The Flagellum Unspun
The Collapse of "Irreducible Complexity"

Kenneth R. Miller
Providence, Rhode Island 02912 USA


Almost from the moment The Origin of Species was published in 1859, the opponents of evolution have fought a long, losing battle against their Darwinian foes. Today, like a prizefighter in the late rounds losing badly on points, they've placed their hopes in one big punch – a single claim that might smash through the overwhelming weight of scientific evidence to bring Darwin to the canvas once and for all. Their name for this virtual roundhouse right is "intelligent design."

In the last several years, the intelligent design movement has attempted to move against science education standards in several American states, most famously in Kansas and Ohio (Holden 1999; Gura 2002).

[Winning the battle at Boards of Education or within any arena relative to the question of which is the preferred philosophy Creationism or Evolution is not an indicator of which is the right or the wrong on any point or overall. As a matter of fact untruth and evil has and will largely win these battles until the end of the this age and of the 7 years of  worldwide violent tribulation when the Intelligent Designer will arrive to fix it all. The greatest discovery that mankind has revealed about himself throughout all of his history is that even in the ‘good’ that he does there is inevitably contained evil]

The principal claim made by adherents of the [creationist] view is that they can detect the presence of "intelligent design" in complex biological systems.

[Certainly this applies to the evolutionist point of view as well, for you all have implied and have outwardly stated that the universe and especially the earth have such an awesome inexplicably complex order about them - far beyond the capacity of man to understand it and create anything within the universe that even compares to the simplest of lifeforms. So I am surprised that you refuse to consider the plausibility / possibility of an Intelligent Agency. You have become attached to the belief system of evolution without scientific proof that there actually has been evolution over great periods of time that creates one species after another, (remember: observability of an actual evolvement of one complete species into another, repeatability of that precise event again and again and FALSIFIABILITY CONTROL of that event over and over again). Your rhetoric is NOT scientific, rather demeaning and ridiculing and shameful. Can a true scientist actually rule out such due to personal preference? Man has not even discovered an accurate progression of a lifeform and how it might have scientifically evolved into another without forcing assumptions to be true in order to prove those assumptions. After so many years have gone by and still there have been no proved out intermediary lifeforms discovered especially one that completely rules out a Creator of far greater intelligence than man can conceive of – Who created all lifeforms even those of similar design without having to have them evolve but including a marvelous capacity within each species of variation within that species Whose motivations are largely not well perceived, albeit they are largely made clear in the one reliable book for all men to understand]

As evidence, they cite a number of specific examples, including the vertebrate blood clotting cascade, the eukaryotic cilium, and most notably, the eubacterial flagellum (Behe 1996a, Behe 2002).

Of all these examples, the flagellum has been presented so often as a counter-example to evolution that it might well be considered the "poster child" of the modern anti-evolution movement. Variations of its image (Figure 1) now appear on web pages of anti-evolution groups like the Discovery Institute, and on the covers of "intelligent design" books such as William Dembski's No Free Lunch (Dembski 2002a). To anti-evolutionists, the high status of the flagellum reflects the supposed fact that it could not possibly have been produced by an evolutionary pathway.

[The elephant in the room is the persistent refusal to consider the plausibility of an Intelligent Creator Designer which is largely ruled out for no good reason – just personal preference. The universe is after all awesomely complex hence ‘intelligent'! ]

Figure 1: The eubacterial flagellum. The flagellum is an ion-powered rotary motor, anchored in the membranes surrounding the bacterial cell. This schematic diagram highlights the assembly process of the bacterial flagellar filament and the cap-filament complex. OM, outer membrane; PG, peptidoglycan layer; IM, cytoplasmic membrane (From Yonekura et al 2000).

There is, to be sure, nothing new or novel in an anti-evolutionist pointing to a complex or intricate natural structure, and professing skepticism that it could have been produced by the "random" processes of mutation and natural selection.

Nonetheless, the "argument from personal incredulity," as such sentiment has been appropriately described, has been a weapon of little value in the anti-evolution movement. Anyone can state at any time that they cannot imagine how evolutionary mechanisms might have produced a certain species, organ, structure. Such statements, obviously, are personal – and they say more about the limitations of those who make them than they do about the limitations of Darwinian mechanisms.

[Could I not say the same about you? Let's see. Nonetheless, the “ ‘argument from personal incredulity,” as such sentiment has been appropriately described, has been a weapon of little value in the anti-creation movement. Anyone can state at any time that they cannot imagine an existence of an Intelligent Designer Who might have produced a certain species, organ, structure. Such statements, obviously, are personal - and they say more about the limitations of those who make them than they do about whether or not an actual Intelligent Designer does exist?]

The hallmark of the intelligent design movement, however, is that it purports to rise above the level of personal skepticism. It claims to have found a reason why evolution could not have produced a structure like the bacterial flagellum, a reason based on sound, solid scientific evidence.

Why does the intelligent design movement regard the flagellum as unevolvable?  Because it is said to possesses a quality known as "irreducible complexity." Irreducibly complex structures, we are told, could not have been produced by evolution, or, for that matter, by any natural process. They do exist, however, and therefore they must have been produced by something. That something could only be an outside intelligent agency operating beyond the laws of nature – an intelligent designer. That, simply stated, is the core of the new argument from design, and the intellectual basis of the intelligent design movement.

[Ignoring the investigation of the probability of the eubacterial flagellum evolving vs the estimated age of the universe vs an intelligent designer’s existence is simply not scientific nor credible. Only because the majority of mankind has been brain washed, (the reason for the worldwide flood in the first place), can man dare to say there is no Creator / Intelligent Designer because we have voted Him out of existence – mankind who can't even find one missing link after all of this time]

The great irony of the flagellum's increasing acceptance as an icon of anti-evolution is that fact that research had demolished its status as an example of irreducible complexity almost at the very moment it was first proclaimed. The purpose of this article is to explore the arguments by which the flagellum's notoriety has been achieved, and to review the research developments that have now undermined they very foundations of those arguments.

