(Part II, Version 1.0)
By Casey Luskin
Copyright © 2006 Casey Luskin. All Rights Reserved.
The entire article can be read here
...Yesterday, I posted Part I of this response. To reiterate, there are three primary problems with Judge Jones's ruling that Ken Miller refuted Michael Behe's arguments that the bacterial flagellum is irreducible complex:
(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.
Yesterday I posted sections addressing parts (A) and (B). Today I will continue with the response, expanding on Part (C):
(C) Miller’s Incorrect Characterization of Irreducible Complexity
To repeat Miller’s assertion, he testified that irreducible complexity is refuted if one sub-system can perform some other function in the cell:
“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.)
The question becomes, “how is Behe’s argument different from that of Ken Miller?” Behe actually formulates irreducible complexity as a test of building an entire system. IC operates on a collection of parts, not each individual part. Even if a separate function could be found for a sub-system, the latter would not refute the irreducible complexity and the unevolvability of the system as a whole. To repeat Behe’s definition, Behe writes:
“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).)
Thus, according to Darwin, evolution requires that a system, or its sub-parts, be functional along each small step of their evolution to the final system. Yet one could find a sub-part that could be useful outside of the final system, and yet the total system would still face many points along an "evolutionary pathway" where it could not remain functional along "numerous, successive, slight modifications" that would be necessary for its gradual evolution. (With regards to the flagellum at least 2/3 of the parts are not known to be shared with any other structure therefore might not be even a sub-part of another system at all.) (*** Note: this footnoted statement has been changed in the official version to reflect newly learned information. See below for details.)
Thus, Miller mischaracterizes Behe's argument as one which focuses on the non-functionality of sub-parts, when in fact, Behe’s argument actually focuses on the ability of the entire system to assemble, even if sub-parts can have functions outside of the final system.
A Car Example for Illustration
To understand how Miller's test fails to accurately apply to Behe's formulation of irreducible complexity, consider the example of a car engine and a bolt. Car engines use various kinds of bolts, and a bolt could be seen as a small “sub-part” or “sub-system” of a car engine. Under Miller's logic, if a vital bolt in my car's engine might also to perform some other function—perhaps as a lugnut--then it follows that my car's whole engine system is not irreducibly complex. Such an argument is obviously fallacious.
In assessing whether an engine is irreducibly complex, one must focus on the function of the engine itself, not on the possible function of some sub-part that may operate elsewhere. Of course a bolt out of my engine could serve some other purpose in my car. However this observation does not explain how many complex parts such as pistons, cylinders, the camshaft, valves, the crankshaft, sparkplugs, the distributor cap, and wiring came together in the appropriate configuration to make a functional car engine. Even if all of these parts could perform some other function in the car (which is doubtful), how were these parts assembled properly to construct a functional engine? The answer requires intelligent design.
Behe asserts that a system is irreducibly complex if the system stops functioning upon the removal of one part. This is the appropriate test of Darwin’s theory because it asks the question, “Is there a minimal level of complexity which is required for functionality of this system?” Clearly my car’s engine has a core set of parts necessary in order for it to function. The ability of an engine bolt to also serve as a lugnut does not refute the irreducibly complex arrangement of parts necessary to make the final engine-system functional. Behe never suggests that subsystems cannot play some other role in the cell—in fact he suggests the opposite. Rather, Behe simply argues that evolution requires that the total system must be built up in a slight, step-by-step fashion, where each step is functional.
Miller has mischaracterized irreducible complexity, and his test is a straw-test for refuting irreducible complexity. The test for irreducible complexity does not ask “can one small part of the macrosystem be used to do something else?” as Miller claims, but rather asks “can the system as a whole be built in a step-by-step fashion which does not require any ‘non-slight’ modifications to gain the final target function?” Any non-slight modifications of complexity required to go from functional sub-part(s), operating outside-of-the-final system, to the entire final functional system, represent the irreducible complexity of a system.
Even if Miller could find that every part of the flagellum existed somewhere else in bacteria (which he cannot—he only accounts for the basal body, which constitutes about 1/4 of the total flagellar proteins), Miller is no where close to providing a plausible account of the evolution of the flagellum until he has explained how all the flagellar parts might have come together to produce a functional bacterial flagellum. Only then that Miller claim that the flagellum is not irreducibly complex.
Other Authorities Agree with Behe
William Dembski captures the essence of the problem with Miller's definition and treatment of IC in Dembski’s expert rebuttal in which Dembski writes:
“[F]inding a subsystem of a functional system that performs some other function is hardly an argument for the original system evolving from that other system. One might just as well say that because the motor of a motorcycle can be used as a blender, therefore the [blender] motor evolved into the motorcycle. Perhaps, but not without intelligent design. Indeed, multipart, tightly integrated functional systems almost invariably contain multipart subsystems that serve some different function. At best the TTSS [Type-III Secretory System] represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn’t constitute a solution to the evolution of the bacterial flagellum. What’s needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we’ve discovered the Hawaiian Islands. Evolutionary biology needs to do better than that.” (William A. Dembski, Rebuttal to Reports by Opposing Expert Witnesses, at
