WorldWatch - Creation and Evolution in the Schools

A few years ago it was "Creation Science" they were trying to teach in the schools.

Creation Science was an attempt by fundamentalist Christians to give the Genesis account, as interpreted by them, a scientific veneer.

But it was only that -- a thin surface -- and any student who actually believed that Creation Science had anything to do with science would have been educationally crippled.

Now the controversy is between advocates of the theory of Intelligent Design vs. strict Darwinists. And some people want you to think it's the same argument.

My first exposure to Intelligent Design theory was Michael Behe's book Darwin's Black Box: The Biochemical Challenge to Evolution. While disavowing any Creationist agenda per se, Behe pointed out serious problems in the strict Darwinian model of evolution.

Basically, Behe's approach was this: Complex systems in advanced organisms depend on many biochemical steps, all of which must be in place for the system to work at all.

So how, Behe asked, could such a complex system have evolved, if the only method available was random variation plus natural selection?

It would be impossible to believe that the entire series of steps in the complex system could randomly appear all at once. But any one step along the way, since it does nothing by itself, could not give the organism that had it any competitive advantage. So why would each of those traits persist and prevail long enough for the complex system to fall into place?

Behe's conclusion is that since complex biochemical systems in advanced organisms could not have evolved through strict Darwinian evolution, the only possible explanation is that the system was designed and put into place deliberately.

In other words, though he shuns the word, complex systems had to have a creator -- they have to be intelligently designed.

The Darwinist answer was immediate. Unfortunately, it was also illogical, personal, and unscientific. The main points are:

3. If you actually understood science as we do, you'd realize that these guys are wrong and we're right; but you don't, so you have to trust us (expertism).

4. They got some details of those complex systems wrong, so they must be wrong about everything (sniping).

6. We can't possibly find a fossil record of every step along the way in evolution, but evolution has already been so well-demonstrated it is absurd to challenge it in the details (prestidigitation).

7. Even if there are problems with the Darwinian model, there's no justification for postulating an "intelligent designer" (true).

1. You have to be ignorant of either Creation Science or Intelligent Design -- or both -- to think that they're the same thing. Creation Science is embarrassing and laughable -- its authors either don't understand science or are deliberately deceiving readers who don't understand it. Frankly, Creation Science is, in my opinion, a pack of pious lies.

But the problems that the Designists raise with the Darwinian model are, in fact, problems. They do understand the real science, and the Darwinian model is, in fact, inadequate to explain how complex systems, which fail without all elements in place, could arise through random mutation and natural selection.

If Darwinists persist in trying to tar the Designists with the Creation-Science brush, then it is bound to appear, to anyone who has actually examined both, that the Darwinists are trying to deceive us. (They're apparently counting on most people to not care enough to discover the difference.)

2. Real science never has to resort to credentialism. If someone with no credentials at all raises a legitimate question, it is not an answer to point out how uneducated or unqualified the questioner is. In fact, it is pretty much an admission that you don't have an answer, so you want the questioner to go away.

3. Expertism is the "trust us, you poor fools" defense. Essentially, the Darwinists tell the general public that we're too dumb to understand the subtleties of biochemistry, so it's not even worth trying to explain to us why the Designists are wrong. "We're the experts, you're not, so we're right by definition."

Behe and his group don't think we're stupid. They actually make the effort to explain the science accurately and clearly in terms that the lay audience can understand. So who is going to win this argument? Some people bow down before experts; most of us resent the experts who expect us to bow.

The irony is that there are plenty of Darwinists who are perfectly good writers, capable of explaining the science to us well enough to show us the flaws in the Designists' arguments. The fact that they refuse even to try to explain is, again, a confession that they don't have an answer.

4. When Darwinists do seem to explain, it's only to point out some error or omission in the Designists' explanation of a biochemical system. Some left-out step, or some point where they got the chemistry wrong. They think if they can shoot down one or two minor points, then the whole problem will go away.

The Designists are explaining things to a lay audience, and Behe, at least, tells us up front that he's leaving out a lot of steps ... but those steps only make the system more complex, not less.

The Designists are working from secondary sources, so they are naturally several years behind. Of course a scientist who is current in the field will understand the processes better, and can easily dismiss the Designists as using old, outmoded models of how the systems work.

What they never seem to show is how the new understanding reveals a system that is not complex after all, one in which each step in the process confers independent benefits on the organism and therefore could have evolved through random mutation and natural selection alone.

They don't do this because the current findings rarely reveal a simpler process than was previously thought. Almost invariably, they find that the system is more complex and therefore harder to explain, and therefore the Designists have even more of a point than they thought.

