protein export apparatus, for example between the b subunit of the ATPase and FliH and between the delta subunit and FliJ.

In 2006, I confirmed one of Nick's hunches through homology searches, showing that part of FliH was homologous to the b subunit. However, things turned out slightly different from Nick's predictions in that FliH is actual of a fusion of domains homologous to the b subunit and the delta subunit.

Last year Namba's group published the structure of FliI and confirmed the striking homology with the F-type ATPase enzymatic subunits. At that stage in the game, it had become clear that the ATPase was a universal component not just of flagellar export systems but also of non-flagellar type III secretion systems. Also, if it was also clear that if one knocked out the gene for FliI, one abolished flagellar biosynthesis. Thus, just about everyone in the field accepted that FliI was an essential component of the flagellar apparatus and that it energised secretion of proteins through the protein export system. In other words, if there were anything to the idea, put forward by Behe and others in the ID movement, that the flagellum showed "irreducible complexity", even experts might have accepted that FliI was one of the "irreducible" components!!

BUT earlier this year, Minamino and Namba (and independently a team headed by Kelly Hughes in the US) overturned all our assumptions by showing that it was perfectly possible to make flagella without FliI--what you needed to do was knock out FliH at the same time. Somehow or other FliH, which usually interacts with FliI, gums up the export apparatus in the absence of FliI. So, bang goes another pillar of support for the ID argument! In fact, it appears that flagellar protein export is powered not primarily by the ATPase but by the proton-motive force.

So, the FliI protein appeared on the face of it to be essential, because knocking out the gene for FliI synthesis destroyed flagellar biosynthesis. But, and here's the part that really throws the spanner into "irreducible complexity" as espoused by Behe, if you knock out the gene coding for FliI, but in addition knock out the gene for FliH, flagellar biosynthesis returns! This rather buggers up "irreducible complexity" in a spectacular manner.

Yet even this is not the whole story. Believe it or not, there is more! Returning to Pallen's blog, we read:

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!

So, now we have deep and broad homologies between the flagellum and the F-type ATPase, just as Nick predicted. This provides another nail in the coffin of the idea that flagellum was intelligently designed. If the flagellum were the product of intelligent design, particularly by an omniscient deity, the designer could have custom-built it from scratch, so it need not resemble anything else in nature. By contrast, the processes of evolution tends to cobble together and tweak already existing components (something Francois Jacob called bricolage)--and slowly but steadily it is become clear that the flagellum has been built this way.

Incidentally, the paper covering the homology between FliI and the alpha and beta subunits of the F-type ATPase is this paper:

Salmonella typhimurium Mutants Defective In Flagellar Filament Regrowth And Sequence Similarity Of FliI to F[sub]0[/sub]F[sub]1[/sub], Vacuolar, And Archaebacterial ATPase Subunits by Alfried P. Vogler, Michio Homma, Vera M. Irikura and Robert M. McNab, Journal of Bacteriology, 173(11): 3564-3572 (June 1991) [Full paper downloadable from here]

so this homology had actually been known even before Behe made his assertions about "irreducible complexity", something he would have known if he had bothered to perform a basic literature search. After all, he has institutional access, whereas I don't currently, yet I was able to find this paper once pointed in the right direction. This paper also covers the knocking out of the gene for FliI and the effect on flagellar biosynthesis.

More pertinently, the following paper:

Evolutionary Links Between FliH/YscL-Like Proteins From Bacterial Type III Secretion Systems And Second-Stalk Components Of The F[sub]0[/sub]F[sub]1[/sub] And Vacuolar ATPases by Mark J. Pallen, Christopher M. Bailey and Scott A. Beatson, Protein Science, 15: 935-941 (2006) [Full paper downloadable from here]

is the one containing the confirmation by Pallen of one of Matzke's predictions as cited above. Another homology was confirmed courtesy of this paper:

Structural Similarity Between The Flagellar Type III ATPase FliI And F[sub]1[/sub]-ATPase Subunits by Katsumi Imada, Tohru Minamino, Aiko Tahara and Keiichi Namba, Proceedings of the National Academy of Sciences of the USA, 104(2): 485-490 [Full paper downloadable from here]

This paper:

Distinct Roles Of The FliI ATPase And Proton Motive Force In Bacterial Flagellar Protein Export by Tohru Minamino and Keiichi Namba, Nature, 451: 485-489 (24th January 2008) [Full paper downloadable from here]

is the paper that covers the knocking out of FliH and FliI resulting in restoration of flagellar biosynthesis.

So, now the only two proteins remaining to find homologies for are FliE and FlgD, and you can bet that this is being worked upon as I type this.

So, another massive nail in the coffin for ID is hammered home, and evolution wins yet again. I'll raise a glass of claret to that. :)