The Argument's Origins

The flagellum owes its status principally to Darwin's Black Box (Behe 1996a) a book by Michael Behe that employed it in a carefully-crafted anti-evolution argument. Building upon William Paley's well-known "argument from design," Behe sought to bring the argument two centuries forward into the realm of biochemistry. Like Paley, Behe appealed to his readers to appreciate the intricate complexity of living organisms as evidence for the work of a designer. Unlike Paley, however, he raised the argument to a new level, claiming to have discovered a scientific principle that could be used to prove that certain structures could not have been produced by evolution. That principle goes by the name of "irreducible complexity."

An irreducibly complex structure is defined as ". . . 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." (Behe 1996a, 39) Why would such systems present difficulties for Darwinism? Because they could not possibly have been produced by the process of evolution:

"An irreducibly complex system cannot be produced directly by numerous, successive, slight modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. .... Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on." (Behe 1996b)

The phrase "numerous, successive, slight modifications" is not accidental. The very same words were used by Charles Darwin in The Origin of Species in describing the conditions that had to be met for his theory to be true. As Darwin wrote, if one could find an organ or structure that could not have been formed by "numerous, successive, slight modifications," his "theory would absolutely break down" (Darwin 1859, 191). To anti-evolutionists, the bacterial flagellum is now regarded as exactly such a case – an "irreducibly complex system" which "cannot be produced directly by numerous successive, slight modifications." A system that could not have evolved – a desperation punch that just might win the fight in the final round – a tool with which the theory of evolution can be brought down.

The Logic of Irreducible Complexity

[So you do admit that there are innumerable complex structures whose detailed evolutionary origins are not known. Have you even considered that they may not have evolved at all – or is that ruled out because of your personal belief system that is not based on science? Are you stubborn about only accepting what you believe and not considering anything else? If another belief system better fits the case why not consider its plausibility. Instead you simply ignore the facts? What about other theories? Ever hear of the God particle? String theory, multi-universes?]

Therefore, in fashioning an argument against evolution one might pick nearly any cellular structure, the ribosome for example, and claim – correctly – that its origin has not 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.

[True if you are objective. Are you? It seems that since you are largely NOT following the scientific method and are operating on your preferences -how many of your ‘theories have been proved wrong over the years and replaced with ones that do no better without proving out a missing link intermediate species?]

As an example, one might consider the question of how left-right asymmetry arises in vertebrate development, a question that was beyond explanation until the 1990s (Belmonte 1999). In 1990 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, the actual molecular mechanism was identified (Stern 2002), and any claim one might have made for the intervention of a designer would have been discarded. The same point can be made, of course, regarding any structure or mechanism whose origins are not yet understood.

[This does not rule out an Intelligent Designer, does it? Were you there to observe, repeat and falsify? Who created the molecular mechanism, since you did not stipulate that it evolved? Oh, that's right, you haven't a clue how it did evolve – if it did at all. Besides that, just because you believe something doesn't make that belief true. The earth was never flat despite so many who believed that it was. What you do believe  and maybe even operate on you may find out was never true. Only future circumstances will tell? Can you think of the things you believed in as a child that did not prove to be true. Is there a supernatural Santa in your past? ]

The utility of the bacterial flagellum is that it seems to rise above this "argument from ignorance." By asserting that it is a structure "in which the removal of an element would cause the whole system to cease functioning" (Behe 2002), 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.

[Have you tested this scientifically, or are you limiting yourself to what you believe? I did not read of any evidence that you took away some of the elements from an active bacteria to see if it would still work. The idea of going to another species with a similar design of flagellum but which does not have the precise components of the first species and comparing them is bad science. Each species has its own design, albeit some species might have a similar design but NOT THE SAME DESIGN. Hence comparison is not legitimate]

In the case of the flagellum, the assertion of irreducible complexity means that a minimum number of protein components, perhaps 30, are required to produce a working biological function. By the logic of irreducible complexity, these individual components should have no function until all 30 are put into place, at which point the function of motility appears.

[Within the same species. Did you do this test?????]

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.

[Within the same species. Did you do this test?????]

 As Behe wrote: " . . . natural selection can only choose among systems that are already working" (Behe 2002), and an irreducibly complex system does not work unless all of its parts are in place. The flagellum is irreducibly complex, and therefore, it must have been designed. Case closed.

[For that particular species is obviously implied]

Answering the Argument

The assertion that cellular machines are irreducibly complex, and therefore provide proof of design, has not gone unnoticed by the scientific community. A number of detailed rebuttals have appeared in the literature, and many have pointed out the poor reasoning of recasting the classic argument from design in the modern language of biochemistry (Coyne 1996; Miller 1996; Depew 1998; Thornhill and Ussery 2000). I have suggested elsewhere that the scientific literature contains counter-examples to any assertion that evolution cannot explain biochemical complexity (Miller 1999, 147), and other workers have addressed the issue of how evolutionary mechanisms allow biological systems to increase in information content (Schneider 2000; Adami, Ofria, and Collier 2000).

The most powerful rebuttals to the flagellum story, however, have not come from direct attempts to answer the critics of evolution. Rather, they have emerged from the steady progress of scientific work on the genes and proteins associated with the flagellum and other cellular structures. Such studies have now established that the entire premise by which this molecular machine has been advanced as an argument against evolution is wrong –the bacterial flagellum is not irreducibly complex.

[So far within the same species, i.e., within this particular bacterial flagellum it appears to work properly only when all the observable parts are in place. That is after all the implication. We are not comparing apples and oranges or even MacIntosh Apples with Green apples, are we?]

As we will see, the flagellum – the supreme example of the power of this new "science of design" – has failed its most basic scientific test. Remember the claim that "any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional?"

[Within the same species. Am I repeating myself here?? Take a human being with a ‘complete’ effectively working blood clotting system and compare it with another human being, (notice same species), who has hemophilia which indicates a defective blood clotting system, i.e., all the components are not in the proper functioning capacity. Now you have a problem with irreducible complexity because not all of the components are functioning properly. This might be attributable to a bad stage of evolution or to the decision of an Intelligent Designer Who because of His judgment upon sinful man. On the other hand, you cannot compare the blood clotting system of a human being with that of a dolphin as you have done in this article and thereby declare something conclusive because the species Dolphin is quite different from the species humankind sufficient to make the comparison inadequate to conclude that evolution is in view or an Intelligent Designer is in view.]