5. The church and state argument is deliberately misleading. First, the Designists are not, in fact, advocating "God." They are very careful not to specify who or what the Intelligent Designer might be. So they are not advocating for any particular religion, or any religion at all. For all anyone knows, the supposed Intelligent Designers might be an alien species of mortal, ungodlike beings.

To the Darwinists, of course, this is hypocrisy and deception -- of course the Designists are religious. They must be. Because only religious people would ever question the Darwinist model.

It comes to this: If you question the Darwinist model, you must be religious; therefore your side of the argument is not admissible in the public arena, and certainly not in the public schools.

This is an attempt to shut down discussion by hiding behind the Constitution. It's what you do when you're pretty sure you can't win on the merits.

6. The "we can't possibly find every step along the way" argument is an old one that doesn't actually fit the current situation. It is the correct answer when defending the idea of evolution against those who believe in an ex nihilo creation in six days.

The fossil record is very clear in showing the divergence of species, with old ones going extinct and new ones arising over a long period of time. And the general progression is from simpler to more-complex organisms. The fact that evolution takes place is obvious. You don't have to find some improbable fossil graveyard where each generation conveniently lay down next to their parents' bodies when it came time to die.

But fossils only show physical structures, and the Intelligent Design argument concedes the point. The Designists (or at least the smart ones) are not arguing for biblical literalism. They freely admit that evolution obviously takes place, that simple organisms were followed by more complex ones.

They also accept the other obvious arguments for evolution, like the similarity of genes among different species. They have no problem with the idea that chimps are so genetically similar to us because we share a common ancestor.

Their argument isn't against evolution per se. Nor are they doubting that natural selection takes place. Their argument is that the Darwinian model is not a sufficient explanation.

So "we can't find fossils representing every step of evolution" has nothing to do with the issues being raised. The Designists are not anti-evolution. They are anti-Darwin.

Here's the place where a lot of scientists indulge in muddy thinking. Evolution and Darwinism have been treated as synonyms for so long that too many people think they're the same thing. But they're not, and never have been.

Darwin did not think up the idea of evolution any more than Columbus proved to a bunch of flat-earthers that the world was round.

In fact, the Columbus analogy is an apt one. Columbus was actually wrong -- he was arguing, not that the Earth was round (everybody knew that already) but that the Earth was much smaller than it really is. His claim was that the Earth was so small that if you sailed west from Spain, you'd find Japan at about the point where in fact you find Cuba.

He was vastly, ridiculously wrong -- but because his expedition got funded, he was able to sail west far enough to bump into a largely unknown (to Europe) land mass, and the civilizations that dwelt on it.

Whereas the sensible people who knew how big the Earth was refused to endanger themselves by sailing west on a voyage so long that no ship could carry enough supplies. And therefore discovered nothing.

Darwin's contribution to biological science is enormous. He posited a means by which science could study the passage of organisms from one species to another over time. Before Darwin (and the others who were working in the same direction), there were many who believed in evolution, but accounted it part of the "great chain of being" ordained by God.

Here's the thing: If you say that things are as they are because God made them that way, then they are off limits to science. Science is simply unsuited to studying God. Science requires impersonal, repeatable testing. Its business is discovering causal relationships, and it can only work with mechanical cause.

So when the answer to the question "why does this natural phenomenon occur?" is "because God wants it that way," then science simply has nothing to add to the conversation. Any more than when the question is "why are you wearing that combination of colors?" If some person -- divine or otherwise -- chose to make things as they are, then we're talking about purpose and motive; science can only work with mechanical causation.

In other words, until Darwin showed us evolution as a machine that did not require divine meddling to be explained, scientists were blocked from answering what seemed to be (and, in some ways, is) a mere historical, not scientific, question: How did this vast variety of life forms come to be?

Of course scientists can't document every step of the historical process of evolution. That wouldn't be science anyway, it would be mere data collection.

What science does is to invent plausible stories of automatic processes by which natural events, systems, and objects come to be as we see them.

Then the story is tested, either by experiments designed to prove the story false, or by making predictions about what else must exist if the story is true, and then seeing if the predictions are right.

Science examines ongoing processes that proceed from mechanical causes; Darwin, by convincingly describing evolution as such a process, opened the door to millions of insights into the workings of organisms of every size.

Make no mistake: Not just the fossil record, but virtually every close examination of biology at every level reveals utterly convincing evidence that evolution takes place, has always taken place, and continues to take place. There is also plenty of evidence that natural selection takes place.

The Designists challenge only the sufficiency of Darwin's model. The claim only that it does not seem adequate to explain systems that were completely unknown at the time he created his theory.

Darwin himself knew that there were sticky places where his theory wasn't a sufficient explanation. He wrestled with the problem of altruism, for instance, and while he found adequate natural-selection explanations for some forms of altruism (for instance, the mother bird that draws off predators, potentially sacrificing her life, to promote the survival of her offspring), there were other behaviors that were inexplicable by means of natural selection (for instance, humans who voluntarily go to war to protect strangers).

