See Challenge to Uncommon Descenters from ID Facebook page: “Hundreds of labs show, it is claimed, that the bacterial flagellum is not irreducibly complex.”
I responded to that paper six years ago, soon after it came out, at Uncommon Descent:
What I didn’t do then at the blog is to say that I had submitted my response as a letter to the Editor of Microbe, which he turned down. My correspondence with him is below.
In “Evolution of the Bacterial Flagellum” (July 2007) Wong et al seek to counter arguments of intelligent design proponents such as myself that the flagellum did not evolve by random mutation and natural selection. Unfortunately, their otherwise-fine review misunderstands design reasoning and so fails to engage that issue. The critical passage from Wong et al is the first paragraph:
Proponents of the intelligent design (ID) explanation for how organisms developed claim that the bacterial flagellum (BF) is irreducibly complex. They argue that this structure is so complicated that it could not have emerged through random selection but had to be designed by an intelligent entity. One part of this claim is that each flagellar component is used solely for the purpose of making a flagellum that, in turn, is used only for motility. Further, each flagellar protein is assumed to have appeared independently of the other component proteins.
Although the first two sentences are correct, the last two sentences are quite wrong. (The authors cite no references for these latter claims.) It is no part of the design argument that each component of an irreducibly complex structure must be used solely for that purpose, nor that each part must arise independently. In my 1996 book Darwin’s Black Box, which brought the concept of irreducible complexity to wide public attention, I pointed out the fact that, for example, proteins of the blood clotting cascade share sequence homology with each other and with other serine proteases, and the fact that ciliary proteins such as tubulin are involved in other tasks in the cell. Yet I explained that neither sequence homology nor multiple functions showed how integrated systems containing many parts could be put together by small random steps. Unfortunately, Wong et al spend their efforts addressing their own erroneous assertions. They fail to address the only pertinent question, the question of whether random, unintelligent processes — even when filtered by natural selection — could plausibly build a structure such as the flagellum.
To address the adequacy of random processes plus selection would require rigorous experiments or calculations showing that the intricate, functional structures are not too improbable given the evolutionary resources available. Recent work bears negatively on this difficult question. In long term laboratory evolution experiments over tens of thousands of generations (Lenski, R.E. 2004. Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. Plant Breeding Reviews 24:225-265), cultures of E. coli were repeatedly seen to lose the ability to make ribose and maltose, and to repair their DNA. Some mutations shut down expression of their flagellar genes, apparently to conserve energy. No selected mutations were observed which could plausibly be argued to be the incipient stages of some new, complex functional system. Similar kinds of results are seen in other well-studied evolutionary systems. For example, in response to strong pressure from the malarial parasite, the human genome has suffered a handful of positively-selected-yet-degradative mutations (Carter, R. and Mendis, K.N. 2002. Evolutionary and historical aspects of the burden of malaria. Clin. Microbiol. Rev. 15:564-594), including ones that render nonfunctional the genes for glucose-6-phosphate dehydrogenase, the alpha and beta chains of hemoglobin, band 3 protein, and others. Again, no selected mutations were observed which could plausibly be argued to be the incipient stages of some new, complex functional system.
To a skeptic such as myself, this does not look like the sort of process which could build complex molecular machinery. Those who would argue persuasively against intelligent design must address this basic issue. – Michael J. Behe, Department of Biological Sciences, Lehigh University
Thank you for your recent letter on Dr. Saier’s article. We are declining to publish the letter as it does not address the main points of the article. The article and Microbe’s decision to publish it were not intended to address the broad question of the validity of evolution. ASM has published its Statement on the Scientific Basis for Evolution which summarizes the views of the Society on the topic:
Knowledge of the microbial world is essential to understanding the evolution of life on Earth. The characteristics of microorganisms—small size, rapid reproduction, mobility, and facility in exchanging genetic information—allow them to adapt rapidly to environmental influences. In microbiology, the validity of evolutionary principles is supported by  readily demonstrated mutation, recombination and selection, which are the fundamental mechanisms of evolution;  comparisons based on genomic data that support a common ancestry of life; and  observable rates of genetic change and the extent of genomic diversity which indicate that divergence has occurred over a very long scale of geologic time, and testify to the great antiquity of life on Earth. Thus, microorganisms illustrate evolution in action, and microbiologists have been able to make use of the microbes’ evolutionary capacity in the development of life-improving and life-saving innovations in medicine, agriculture, and for the environment. By contrast, proposed alternatives to evolution, such as intelligent design and other forms of creationism, are not scientific, in part because they fail to provide a framework for useful, testable predictions. The use of the supposed “irreducible complexity” of the bacterial flagellum as an argument to endow nonscientific concepts with what appears to be legitimacy, is spurious and not based on fact. Evolution is not mere conjecture, but a conclusive discovery supported by a coherent body of integrated evidence. Overwhelmingly, the scientific community, regardless of religious belief, accepts evolution as central to an understanding of life and the life sciences. A fundamental aspect of the practice of science is to separate one’s personal beliefs from the pursuit of understanding of the natural world. It is important that society and future generations recognize the legitimacy of testable, verified, fact-based learning about the origins and diversity of life. – Patrick Lacey, production Manager, Microbe (formerly ASM News)
Dear Dr. Lacey,
Thanks very much for your email. However, your statement that my letter “does not address the main points of the article” is quite difficult to understand. The clearly stated purpose of the Wong et al article is to refute intelligent design reasoning. My letter shows that the authors misunderstand design reasoning, so that the supposed refutation addresses a straw man. How can that not be “address[ing] the main points”?
If you will read my letter with attention, Dr. Lacey, you will notice that I did not question “the validity of evolution”. In fact, although many people are confused on this point, the concept of intelligent design has no proper quarrel with the validity of evolution. Intelligent design is quite compatible with descent with modification. It simply argues that some facets of life resulted from intelligent planning or direction, rather than relying exclusively on random events, as Darwinian theory proposes. My discussion in the letter of the results of random mutations in experiments on E. coli, and in human/malaria evolutionary warfare underscores this point.
Dr. Lacey, most publications consider it responsible journalism to publish letters by well-known advocates of views attacked in articles. The purpose, of course, is to avoid misleading readers of the journal by unknowingly misstating or caricaturing a position. In order that your readers will not form a mistaken view of what the intelligent design argument actually states, I ask you to reconsider the decision not to publish my letter. – Best wishes, Mike Behe
Of course the letter was never published! Why ever should it be? Lacey is just another feeder at the government teat of Darwinism. He gets a salary from helping suppress growing doubt.
Just think how many tenured Darwin mediocrities batten off your taxes, knowing that, like him, they need fear no challenge from facts. They also teach at the high schools your taxes pay for.