As the evidence has shown, nature is filled with examples of "precursors" to the flagellum that are indeed "missing a part," and yet are fully-functional.

[Not proved because a system in one species might be different from a system in another and are thereby NOT interchangeable. Have you actually tested your hypothesis by taking out a part and replacing it with a less complex part that appears to be of similar design less a few components and then observing if the species still performs as it did? Answer: No.]

Functional enough, in some cases, to pose a serious threat to human life.


The point is that within that particular species that you have observed with the more complex system of locomotion you have NOT observed to have the less complex system from another species that provides a toxic delivery system instead – an entirely different function! So you do not know if the bacteria would actually function properly or not, having not actually tested it in real life. You’re just guessing. Also the toxic bacteria might not function with the more complex system of locomotion either. You’re just guessing again. Perhaps the missing component observed in the first bacteria was required for some function in the first species that was not observed functioning via your investigation hence viewed by you as not ‘required’ in the second species that did not have that part. You’re just guessing. You did not stipulate that your ‘scientific’ investigation addressed these all important issues. In any case getting all those parts together in that first species in the manner in which they were observed presents a problem to do that over time and yet have that species function the way it was observed functioning, i.e., it nevertheless is irreducibly complex and demands an Intelligent Designer relative to at least that one species, but the scope of your investigation may not be applicable to all species. But if there is an Intelligent Designer it stands to reason that being that intelligent He is Creator of all species in a short, convenient and amazing period of time]

The Type -III Secretory Apparatus

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 – even essential – to human life. 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 this diabolical work, bacteria must not only produce the protein toxins that bring about the demise of their hosts, but they must efficiently inject them across the cell membranes and into the cells of their hosts. They do this by means of any number of specialized protein secretory systems. One, known as the type III secretory system (TTSS), allows gram negative bacteria to translocate proteins directly into the cytoplasm of a host cell (Heuck 1998). The proteins transferred through the TTSS include a variety of truly dangerous molecules, some of which are known as "virulence factors," and are directly responsible for the pathogenic activity of some of the most deadly bacteria in existence (BŁttner and Bonas 2002; Heuck 1998).

At first glance, the existence of the TTSS, a nasty little device that allows bacteria to inject these toxins through the cell membranes of its unsuspecting hosts, 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 directly homologous to the proteins in the basal portion of the bacterial flagellum. As figure 2 (Heuck 1998) shows, these homologies extend to a cluster of closely-associated proteins found in both of these molecular "machines." On the basis of these homologies, McNab (McNab 1999) has argued that the flagellum itself should be regarded as a type III secretory system. Extending such studies with a detailed comparison of the proteins associated with both systems, Aizawa has seconded this suggestion, noting that the two systems "consist of homologous component proteins with common physico-chemical properties" (Aizawa 2001, 163). It is now clear, therefore, that a smaller subset of the full complement of proteins in the flagellum makes up the functional transmembrane portion of the TTSS.

Figure 2: There are extensive homologies between type III secretory proteins and proteins involved in export in the basal region of the bacterial flagellum. These homologies demonstrate that the bacterial flagellum is not "irreducibly complex."

[They do NOT demonstrate that the bacterial flagellum is not “irreducibly complex” because there are two species involved in your investigation wherein you are presupposing one system in one species is capable of operating within a second species replacing a more complex system and function perfectly well within that species for the function that the more complex system was performing; or you offer a different function which would obfuscate the first function which was locomotion which would cause the rapid demise of the species! And it appears you have not tested this hypothesis. Just because you might observe a simpler transmission in a functioning Ford with components that are the same as in a Toyota which has a more complex transmission with more components; this does not then lead to the conclusion that the simpler transmission would work as well in the Toyota unless you properly test this hypothesis. The Ford might be similar in design relative to a number of components identical to those in the Toyota, but you do not have sufficient evidence that the simpler transmission in the Ford could perform the same or another kind of function in the more complex Toyota, such as a carburetor. This point was never thoroughly tested. Besides that, ‘another function” would leave the Toyota without a transmission leading to its rapid ‘demise.’ The overall complexity of the Ford vs the Toyota and how all of its components function together in performing ALL of the functions was not investigated. After all, Ford is one species, and Toyota another.

So the evidence of whether or not a lifeform was created by an Intelligent Designer or evolved from another / other lifeform(s) is scientifically dependent, by and large, upon that original lifeform, not upon another species from which one is ‘guessing’ it evolved into / from which has a different history / existence; and especially not if the species has significant differences from the original species – which most species do. Cherry picking features without presenting detailed evidence from one species without connecting the dots of evidence to another species is hardly scientific. Two or more species that are of similar design may well have been created by an intelligent designer with significant yet original differences as opposed to evolving from a common ancestor in a non-identical manner. The point is that if either species evidences that all components must be available and in place at the same time in order to function properly, then that species is irreducibly complex, probability / statistically-wise not evolvable. It must have been created by an Intelligent Designer. ONE SPECIES AT A TIME]

In this diagram (redrawn from Heuck 1998), the shaded portions of the basal region indicate proteins in the E. coli flagellum homologous to the Type III secretory structure of Yersinia. . OM, outer membrane; PP, periplasmic space; CM, cytoplasmic membrane.

Stated directly, the TTSS does its dirty work using a handful of proteins from the base of the flagellum. From the evolutionary point of view, this relationship is hardly surprising. In fact, it's to be expected that the opportunism of evolutionary processes would mix and match proteins to produce new and novel functions.

[The evolutionary point of view is largely one of innumerable repeated failures over eons of time until something of value is produced which probability-wise is usually older than the universe is estimated to be, hence unlikely – hence not plausible. Hence the more plausible conclusion is that the species was created by an Intelligent Designer instantly and recently. Even if plausibility is significant for the evolutionary model, THIS DOES NOT RULE OUT THE INTELLIGENT DESIGNER MODEL which is in any case far more convenient, efficient and promising. For the evolutionary mindset is hardly an opportunistic process because it is built into their thinking that there will be innumerable failures until one miniscule success is ‘achieved.’ Furthermore, the TTSS species is not the same as the flagellum of a bacteria. There are similarities amongst these two species, but they are not identical especially not relative to the question as to whether either or both species was created by an Intelligent Designer or evolved over eons after the ‘necessary’ innumerable repeated failures]

According to the doctrine of irreducible complexity, however, this should not be possible.

