Flagellated!

Kenneth R. Miller gave expert testimony at the "Dover trial" (Kitzmiller v. Dover Area School District) which concluded that "intelligent design" is not science, and that the teaching of it as if it was science would violate the U.S. "constitutional principle of separation of powers.

Part of his testimony, regarding the supposed "irreducible complexity" of the bacterial flagellum, he explains here. Other commentators are welcome to use this in reply whenever someone starts to try to flagellate them. ;)

From Kenneth R. Miller, Only a Theory: Evolution and the Battle for America's Soul, Chapter 3, Embracing Design, The Poison Pump.

//If the mousetrap is ID's favorite mechanical analogy, then the bacterial flagellum is clearly its favorite biological example of irreducible complexity. As we saw in chapter 2, the flagellum is one nifty machine—a reversible, high-torque rotary engine, powered by ion gradients and capable of propelling a bacterial cell with all the dispatch of a miniature outboard motor. One could, as creation- ists have been doing for decades, point to its mere complexity and profess profound skepticism that it could have been produced by random mutation and natural selection. In fashioning an argument against evolution, one might well pick nearly any other cellular structure and claim-correctly—that its origin has not yet been explained in detail by evolution. 

Such arguments are easy to make, of course, but the nature of scientific progress renders them far from compelling. The lack of a detailed current explanation for a structure, organ, or process does not mean that science will never come up with one. As an example, consider the question of how the left-right asymmetry that is part of our body plan arises in development, a question that was beyond explanation until the 1990s. Back then one might have argued that the body's left-right asymmetry could just as well be explained by the intervention of a designer as by an unknown molecular mechanism. Only a decade later that actual mechanism was identified, and any claim one might have made for the intervention of a designer would have to have been discarded. The same point can be made, of course, with respect to any structure or mechanism whose origins are not yet understood. 

The power of ID's story about the bacterial flagellum is that it seems to rise above an argument from ignorance in which we choose the explanation of "design" because we cannot imagine anything else. By asserting that it is a structure "in which the removal of an element would cause the whole system to cease functioning," the flagellum is presented as a molecular machine whose individual parts must have been specifically crafted to work as a unified assembly. The existence of such a multipart machine therefore provides genuine scientific proof of the actions of an intelligent designer.

In the case of the flagellum, irreducible complexity means that a minimum number of protein components, perhaps thirty, must be present to produce a viable biological function. These individual components should have no function until all thirty are put into place, at which point the flagellum spins into action. What this means, of course, is that evolution could not have fashioned those components a few at a time, since they do not have functions that could be favored by natural selection. As Behe wrote, "Natural selection can only choose among systems that are already working," and an irreducibly complex system does not work unless all of its parts are accounted for. The flagellum must therefore have been designed and crafted to function as a single, irreducible unit. Case closed? 

Maybe not. In the popular imagination bacteria are "germs"- tiny microscopic bugs that make us sick. Microbiologists smile at that generalization, knowing that most bacteria are perfectly benign, and many are beneficial. Nonetheless, there are indeed bacteria that produce diseases, ranging from the mildly unpleasant to the truly dangerous. Pathogenic, or disease-causing, bacteria threaten the organisms they infect in a variety of ways, one of which is to produce poisons and inject them directly into the cells of the body. Once inside, these toxins break down and destroy the host cells, producing illness, tissue damage, and sometimes even death. 

In order to carry out their diabolical work, these bacteria must not only synthesize powerful and deadly toxins, but must also produce an apparatus to inject them efficiently into the cells of their hosts. They do so by means of any number of specialized protein secretory systems. One, known as the type III secretory system (TTSS), enables bacteria to pump proteins directly into the cytoplasm of a host cell. The proteins transferred through the TTSS include a variety of truly dangerous molecules, among which are the "virulence factors" that are directly responsible for the pathogenic activity of some of the most deadly bacteria in existence. The TTSS is, in effect, a poison pump that bacteria use to kill other cells. 

At first glance this nasty little device would seem to have little to do with the flagellum. However, molecular studies of proteins in the TTSS have revealed a surprising fact-the proteins of the TTSS are remarkably similar to the proteins in the bottom portion of the bacterial flagellum. As figure 3.3 shows, these similarities extend to a cluster of closely associated proteins found in both of these molecular "machines," and on that basis, it's now clear that the flagellum itself can be regarded as a type III secretory system. In technical terms researchers have noted that the two systems "consist of homologous component proteins with common physico-chemical properties." In other words, about ten of the full complement of thirty or so proteins in the flagellum function perfectly well as the TTSS. In plain language, the TTSS is just like my spitball catapult a small part of a larger system that works just fine for an entirely different purpose. 