There are other problems with Darwin's model. For instance, the idea of gradual change at a consistent rate is challenged in some respects by the fossil record. Some organisms have persisted virtually unchanged for millions of years, only to suddenly disappear; others have seemed to spring up suddenly, with few or seemingly no precursors.

The result was a modification in doctrinaire Darwinism, called the "punctuational model," which proposed that evolution can happen in bursts that are much more rapid than the normal pace. It is not really so much a contradiction of Darwinism as an elaboration of it, a revision to help it fit observed reality better.

It is vital to keep in mind that Darwin's theory is a theory, not in the way that Creationists mean (i.e., a theory and therefore not a fact), but in the way that scientists use the word "theory": a story that accounts for all the data that we've found so far.

But good science always examines its theories and compares them to the evidence, to see if they are still adequate. That's how Newton's "laws" (i.e., theoretical constants) were able to be superseded by Einstein's -- not because they weren't true, but because they couldn't adequately explain all the phenomena that were being observed.

I specify "good science" because if, at any point, any theory becomes a dogma that no one is allowed to question, it stops being good science. Indeed, it stops being science at all, and becomes its opposite -- its enemy.

Darwin himself was a scientist, and a great one, in part because he was constantly probing and questioning his own ideas.

But an astonishing number of his defenders today are, at least when discussing Darwinism, not scientists at all.

They instead behave like religious fanatics whose favorite dogmas are being challenged. That's why they answer their serious critics with name-calling, credentialism, expertism, sniping, politics, and misdirection, answering questions that have not been asked, using answers that have nothing to do with the real questions.

They have no good answers, and yet they have an unshakable faith in Darwinism; so they fervently and vehemently attack their attackers, waging, not one side in a scientific conversation, but a crusade against those who do not treat their Prophet with enough respect.

More respect, in fact, than Darwin would have wanted or ever showed for his own ideas. Darwin had no problem with questioning Darwinism. He constantly entertained the possibility that he was wrong about this, that, or everything. Would that his disciples today would adopt the same attitude.

7. Yes, there are problems with the Darwinian model. But those problems are questions. "Intelligent design" is an answer, and you have no evidence at all for that.

Intelligent design uses the evil "must" word: Well, if random mutation plus natural selection can't account for the existence of this complex system, then it must have been brought into existence by some intelligent designer

Just because the Darwinian model seems to be inadequate at the molecular level does not imply in any way that the only other explanation is purposive causation.

There might be several or even many other hypotheses. To believe in Intelligent Design is still a leap of faith.

But the normal answer of the Darwinists is also a leap of faith. In effect, their arguments boil down to this: We have no idea right now how these complex systems came to be, but we have fervent, absolute faith that when we do figure it out, it will be found to have a completely mechanical, natural cause that requires no "intelligent designer" at all.

If the Darwinists' faith is eventually proved correct, and we find completely natural, mechanical explanations for the evolution of complex biochemical systems, then these matters will remain within the purview of the scientific method. They will still be teachable in science class.

But if the Designists are right, and there is no natural explanation, no process of mechanical causation that can possibly lead to the automatic evolution of complex biochemical systems, then at that moment the subject ceases to be science at all, and becomes either history (what did the Designers do and why did they do it?) or theology (what does God mean by all this?).

That's fine. There are lots of subjects in this world that are worth studying, and in which true and valuable things can be discovered, which are not and cannot be science.

But when you purport to teach science in school, the subject you teach had better be science, and not somebody's religion in disguise.

That's the problem with both sides in this squabble. They are both functioning as religions, and they should stop it at once.

If both sides would behave like scientists, there wouldn't even be a controversy, because everyone would agree on this statement:

Evolution happens and obviously happened in the natural world, and natural selection plays a role in it. But we do not have adequate theories yet to explain completely how evolution works and worked at the biochemical level.

That is a true statement, according to our present state of scientific knowledge.

And when Darwinists scream that we do too know how to explain evolution, and it's natural selection, so just stop talking about it, they are dogmatists demanding that their faith -- the faith that Darwin's model will be found to explain everything when we just understand things better -- be taught in the public schools.

There is no reason for science teachers in the public schools to take a single step beyond that statement I made above. It allows the teaching of every speck of scientific biology; and it makes moot the as-yet-unknowable issue of how each specific complex biochemical system came into existence.

In fact, what every school board in this country should decide is to ignore both sides' demands that the schools teach their faith, and allow the public schools to perform their public service: educating children in our shared culture, including what we have learned through the scientific method.