[Within the same species so far it has not been proved to be possible to put the simpler component referred to in the TTSS into the more complex bacteria and have it function properly either as a replacement method of locomotion or a dispenser of toxins]

If the flagellum is indeed irreducibly complex, then removing just one part, let alone 10 or 15, should render what remains "by definition nonfunctional."

[Has this actually been tested???? You don’t stipulate that you have done this. So how can you conclude that the species in view does not need the specified components and yet still operate as before???]

Yet the TTSS is indeed fully-functional, even though it is missing most of the parts of the flagellum. The TTSS may be bad news for us, but for the bacteria that possess it, it is a truly valuable biochemical machine.

[The TTSS and the flagellum of a bacteria are not the same species. Apples and oranges. If the TTSS is a legitimate species to consider, your examination of it was insufficient to prove that the flagellum of a bacteria could indeed operate properly with the same system that is in the TTSS as before or operate properly but differently. You haven’t provided that proof. The system in the TTSS is different from the system in the flagellum! So it most likely would NOT operate in the same way to provide locomotion for the bacteria or any other way because you have not stipulated that you have found such bacteria in existence which does!!!]

The existence of the TTSS in a wide variety of bacteria demonstrates that a small portion of the "irreducibly complex" flagellum can indeed carry out an important biological function.

[But not the same function as in a different species]

Since such a function is clearly favored by natural selection, the contention that the flagellum must be fully-assembled before any of its component parts can be useful is obviously incorrect.

[Your 'science' is faulty. Have you placed the mechanism in the TTSS in the bacteria to test this?]

What this means is that the argument for intelligent design of the flagellum has failed.

[No. You are testing the wrong hypothesis, proved something that is irrelevant and boasted that you have defeated the concept of an intelligent designer. Even if what you have determined is true, and it is not, an intelligent designer could have created both species from nothing in far less time]


Classically, one of the most widely-repeated charges made by anti-evolutionists is that the fossil record contains wide "gaps" for which transitional fossils have never been found. Therefore, the intervention of a creative agency, an intelligent designer, must be invoked to account for each gap. Such gaps, of course, have been filled with increasing frequency by paleontologists – the increasingly rich fossil sequences demonstrating the origins of whales are a useful examples (Thewissen, Hussain, and Arif 1994; Thewissen, Williams, Roe, and Hussain 2001).

[Species with similarly designed components do not nullify an Intelligent Designer Who could create those species out of nothing in an instant. It is a far better solution than to ‘wait’ for millions / billions of years for a unique species to evolve – which time span is most likely older than estimates of the age of the universe thus disqualifying itself as a rationale /  plausible means for how the species exists. Why not have all of the species be created and present at once and the interdependence for food, survival, water and other benefits be immediately available as observed in the universe today – albeit with fewer and fewer species as time goes by? It appears this is more plausible especially because there has not been observed any actually new species that have arrived on the planet. The number of species appears to be diminishing not increasing. So the world wide flood is a plausible and well corroborated event which event is more plausible than the concept of millions / billions of years of time going by because all that water would have destroyed the fossil record if there had been one, leaving one with a recent creation not an ages old one]

Ironically, the response of anti-evolutionists to such discoveries is frequently to claim that things have only gotten worse for evolution.

[They have]

Where previously there had been just one gap, as a result of the transitional fossil, now there are two (one on either side of the newly-discovered specimen).

[There have not been found ANY actual transitional fossils that one can prove was a descendant of another fossil. More plausible is that there are uncountable fossils of similar design, not descendants of one another. Furthermore, the spaces between fossils in the frequently different fossil order in the rock strata – which speaks more of a worldwide flood – contains nothing!! How do you make something out of nothing unless you are an Intelligent Designer / Creator?? Are you?]

As word of the relationship between the eubacterial flagellum and the TTSS has begun to spread among the "design" community, the first hints of a remarkably similar reaction have emerged. The TTSS only makes problems worse for evolution, according to this response, because now there are two irreducibly-complex systems to deal with. The flagellum is still irreducibly complex – but so is the TTSS. But now there are two systems for evolutionists to explain instead of just one.

Unfortunately for this line of argument, the claim that one irreducibly-complex system might contain another is self-contradictory. To understand this, we need to remember that the entire point of the design argument, as exemplified by the flagellum, is that only the entire biochemical machine, with all of its parts, is functional. For the intelligent design argument to stand, this must be the case, since it provides the basis for their claim that only the complete flagellum can be favored by natural selection, not any its component parts. For the intelligent design argument to stand, this must be the case, since it provides the basis for their claim that only the complete flagellum can be favored by natural selection, not any [of ] its component parts. However, if the flagellum contains within it a smaller functional set of components like the TTSS, then the flagellum itself cannot be irreducibly complex – by definition. Since we now know that this is indeed the case, it is obviously true that the flagellum is not irreducibly complex.

A second reaction, which I have heard directly after describing the relationship between the secretory apparatus and the flagellum, is the objection that the TTSS does not tell us how either it or the flagellum evolved. This is certainly true, although Aizawa has suggested that the TTSS may indeed be an evolutionary precursor of the flagellum (Aizawa 2001). Nonetheless, until we have produced a step-by-step account for the evolutionary derivation of the flagellum, one may indeed invoke the argument from ignorance for this and every other complex biochemical machine.

However, in agreeing to this, one must keep in mind that the doctrine of irreducible complexity was intended to go one step beyond the claim of ignorance. It was fashioned in order to provide a rationale for claiming that the bacterial flagellum couldn't have evolved, even in principle, because it is irreducibly complex. Now that a simpler, functional system (the TTSS) has been discovered among the protein components of the flagellum, the claim of irreducible complexity has collapsed, and with it any "evidence" that the flagellum was designed.