Figure 3.3: The bacterial flagellum and the type III secretory system. Electron microscope images (top) and computer-drawn representations (bottom) of the bacterial flagellum (left top and bottom) and the type III secretory system, or injectisome (right top and bottom). The structural similarities between the base of the flagellum and the base of the injectisome are striking. The reason for this is that the proteins of the injectisome are nearly identical to proteins in the flagellar base. The injectisome, even though it does not produce rotational movement like the flagellum, acts as an effective protein-injecting system. The fact that a subset of proteins from the flagellum is fully functional in the injectisome shows that the flagellum is not, as advocates of intelligent design claim, irreducibly complex. (Top left: Provided by Professor David DeRosier, Brandeis University. Top right: Provided by Professor Ariel Blocker, Oxford University. Bottom left and right: WGBH Television, from the NOVA science series.)

Now we can see the importance of the TTSS. It means that the flagellum is not irreducibly complex. 

Given that science is the search for knowledge, one would think that the design community would have welcomed all this new information about its favorite icon. That hasn't been the case. In fact, ID proponents have reacted with great fury at any suggestion that the bacterial flagellum has lost its value in making the case for design. Some have vainly argued that both the flagellum and the TTSS are irreducibly complex, which makes sense only if one redefines the word "irreducible." Others have pointed to speculation that the TTSS evolved from the flagellum as proving that the smaller system couldn't be the actual ancestor of the flagellum. That might be so, but other scientists have suggested quite the opposite, and in any case, it actually doesn't matter if today's TTSS is the ancestor of anything. It is absolutely correct to argue that the existence of the TTSS today doesn't answer the question of how the flagellum actually evolved. But that overlooks why the ID camp believed that irreducible complexity was so critical in the first place: They thought it proved that the flagellum couldn't have evolved. It doesn't. 

It's quite one thing to point to the flagellum and challenge evolution by saying, "Evolve this!" But intelligent design has always claimed something more, something that sounds testable and scientific. It claims to have discovered a truth (irreducible complexity) that makes biochemical machines like the flagellum unevolvable, even in principle. However, once one discovers a useful, selectable function in part of such a machine, that claim falls apart, and that's exactly what has happened to the flagellum as an argument against evolution. 

New research suggests, in fact, that nearly every one of the proteins in the flagellum shows significant homology to proteins that perform important functions elsewhere in the cell. In addition to the ten proteins found in the TTSS, another group of proteins in the flagellum belongs to the "axial protein" family, several are related to another secretion machine known as the type II apparatus, two are a close match for ion transport proteins, and a half dozen are involved in signal transduction pathways. In short, the flagellum isn't the custom-made, designed-from-scratch collection of closely matched elements that ID likes to claim. It's much more like a collection of borrowed, copied, and jerry-rigged parts that have been cobbled together from the spare-parts bin of the cell. In short, it's exactly the sort of thing that you'd expect from evolution. 

DISSECTING RUBE 

A scientific idea usually doesn't rise or fall on one example, so the demise of the flagellum doesn't mean that there might not be other examples of irreducible complexity. The blood-clotting cascade, that intricate pathway of enzymes and cofactors, looks like a good place on which to fall back, so let's go there next. Every protein in the pathway is essential to the clotting process. As Michael Behe has written, the entire system has to be in place for clotting to work properly, and in the absence of any of the components, blood does not clot and the system fails. That should make it impossible even to imagine how the system could have arisen by evolution. To reinforce the case for design, we might draw upon the enormous amount of whole-genome analysis that has been done using high- efficiency DNA sequences techniques. What we should find, as ID theorists have made clear, is that the complete vertebrate blood- clotting pathway is present in the genome of each and every organism we analyze. 

It's a bit of a surprise, therefore, to discover that ID advocates have not been vigorously combing the databases of vertebrate genome sequences to reinforce their argument. After all, what better way to establish the irreducible complexity of this system as a genuine scientific principle than to show that their bold predictions about the need for all of the components to be present are absolutely true? Unless, of course, those predictions are wrong—which now clearly seems to be the case. //

Miller continues with discussing the blood-clotting cascade.

See also https://www.millerandlevine.com/km/evol/design2/article.html

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