http://www.designinference.com/documents/2005.09.Expert_Rebuttal_Dembski.pdf.)
Though Miller has accounted for the origin of only a fraction of the flagellar parts, Scott A. Minnich and Stephen C. Meyer also explain how mere availability of parts is insufficient to explain the evolution of a system:
“[E]ven if all the protein parts were somehow available to make a flagellar motor during the evolution of life, the parts would need to be assembled in the correct temporal sequence similar to the way an automobile is assembled in factory. Yet, to choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions. Arguably, this system is itself irreducibly complex. In any case, the co-option argument tacitly presupposes the need for the very thing it seeks to explain—a functionally interdependent system of proteins.” (Scott A. Minnich and Stephen C. Meyer, Genetic Analysis of coordinate flagellar and type III regulatory circuits in pathogenic
bacteria, pg. 8, at http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=389.)
Similarly, philosopher Angus Menuge lays out a number of obstacles which must be overcome by "co-option" or "exaptation" explanations, none of which were addressed by Miller during the trial. Menuge writes:
“For a working flagellum to be built by exaptation, the five following conditions would all have to be met:
“C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.
“C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
“C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.
“C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
“C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.”
(Angus Menuge, Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004).)
William Dembski takes a similar approach to that of Menuge. Dembski effectively combines some of Menuge’s criteria in order to develop a means of calculating the probability of constructing an irreducibly complex object. In calculating the probability of a “discrete combinatorial object” one must take into account the probability of originating the parts, the probability of localizing the parts all in once place, and the probability of configuring the parts together:
Table 1. Comparison of Dembski and Menuge’s required explanatory components for any exaptation-based account of evolution (Table based upon the descriptions in William A. Dembski, No Free Lunch: Why Specified Complexity Cannot be Purchased Without Intelligence, pg. 291 (Rowman & Littlefield, 2002)):
| Dembski’s Factor | Description | Analogue in Menuge’s Criteria |
| Porig | Probability of originating the building blocks for that objects. | C1 |
| Plocal | Probability of locating the building blocks in one place once they are given. | C2, C3 |
| Pconfig | Probability of configuring the building blocks once they are given and in one place. | C4, C5 |
It is clear that Miller has found that the probability for originating about 1/4 of the flagellar proteins might be “1/1” if the TTSS (or perhaps a similar structure) existed prior to the flagellum. However he has not accounted for the origin of the remaining the flagellar proteins, nor has he addressed Plocal or Pconfig in his evolutionary scenario. In light of Menuge's and Dembski’s criteria, it seems fair to demand answers from Miller to the following questions:
- What function was performed by the paddle, rotor, or motor outside of the flagellum? (At trial, Miller explained the function for the basal body of the flagellum via the TTSS, but left the most complex and vital motorized portions of the flagellum unexplained.)
- How did the parts become synchronized in the flagellum? (At trial, Miller never discussed this.)
- How did the parts become localized within the flagellum at the same construction site? (At trial, Miller never addressed this issue.)
- How did the parts become structurally coordinated so as to interact when assembled to produce the flagellar swimming function? (Again, Miller also never addressed this issue at trial.)
Thus Miller never answered any of these important questions at the trial. Rather, he presented a straw version of testing irreducible complexity whereby he convinced the Judge in a fashion which did not come remotely close to accounting for how the flagellum might have actually evolved.
A Final Analogy: The Arch
Miller’s treatment of the bacterial flagellum did not refute its irreducibly complexity, as Miller did not address questions about how the final flagellar systems might arise. The existence of other functions for the TTSS does not imply that the flagellar system would not still require large leaps in complexity (or to use Darwin's words, non-slight modifications) in order to ultimately achieve a functional flagellum. To use a final analogy to show the deficiency of Miller’s explanation, consider an attempt to build an irreducibly complex arch (Figure A):

Figure A: An arch is irreducibly complex: if one removes a piece, the remaining pieces will fall down. (Note: For the purpose of illustration, I am temporarily ignoring the common objection that an irreducibly complex arch might be made using natural erosional processes. I am aware of no appropriate "scaffolding" analogy within the biological realm, but it is not the present purpose of this discussion to rebut that objection.)
According to Miller, if we can find a function for some sub-piece, then a system is not irreducibly complex. Now, let’s now break this arch into sub-pieces:

Figure B: Here an arch has been broken up into subpieces. Similarly, Miller has apparently found a flagellar sub-piece (the TTSS) which can perform some other function. The TTSS comprises no more than 1/4 of the total flagellar parts. Similarly, in this arch, there is one large sub-section (labeled “S”) which comprises approximately 1/4 of the total arch. Sub-section “S” can have a function outside of the arch (i.e. here, it can stand on its own). However, this exposes the fallacy of Miller’s test: the ability of sub-section “S” to stand on its own does not therefore dictate that the arch is not irreducibly complex. Thus if one were to removes the top piece (t), the arch crumbles, even if sub-section “S” can still remain standing (Figure C):

Fig