[You evidently have NOT taken out one component in a system in a species such as the locomotion system in a particular bacterium and replaced it with a simpler one from another species such as the TTSS species that uses it to toxify its host, in order to see if the first species of bacteria works properly, have you? And if this works, such as with heart transplants, it STILL does not refute an Intelligent Designer by using His designs to repair / alter something He created in the first place. So an Intelligent Designer remains plausible and the best answer to this question of which is the better model: Creationism or Evolution because it takes a lot less time and the Intelligent Designer evidently fails less and evidently cares more for His Creation]

Combinatorial Argument

At first glance, William Dembski's case for intelligent design seems to follow a distinctly different strategy in dealing with biological complexity. His recent book, No Free Lunch (Dembski 2002a), lays out this case, using information theory and mathematics to show that life is the result of intelligent design. Dembski makes the assertion that living organisms contain what he calls "complex specified information" (CSI), and claims to have shown that the evolutionary mechanism of natural selection cannot produce CSI. Therefore, any instance of CSI in a living organism must be the result of intelligent design. And living organisms, according to Dembski, are chock-full of CSI.

Dembski's arguments, couched in the language of information theory, are highly technical and are defended, almost exclusively, by reference to their utility in detecting information produced by human beings. These include phone and credit card numbers, symphonies, and artistic woodcuts, to name just a few. One might then expect that Dembski, having shown how the presence of CSI can be demonstrated in man made objects, would then turn to a variety of biological objects. Instead, he turns to just one such object, the bacterial flagellum.

Dembski then offers his readers a calculation showing that the flagellum could not have possibly have evolved. Significantly, he begins that calculation by linking his arguments to those of Behe, writing: "I want therefore in this section to show how irreducible complexity is a special case of specified complexity, and in particular I want to sketch how one calculates the relevant probabilities needed to eliminate chance and infer design for such systems" (Dembski 2002a, 289). Dembski then tells us that an irreducibly complex system, like the flagellum, is a "discrete combinatorial object." What this means, as he explains, is that the probability of assembling such an object can be calculated by determining the probabilities that each of its components might have originated by chance, that they might have been localized to the same region of the cell, and that they would be assembled in precisely the right order. Dembski refers to these three probabilities as Porig, Plocal, and Pconfig, and he regards each of them as separate and independent (Dembski 2002a, 291).

This approach overlooks the fact that the last two probabilities are actually contained within the first. Localization and self-assembly of complex protein structures in prokaryotic cells are properties generally determined by signals built into the primary structures of the proteins themselves.

The same is likely true for the amino acid sequences of the 30 or so protein components of the flagellum and the approximately 20 proteins involved in the flagellum's assembly (McNab 1999; Yonekura et al 2000). Therefore, if one gets the sequences of all the proteins right, localization and assembly will take care of themselves.

[Actually not. Signals might be sent out while the components have not yet ‘evolved’ by chance in which case nothing would be accomplished yet, and the configuration activity might be working but with no component in the proper position to make installation effective. So it is evident that all three have to occur at once.]

To the ID enthusiast, however, this is a point of little concern. According to Dembski, evolution could still not construct the 30 proteins needed for the flagellum. His reason is that the probability of their assembly falls below what he terms the "universal probability bound." According to Dembski, the probability bound is a sensible allowance for the fact that highly improbable events do occur from time to time in nature. To allow for such events, he agrees that given enough time, any event with a probability larger than 10-150 might well take place. Therefore, if a sequence of events, such as a presumed evolutionary pathway, has a calculated probability less than 10-150, we may conclude that the pathway is impossible. If the calculated probability is greater than 10-150, it's possible (even if unlikely).

When Dembski turns his attention to the chances of evolving the 30 proteins of the bacterial flagellum, he makes what he regards as a generous assumption. Guessing that each of the proteins of the flagellum have about 300 amino acids, one might calculate that the chances of getting just one such protein to assemble from "random" evolutionary processes would be 20-300 , since there are 20 amino acids specified by the genetic code. Dembski, however, concedes that proteins need not get the exact amino acid sequence right in order to be functional, so he cuts the odds to just 20-30, which he tells his readers is "on the order of 10-39" (Dembski 2002a, 301). Since the flagellum requires 30 such proteins, he explains that 30 such probabilities "will all need to be multiplied to form the origination probability"(Dembski 2002a, 301). That would give us an origination probability for the flagellum of 10 -1170, far below the universal probability bound. The flagellum couldn't have evolved, and now we have the numbers to prove it. Right?

[Suppose the time frame for this exceeds the proposed age of the universe just for this one simple life form, never mind mammals and man]

Assuming Impossibility

I have no doubt that to the casual reader, a quick glance over the pages of numbers and symbols in Dembski's books is impressive, if not downright intimidating. Nonetheless, the way in which he calculates the probability of an evolutionary origin for the flagellum shows how little biology actually stands behind those numbers. His computation calculates only the probability of spontaneous, random assembly for each of the proteins of the flagellum. Having come up with a probability value on the order of 10 -1170, he assures us that he has shown the flagellum to be unevolvable. This conclusion, of course, fits comfortably with his view is that "The Darwinian mechanism is powerless to produce irreducibly complex systems..." (Dembski 2002a, 289).

However complex Dembski's analysis, the scientific problem with his calculations is almost too easy to spot. By treating the flagellum as a "discrete combinatorial object" he has shown only that it is unlikely that the parts flagellum could assemble spontaneously. Unfortunately for his argument, no scientist has ever proposed that the flagellum or any other complex object evolved that way. Dembski, therefore, has constructed a classic "straw man" and blown it away with an irrelevant calculation.

By treating the flagellum as a discrete combinatorial object he has assumed in his calculation that no subset of the 30 or so proteins of the flagellum could have biological activity. As we have already seen, this is wrong. Nearly a third of those proteins are closely related to components of the TTSS, which does indeed have biological activity. A calculation that ignores that fact has no scientific validity.

More importantly, Dembski's willingness to ignore the TTSS lays bare the underlying assumption of his entire approach towards the calculation of probabilities and the detection of "design." He assumes what he is trying to prove.

