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Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones’s Straw Tests of Irreducible Complexity for the Bacterial Flagellum (Part I)

(Part I, Version 1.0)

By Casey Luskin

Copyright © 2006 Casey Luskin. All Rights Reserved.

The entire article can be read here

In Kitzmiller v. Dover, Judge John E. Jones ruled harshly against the scientific validity of intelligent design. Judge Jones ruled that the irreducible complexity of the bacterial flagellum, as argued by intelligent design proponents during the trial, was refuted by the testimony of the plaintiffs’ expert biology witness, Dr. Kenneth Miller. Dr. Miller misconstrued design theorist Michael Behe’s definition of irreducible complexity by presenting and subsequently refuting only a straw-characterization of the argument. Accordingly, Miller claimed that irreducible complexity is refuted if a separate function can be found for any sub-system of an irreducibly complex system, outside of the entire irreducible complex system, suggesting the sub-system might have been co-opted into the final system through the evolutionary process of exaptation. However, Miller’s characterization ignores the fact that irreducible complexity is defined by testing the ability of the final system to evolve in a step-by-step fashion in which function may not exist at each step. Only by reverse-engineering a system to test for function at each transitional stage can one determine if a system has “reducible complexity” or “irreducible complexity.” The ability to find function for some sub-part, such as the injection function of the Type III Secretory System (which contains approximately ¼ of the genes of bacterial flagellum), does not negate the irreducible complexity of the final system. Moreover, Miller ignored the fact that any evolutionary explanation of a system must account for much more than simply the availability of the parts. In the final analysis, Miller’s testimony did not actually refute irreducible complexity, leaving readers of the Kitzmiller ruling with the unfortunate perception that the evolutionary origin of the bacterial flagellum has been solved.

Introduction: The Definition of Irreducible Complexity
Design theorist and biologist, Michael Behe, defines “irreducible complexity” by looking at a biological system to see if it can be produced in a step-by-step evolutionary fashion. Behe defines irreducible complexity in his book Darwin’s Black Box:

“In The Origin of Species Darwin stated:

‘If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.’

A system which meets Darwin’s criterion is one which exhibits irreducible complexity. By irreducible complexity I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.”

(Michael Behe, Darwin’s Black Box, pg. 39 (Free Press, 1996) (emphasis added).)

During the Kitzmiller trial, Michael Behe testified in favor of intelligent design by arguing that the bacterial flagellum represents one such biological structure which is irreducibly complex. The bacterial flagellum is a motor-driven propeller for bacterial swimming. (For a technical discussion of the various components of the bacterial flagellum, see David J. DeRosier, Spinning Tails, Current Opinion in Structural Biology, 5:187-193 (1995).) In the Kitzmiller trial, however, Judge Jones’ ruling disagreed with Behe’s claims and alleged that Behe ignored how evolution can effectively produce complex structures like the bacterial flagellum:

“Drs. Miller and Padian testified that Professor Behe’s concept of irreducible complexity depends on ignoring ways in which evolution is known to occur. Although Professor Behe is adamant in his definition of irreducible complexity when he says a precursor “missing a part is by definition nonfunctional,” what he obviously means is that it will not function in the same way the system functions when all the parts are present. For example in the case of the bacterial flagellum, removal of a part may prevent it from acting as a rotary motor. However, Professor Behe excludes, by definition, the possibility that a precursor to the bacterial flagellum functioned not as a rotary motor, but in some other way, for example as a secretory system.”

(Kitzmiller ruling, pg. 74. All references to Kitzmiller ruling from Judge Jones original ruling at

What follows is an assessment of the Judge’s findings with respect to the irreducible complexity of the bacterial flagellum.

Ignoring Exaptation?
In the Kitzmiller ruling, Judge Jones uses the term “exaptation” (also called “co-option,” or “preadaptation”) to describe how a part may initially serve a role in the cell, only to be later employed by an irreducibly complex system to perform some different function. The widely used college text Evolutionary Biology describes exaptation as follows:

“Stephen Jay Gould and Elisabeth Vrba (1982) suggest that if an adaptation is a feature evolved by natural selection for its current function, a different term is required for features that, like the hollow bones of birds or the sutures of a young mammal’s skull, did not evolve because of the use to which they are now put. They suggest that such characters that evolved for other functions, or for no function at all, but which have been co-opted for a new use be called exaptations.”

(Douglas J. Futuyma, Evolutionary Biology (3rd ed. 1998), pg. 355 (emphasis in original).)

Judge Jones alleges in his ruling that Michael Behe ignores exaptation as a way of accounting for the origin of biological complexity:

“By defining irreducible complexity in the way that he has, Professor Behe attempts to exclude the phenomenon of exaptation by definitional fiat, ignoring as he does so abundant evidence which refutes his argument.”

(Kitzmiller ruling, pg. 76.)

Judge Jones’s claim that Behe ignores “exaptation” was based upon the testimony of Dr. Kenneth R. Miller, an evolutionist and the plaintiff’s lead-expert biology witness during the trial. Dr. Miller testified that irreducible complexity is refuted if one can find any use for some sub-part of the total system:

“Dr. Behe’s prediction is that the parts of any irreducibly complex system should have no useful function. Therefore, we ought to be able to take the bacterial flagellum, for example, break its parts down, and discover that none of the parts are good for anything except when we’re all assembled in a flagellum.”

(Dr. Kenneth Miller Testimony, Day 1, PM Session, page 16.)

