Literature

The iconic status of the bacterial flagellum as an irreducibly complex structure has stimulated interest among evolutionary biologists and an extensive literature. The latest is by Liu and Ochman who claim not only that the bacterial flagellum has originated in a stepwise manner from simple precursors, but also that "a single gene that underwent successive duplications and subsequent diversification during the early evolution of Bacteria."
ScienceNow has a report on this paper, with quotes drawn from the science community: "Complexity builds out of simplicity, and this is a well-documented argument for how that can happen," and "By testing the hypothesis of common ancestry of the flagellum in so many different species, the researchers clearly show these genes were derived from one another through gene duplication."
The major claim of the authors is to have traced the history of a set of core flagellum genes. "Our results show that flagellum originated very early, before the diversification of contemporary bacterial phyla, and evolved in a stepwise fashion through a series of gene duplication, loss and transfer events." They have adopted a methodology based on gene sequencing: "Comparisons of the complete genome sequences of flagellated bacteria revealed that the flagellum is based on an ancestral set of 24 core genes for which homologs are present in genomes of all bacterial phyla. The most striking finding from our analysis is that these core genes originated from one another through a series of duplications, an inference based on the fact that they still retain significant sequence homology."
So, have ID scientists got it wrong? The first point to be made is that the problem of actually forming the flagellum has not been addressed in the paper at all! There is no engagement with the challenge of irreducible complexity. Instead, this paper simply compares sequences of proteins, looking for similarities and differences in amino acid order. The analysis is concerned with sequence data, and the interpretation is dependent on the conceptual framework adopted by the researchers. In this case, the conceptual framework is Darwinism. The researchers have assumed that sequence similarity is related to ancestry, even though they cannot show that Darwinian processes produced the flagellum using their data set. This is a basic methodological point, and ID scholars have been making it for at least a decade. Consequently: 'Darwinism in - Darwinism out' sums up the findings.
There are many other detailed criticisms that can be made. Happily, a good start has been made here by Nick Matzke, who refers to "canine qualities" of the paper. By this he means that "there is nothing for it but to suck it up and declare this paper a dog." Of the claim that all flagellar proteins come from one gene, Matzke writes: "Frankly it is a flabbergasting thing to say, and I can't understand how it got published." Also: "There is just no way that the flagellum evolved by diversification of a single gene." However, Matzke misses the main methodological flaw in the research, which concerns their interpretation of sequence homologies in terms of descent with stepwise modification.
Jennifer Cutraro wrote that the study "not only answers an important question about the evolution of complex structures but also provides additional ammunition to counter arguments from evolution's foes." ID scientists are opposed to the 'just-so' stories and unwarranted extrapolations which are often found associated with evolutionary biology. By overstepping the mark so badly, perhaps this new paper will help people to understand the importance of paradigms in science and why critical issues are continually being overlooked.

Stepwise formation of the bacterial flagellar system
Renyi Liu and Howard Ochman
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0700266104, Published online before print April 16, 2007 [OPEN ACCESS ARTICLE]

Abstract: Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

See also:

Cutraro, J., A Complex Tail, Simply Told, ScienceNOW Daily News, 17 April 2007

Matzke, N., Flagellum evolution paper exhibits canine qualities, Panda's Thumb, April 16, 2007

Behe, M. DARWINISM GONE WILD: Neither sequence similarity nor common descent address a claim of Intelligent Design, Evolution News & Views, 19 April 2007.