According to Dembski, the detection of "design" requires that an object display complexity that could not be produced by what he calls "natural causes." In order to do that, one must first examine all of the possibilities by which an object, like the flagellum, might have been generated naturally. Dembski and Behe, of course, come to the conclusion that there are no such natural causes. But how did they determine that? What is the scientific method used to support such a conclusion? Could it be that their assertions of the lack of natural causes simply amount to an unsupported personal belief? Suppose that there are such causes, but they simply happened not to think of them? Dembski actually seems to realize that this is a serious problem. He writes: "Now it can happen that we may not know enough to determine all the relevant chance hypotheses [which here, as noted above, means all relevant natural processes (hvt)]. Alternatively, we might think we know the relevant chance hypotheses, but later discover that we missed a crucial one. In the one case a design inference could not even get going; in the other, it would be mistaken" (Dembski 2002, 123 (note 80)).

What Dembski is telling us is that in order to "detect" design in a biological object one must first come to the conclusion that the object could not have been produced by any "relevant chance hypotheses" (meaning, naturally, evolution). Then, and only then, are Dembski's calculations brought into play. Stated more bluntly, what this really means is that the "method" first involves assuming the absence of an evolutionary pathway leading to the object, followed by a calculation "proving" the impossibility of spontaneous assembly. Incredibly, this a priori reasoning is exactly the sort of logic upon which the new "science of design" has been constructed.

Not surprisingly, scientific reviewers have not missed this point – Dembski's arguments have been repeatedly criticized on this issue and on many others (Orr 2002; Charlesworth 2002; Padian 2002).

Designing the Cycle

In assessing the design argument, therefore, it only seems as though two distinct arguments have been raised for the unevolvability of the flagellum. In reality, those two arguments, one invoking irreducible complexity and the other specified complex information, both depend upon a single scientifically insupportable position. Namely, that we can look at a complex biological object and determine with absolute certainty that none of its component parts could have been first selected to perform other functions. The discovery of extensive homologies between the Type III secretory system and the flagellum has now shown just how wrong that position was.

[But have you actually observed a bacterium with the locomotion component in which you replaced that component with another functioning component that is similar or identical found in another species that is similar to the first bacterium to see if it functions properly either for locomotion or for other purposes such as producing toxins? Have you found any bacterium without a functioning locomotion component? If you have not done any of these things, then your conclusions are pure speculation with no real basis for speculating, hence a waste of time. Note that an Intelligent Designer cannot be ruled out in any case, because He could have created such functioning components as well to be received by the lifeforms He created. For just as He created sources of liquid and food to have it readily available for the lifeforms He created to utilize in order to sustain itself, so He could have created such components for the lifeforms to receive and placed them in such a manner and in such quantities to assist His creation in surviving. The question is have you found any of these components floating around in the environments that the bacteria occupy. If not then don’t speculate further. None of these things has to evolve over a long time, but be made immediately available for the lifeforms He created which live upon the earth that He created]

When anti-evolutionary arguments featuring the bacterial flagellum rose into prominence, beginning with the 1996 publication of Darwin's Black Box (Behe 1996a), they were predicated upon the assertion that each of the protein components of the flagellum were crafted, in a single act of design, to fit the specific purpose of the flagellum. The flagellum was said to be unevolvable since the entire complex system had to be assembled first in order to produce any selectable biological function. This claim was broadened to include all complex biological systems, and asserted further that science would never find an evolutionary pathway to any of these systems. After all, it hadn't so far, at least according to one of "design's" principal advocates:

There is no publication in the scientific literature – in prestigious journals, specialty journals, or books – that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred. (Behe 1996a, 185) 

[Note that in this article you actually do admit to not knowing the details of how anything evolved: “Living cells are filled, of course, with complex structures whose detailed evolutionary origins are not known.”]

As many critics of intelligent design have pointed out, that statement is simply false. Consider, as just one example, the Krebs cycle, an intricate biochemical pathway consisting of nine enzymes and a number of cofactors that occupies center stage in the pathways of cellular metabolism. The Krebs cycle is "real," "complex," and "biochemical." Does it also present a problem for evolution? Apparently yes, according to the authors of a 1996 paper in the Journal of Molecular evolution, who wrote:

"The Krebs cycle has been frequently quoted as a key problem in the evolution of living cells, hard to explain by Darwin’s natural selection: How could natural selection explain the building of a complicated structure in toto, when the intermediate stages have no obvious fitness functionality? (Melendez-Hevia, Wadell, and Cascante 1996)

Where intelligent design theorists throw up their hands and declare defeat for evolution, however, these researchers decided to do the hard scientific work of analyzing the components of the cycle, and seeing if any of them might have been selected for other biochemical tasks. What they found should be a lesson to anyone who asserts that evolution can only act by direct selection for a final function. In fact, nearly all of the proteins of the complex cycle can serve different biochemical purposes within the cell, making it possible to explain in detail how they evolved:

[Although you stipulate that a number of the components of the Kreb’s cycle have been observed to participate in different biochemical purposes within a cell or other cells; this does not make it possible for you to explain in detail how they evolved. There has to be more information which indicates the progression of that evolution stage by stage, failure by failure, success by success over many years – lots of details which most likely require you to be very very old – millions, billions of years old. For evolution by its own self description is not straight forward progress but a series of virtually endless failures interspersed with successes here and there until a huge amount of trials / uncountable years go by and you have some constructive results that you have called “random processes and natural selection” as well as “survival of the fittest.” Since both Creationism and Evolution are faith based models of how the universe / earth came about because neither is sufficiently observable in how it came about – to be there as each species evolved or did not evolve successfully; nor repeatable nor falsifiable in order to arrive at sufficient scientific, objective data; and since there is evidently a quality of design prevalent everywhere in the universe that is way beyond the imagination and capacity of mankind so far, then there remains the plausibility of an Intelligent Designer Who created the universe]