Miller’s characterization of irreducible complexity is grossly inaccurate. In particular, Miller applied his argument to real biological situations when he claimed that some sub-systems of the bacterial flagellum can perform a different role in some organisms. For example, Miller observed that the Type III Secretory System (TTSS), which uses approximately 1/4 of the genes involved in the flagellum, can be used by predatory bacteria to inject toxins into Eukaryotic cells. (See Scott A. Minnich and Stephen C. Meyer, Genetic Analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria, pg. 8, at According to Miller, the presence of the TTSS shows that the bacterial flagellum is not irreducibly complex. However, Miller’s Type III Secretory System argument contains three primary problems:

  • (A) Experts say the evidence suggests that the TTSS evolved from the flagellum, and not the other way around.
  • (B) Behe and other ID-proponents have long-acknowledged “exaptation” or “co-option” as an attempt to evolve biological complexity, and have observed many problems with “co-option” explanations.
  • (C) Miller has inaccurately characterized how one tests for irreducible complexity, thus refuting only a straw-version of Behe’s concept of irreducible complexity.

(A) Which came first: the TTSS or the Flagellum (or neither)?
Firstly, it is worth noting that a leading authority on bacterial systematics, Milton Saier, still believes that TTSS evolved FROM the flagellum, not the other way around, making Miller’s claim highly dubious. While Saier acknowledges some may disagree with him, he maintains that the TTSS evolved from the flagellum:

“Regarding the bacterial flagellum and TTSSs, we must consider three (and only three) possibilities. First, the TTSS came first; second, the Fla system came first; or third, both systems evolved from a common precursor. At present, too little information is available to distinguish between these possibilities with certainty. As is often true in evaluating evolutionary arguments, the investigator must rely on logical deduction and intuition. According to my own intuition and the arguments discussed above, I prefer pathway 2. What’s your opinion?”

(Milton Saier, “Evolution of bacterial type III protein secretion systems,” Trends in Microbiology, Vol 12 (3) pg. 113-15, March, 2004.)

(B) Behe’s Clear Responses to Evolutionary Appeals to Exaptation:
Secondly, refuting both Judge Jones’s claim that Behe “attempts to exclude the phenomenon of exaptation by definitional fiat” and also Miller’s statement that “Behe’s prediction is that the parts of any irreducibly complex system should have no useful function,” consider these passages from Darwin’s Black Box in which Behe presents the problems of exaptational arguments when discussing the evolution of the cilium:

“Because the cilium is irreducibly complex, no direct gradual route leads to its production. So an evolutionary story for the cilium must envision a circuitous route, perhaps adapting parts that were originally used for other purposes.” (Michael Behe, Darwin’s Black Box, pg. 65-66.)

“For example, suppose you wanted to make a mousetrap. In your garage you might have a piece of wood from an old Popsicle stick (for the platform), a spring from an old wind-up clock, a piece of metal (for the hammer) in the form of a crowbar, a darning needle for the holding bar, and a bottle cap that you fancy to use as a catch. But these pieces couldn’t form a functioning mousetrap without extensive modification, and while the modification was going on, they would be unable to work as a mousetrap. Their previous functions make them ill- suited for virtually any new role as part of a complex system. In the case of the cilium, there are analogous problems. The mutated protein that accidentally stuck to microtubules would block their function as “highways” of transport. A protein that indiscriminately bound microtubules together would disrupt the cell’s shape–just as a building’s shape would be disrupted by an erroneously placed cable that accidentally pulled together girders supporting the building. A linker that strengthened microtubule bundles for structural supports would tend to make them inflexible, unlike the flexible linker nexin. An unregulated motor protein, freshly binding to microtubules, would push apart micrutubules that should be close together. The incipient cilium would not be at the cell surface. If it were not at the cell surface, then internal beating could disrupt the cell; but even if it were at the cell surface, the number of motor proteins would probably not be enough to move the cilium. And even if the cilium moved, an awkward stroke would not necessarily move the cell. And if the cell did move, it would be an unregulated motion using energy and not corresponding to any need of the cell.” (Michael Behe, Darwin’s Black Box, pg. 66-67.)

Previously Behe had also explained evolution does not always necessarily proceed in such a direct route:

“Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin’s criterion of failure has been met skyrockets toward the maximum that science allows.”

(Michael Behe, Darwin’s Black Box, pg. 40.)

Thus contrary to both the Judge’s and Miller’s claims, Behe addresses the possibility that parts can be “co-opted” from other systems and does not shy away from this objection at all. (Indeed, even the basic and introductory pro-ID video entitled “Unlocking the Mystery of Life” deals with the co-option objection.) Behe explains that simply having all of the parts for a system is not enough: one must also have the proper assembly instructions for those parts. Thus, it should be clear that Miller has misrepresented Behe’s argument both by ignoring Behe’s refutation of the co-option theory and by falsely suggesting that Behe holds, “that the parts of any irreducibly complex system should have no useful function [outside of the total irreducibly complex system].”
…to be continued tomorrow. To read the full article, click here. Tomorrow, will be the main section of this article, explaining this issue:

(C) Miller has inaccurately characterized how one tests for irreducible complexity, thus refuting only a straw-version of Behe’s concept of irreducible complexity.

Casey Luskin

Associate Director and Senior Fellow, Center for Science and Culture
Casey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.



__editedflagellumJudge John E. JonesKen MillerKitzmiller v. Dover Area School District