In the Krebs cycle problem the intermediary stages were also useful, but for different purposes, and, therefore, its complete design was a very clear case of opportunism. . . . the Krebs cycle was built through the process that Jacob (1977) called ‘‘evolution by molecular tinkering,’’ stating that evolution does not produce novelties from scratch: It works on what already exists. The most novel result of our analysis is seeing how, with minimal new material, evolution created the most important pathway of metabolism, achieving the best chemically possible design. In this case, a chemical engineer who was looking for the best design of the process could not have found a better design than the cycle which works in living cells." (Melendez-Hevia, Wadell, and Cascante 1996)

Since this paper appeared, a study based on genomic DNA sequences has confirmed the validity of this approach (Huynen, Dandekar, and Bork 1999). By contrast, how would intelligent design have approached the Krebs Cycle? Using Dembski's calculations as our guide, we would first determine the amino acid sequences of each of the proteins of the cycle, and then calculate the probability of their spontaneous assembly. When this is done, an origination probability of less than 10 -400 is the result. Therefore, the result of applying "design" as a predictive science would have told both groups of researchers that their ultimately successful studies would have been fruitless, since the probability of spontaneous assembly falls below the "universal probability bound."

We already know, however, the reason that such calculations fail. They carry a built-in assumption that the component parts of a complex biochemical system have no possible functions beyond the completely assembled system itself. As we have seen, this assumption is false. The Krebs cycle researchers knew better, of course, and were able to produce two important studies describing how a real, complex, biochemical system might have evolved – the very thing that design theorists once claimed did not exist in the scientific literature.

The Failure of Design

It is no secret that concepts like "irreducible complexity" and "intelligent design" have failed to take the scientific community by storm (Forrest 2002). Design has not prompted new research studies, new breakthroughs, or novel insights on so much as a single scientific question. Design advocates acknowledge this from time to time, but they often claim that this is because the scientific deck is stacked against them. The Darwinist establishment, they say, prevents them from getting a foot in the laboratory door.

I would suggest that the real reason for the cold shoulder given "design" by the scientific community, particularly by life science researchers, is because time and time again its principal scientific claims have turned out to be wrong. Science is a pragmatic activity, and if your hypothesis doesn't work, it is quickly discarded.

The claim of irreducible complexity for the bacterial flagellum is an obvious example of this, but there are many others. Consider, for example, the intricate cascade of proteins involved in the clotting of vertebrate blood. This has been cited as one of the principal examples of the kind of complexity that evolution cannot generate, despite the elegant work of Russell Doolittle (Doolittle and Feng 1987; Doolittle 1993) to the contrary. A number of proteins are involved in this complex pathway, as described by Behe:

When an animal is cut, a protein called Hagemann factor (XII) sticks to the surface of cells near the wound. Bound Hagemann factor is then cleaved by a protein called HMK to yield activated Hagemann factor. Immediately the activated Hagemann factor converts another protein, called prekallikrein, to its active form, kallikrein. (Behe 1996a, 84)

How important are each of these proteins? In line with the dogma of irreducible complexity, Behe argues that each and every component must be in place before the system will work, and he is perfectly clear on this point:

. . . none of the cascade proteins are used for anything except controlling the formation of a clot. Yet in the absence of any of the components, blood does not clot, and the system fails. (Behe 1996a, 86)

As we have seen, the claim that every one of the components must be present for clotting to work is central to the "evidence" for design. One of those components, as these quotations indicate, is Factor XII, which initiates the cascade. Once again, however, a nasty little fact gets in the way of intelligent design theory. Dolphins lack Factor XII (Robinson, Kasting, and Aggeler 1969), and yet their blood clots perfectly well. How can this be if the clotting cascade is indeed irreducibly complex? It cannot, of course, and therefore the claim of irreducible complexity is wrong for this system as well. I would suggest, therefore, that the real reason for the rejection of "design" by the scientific community is remarkably simple – the claims of the intelligent design movement are contradicted time and time again by the scientific evidence.

[In this case it is NOT contradicted. Apples and oranges. A human being is not the same as a dolphin. Have you tried to find a human being that does not have Factor XII in his / her blood clotting system to see if it operates? Evidently not. Don’t dolphins have a different environment to live in that might not need Factor XII? Yes. Have you refuted an Intelligent Designer because Factor XII is redundant? No. For you may discover that Factor XII is essential for human clotting but not for Dolphin clotting. An Intelligent Designer is nevertheless not refuted because there is not proved out that there is NO irreducible complexity present in the universe at all, therefore no evidence that one might be required. It’s all about evidence] 

The Flagellum Unspun

In any discussion of the question of "intelligent design," it is absolutely essential to determine what is meant by the term itself. If, for example, the advocates of design wish to suggest that the intricacies of nature, life, and the universe reveal a world of meaning and purpose consistent with an overarching, possibly Divine intelligence, then their point is philosophical, not scientific.

[And so is yours philosophical because yours is not based on scientific facts either because there has been not any opportunity for observing one species evolving into another in a reasonable timeframe that does not exceed the age of the universe, nor an opportunity for repeating and falsifying. Furthermore, information that may contribute toward corroborating one view does not refute the other which view might also be corroborated by the same evidence]

It is a philosophical point of view, incidentally, that I share, along with many scientists. As H. Allen Orr pointed out in a recent review:

Plenty of scientists have, after all, been attracted to the notion that natural laws reflect (in some way that's necessarily poorly articulated) an intelligence or aesthetic sensibility. This is the religion of Einstein, who spoke of "the grandeur of reason incarnate in existence" and of the scientist's "religious feeling [that] takes the form of a rapturous amazement at the harmony of natural law." (Orr 2002).

This, however, is not what is meant by "intelligent design" in the parlance of the new anti-evolutionists. Their views demand not a universe in which the beauty and harmony of natural law has brought a world of vibrant and fruitful life into existence, but rather a universe in which the emergence and evolution of life is made expressly impossible by the very same rules.

Their view requires that the source of each and every novelty of life was the direct and active involvement of an outside designer whose work violated the very laws of nature he had fashioned. The world of intelligent design is not the bright and innovative world of life that we have come to know through science. Rather, it is a brittle and unchanging landscape, frozen in form and unable to adapt except at the whims of its designer.

[The Creationist worldview is far more beautiful and will be even moreso when the Creator comes to fix everything and bring us back to the world of the Garden of Eden before the Fall, including man. No more natural disasters, cruelties to fellow man by man, perfect climate, no death, only eternal life. Or don’t you read the Bible logically in accordance with the normative rules of language, context and logic to determine what it really says and not what someone tells you it says?]

Certainly, the issue of design and purpose in nature is a philosophical one that scientists can and should discuss with great vigor.

[Of course. You’ve supported my very point. Both evolutionists’ and creationists’ statements about the design and purpose of the universe / nature must of necessity be philosophical because there is no a means by which true scientific evidence can be arrived at that because such evidence is neither wholly observable, nor wholly repeatable nor wholly falsifiable.]

However, the notion at the heart's of today intelligent design movement is that the direct intervention of an outside designer can be demonstrated by the very existence of complex biochemical systems.

[If a complex biochemical or other kind of system cannot gradually evolve because the time involved would be greater than the supposed age of the universe, then it demands an Intelligent Designer because the probability of their evolving is too long – longer than the supposed age of the universe]

What even they acknowledge is that their entire scientific position rests upon a single assertion – that the living cell contains biochemical machines that are irreducibly complex.

[There are other assertions which creationists make as well. For example, the world wide flood of which evidence is everywhere on the planet testifies to a recent creation, which evidence would have destroyed the fossil evidence of evolution in a very short time, (if there was evidence in the first place), which thus demands an Intelligent Designer to create the universe so quickly. But One assertion at a time please. And the bacterial flagellum is the prime example of such a machine. One of the innumerable examples. To refute one is not to refute them all. Each one must be adequately examined]

Such an assertion, as we have seen, can be put to the test in a very direct way. If we are able to search and find an example of a machine with fewer protein parts, contained within the flagellum, that serves a purpose distinct from motility, the claim of irreducible complexity is refuted.

[Not so. And Intelligent Designer is not refuted just because He created a particular design with multipurposes. I would think that what He did was rather intelligent and amazing, wouldn’t you?]

As we have also seen, the flagellum does indeed contain such a machine, a protein-secreting apparatus that carries out an important function even in species that lack the flagellum altogether. A scientific idea rises or falls on the weight of the evidence, and the evidence in the case of the bacterial flagellum is abundantly clear.

[And the evidence is that a particular design has a number of variations in it which performs a number of functions in a number of species. That’s rather intelligent, don’t you think? Does that refute an intelligent designer??? Not even if you can figure out that that species might evolve before the universe is old. Otherwise there needs to be Someone Who can do it faster, right?]

As an icon of anti-evolution, the flagellum has fallen.

[Only if you can provide the stages of evolution in this amazing microscopic engine that seems as complex as an automobile]

The very existence of the Type III Secretory System shows that the bacterial flagellum is not irreducibly complex.

[More than one function of this system in more than one species is not what irreducible complexity is referring to. How did that system evolve in the ONE species in view – stage by stage; and how did that system evolve in the OTHER species in view is the issue and in how much time? If that time is longer than the universe is old. Then look for another solution. You have not provided this all important information]

It also demonstrates, more generally, that the claim of "irreducible complexity" is scientifically meaningless, constructed as it is upon the flimsiest of foundations – the assertion that because science has not yet found selectable functions for the components of a certain structure, it never will.

[I am going to stick with what is the best explanation we have so far until something better comes along. So far we have a very complex universe in which you have not fully explained every detail for over 150 years. It appears so far to be left up to an Intelligent Designer over a very short period of time, especially because of the overwhelming evidence of a worldwide flood that would have destroyed the fossil record if there was one and produced its own because of all of that water and sediment. A recent creation demands an Intelligent Designer]

In the final analysis, as the claims of intelligent design fall by the wayside, its advocates are left with a single, remaining tool with which to battle against the rising tide of scientific evidence. That tool may be effective in some circles, of course, but the scientific community will be quick to recognize it for what it really is – the classic argument from ignorance, dressed up in the shiny cloth of biochemistry and information theory.

[You state that creation is wonderfully complex and so far beyond your comprehension to explain in detail, species by species. How does that rule out an Intelligent Designer?]

When three leading advocates of intelligent design were recently given a chance to make their case in an issue of Natural History magazine, they each concluded their articles with a plea for design. One wrote that we should recognize "the design inherent in life and the universe" (Behe 2002), another that "design remains a possibility" (Wells 2002), and another "that the natural sciences need to leave room for design" (Dembski 2002b). Yes, it is true. Design does remain a possibility, but not the type of "intelligent design" of which they speak.

[Why not? Can you prove there is not an Intelligent Designer of some sort until you can explain evolution a bit better?]

As Darwin wrote, there is grandeur in an evolutionary view of life, a grandeur that is there for all to see, regardless of their philosophical views on the meaning and purpose of life.

[Creationists and the Bible itself have a wonder about the marvelous creation that appears before them – they consider it so incredible that there must be some marvelous Creator responsible for its beauty and unfathomable complexity, and responsible for a solution for all of the deaths and disasters that nevertheless have occurred throughout the ages. The solution is quite plausible if there is an Intelligent Designer. So far evolution has not promised an offer for this solution]

I do not believe, even for an instant, that Darwin's vision has weakened or diminished the sense of wonder and awe that one should feel in confronting the magnificence and diversity of the living world. Rather, to a person of faith it should enhance their sense of the Creator's majesty and wisdom (Miller 1999).  Against such a backdrop, the struggles of the intelligent design movement are best understood as clamorous and disappointing double failures – rejected by science because they do not fit the facts,

[Actually Creation does indeed fit the facts especially since there is not enough time for the universe to have evolved from its beginning via random selection, especially since the worldwide flood demands a recent universe]

and having failed religion because they think too little of God.

[What!!! Explain. Are you writing of a god who lets death and random selection go on for billions of years??? Or according to the Bible the God Who created everything out of nothing into a grand and perfect universe, and then allows mankind to have his way and mess it up and then provides a Savior to restore it all as it was originally created, allowing all mankind to participate in that salvation by a moment of faith alone in His Son Jesus Christ alone. No I don’t think that’s less, the God of the Bible is far more than you think!]