Real science does not in any way impinge on a belief that God (or some other Intelligent Designer) created the world and everything that dwells in it. At the same time, real science does not -- and never can -- prove or even support the hypothesis.

But real science also does not support a misguided faith in the teachings of a scientist who is now regarded as a prophet, and whose disciples have an emotional commitment to his theories, even when they can be shown to be inadequate to explain the data as we presently have it.

Physicists know this -- they don't get their dander up and demand that non-Einsteinian physics never be taught in the public schools, for instance. They recognize that at the bleeding edge of science we simply don't know stuff yet, and no past genius has authority today, if and when we come up with data that may not support his theories.

Biology is no different. Darwin gave us a huge leap forward. But he did not take us all the way to final truth -- no scientist ever can or ever will, by the definition of what science is and scientists do.

When somebody -- anybody -- asks hard questions of a theory, then the scientific answer is never "shut up and go away." The scientific answer is, "Let's see if we can find out."

Meanwhile ... what do I believe about the origin of life? I believe that God created it, employing and obeying natural laws, but at levels beyond our understanding. I believe we're here on this earth for God's beneficent purposes.

But I have no interest whatsoever in having schoolteachers train my or anyone else's children in any religion. My wife and I teach our beliefs to our children and help them put what they learn at school in perspective. We encourage them to question everything -- including what we teach them -- but we expect them to adhere to rigorous standards in deciding what they should believe.

I don't have to call upon religious faith to contradict the claims of bad science. I'll reserve it to deal with the claims of bad religion. An understanding of good science is always enough to sweep away the overclaiming of those "scientists" who, as the religious fanatics they are, wish to impose their faith on everyone.

What Orson Scott Card doesn't realize about the fatal flaws in Behe's "Irreducible Complexity" argument would fill volumes.

Here are my own analyses of it:

The next idea you probably will not like, and that is irreducible complexity.
As an "idea" I like it just fine, and so do evolutionary scientists. The problem is that Behe (and the creationists who follow him) have created a "straw man" version of "IC" which is quite simply incorrect -- but appears to give the conclusion they want.
The original notion of "IC" goes back to Darwin himself. He wrote:
"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."
-- Charles Darwin, "On the Origin of Species", 1859
That's "Irreducible Complexity" in a nutshell. It's not as if Behe has pointed out anything that biologists (or Darwin) didn't already realize.
But let's examine Darwin's description of "IC" in a bit more detail (emphasis mine):
No doubt many organs exist of which we do not know the transitional grades, more especially if we look to much-isolated species, round which, according to my theory, there has been much extinction. Or again, if we look to an organ common to all the members of a large class, for in this latter case the organ must have been first formed at an extremely remote period, since which all the many members of the class have been developed; and in order to discover the early transitional grades through which the organ has passed, we should have to look to very ancient ancestral forms, long since become extinct.
We should be extremely cautious in concluding that an organ could not have been formed by transitional gradations of some kind. Numerous cases could be given amongst the lower animals of the same organ performing at the same time wholly distinct functions; thus the alimentary canal respires, digests, and excretes in the larva of the dragon-fly and in the fish Cobites. In the Hydra, the animal may be turned inside out, and the exterior surface will then digest and the stomach respire. In such cases natural selection might easily specialise, if any advantage were thus gained, a part or organ, which had performed two functions, for one function alone, and thus wholly change its nature by insensible steps. Two distinct organs sometimes perform simultaneously the same function in the same individual; to give one instance, there are fish with gills or branchiae that breathe the air dissolved in the water, at the same time that they breathe free air in their swimbladders, this latter organ having a ductus pneumaticus for its supply, and being divided by highly vascular partitions. In these cases, one of the two organs might with ease be modified and perfected so as to perform all the work by itself, being aided during the process of modification by the other organ; and then this other organ might be modified for some other and quite distinct purpose, or be quite obliterated.
The illustration of the swimbladder in fishes is a good one, because it shows us clearly the highly important fact that an organ originally constructed for one purpose, namely flotation, may be converted into one for a wholly different purpose, namely respiration. The swimbladder has, also, been worked in as an accessory to the auditory organs of certain fish, or, for I do not know which view is now generally held, a part of the auditory apparatus has been worked in as a complement to the swimbladder. All physiologists admit that the swimbladder is homologous, or 'ideally similar,' in position and structure with the lungs of the higher vertebrate animals: hence there seems to me to be no great difficulty in believing that natural selection has actually converted a swimbladder into a lung, or organ used exclusively for respiration.
[Example snipped]
In considering transitions of organs, it is so important to bear in mind the probability of conversion from one function to another, that I will give one more instance. [Long detail of example snipped] If all pedunculated cirripedes had become extinct, and they have already suffered far more extinction than have sessile cirripedes, who would ever have imagined that the branchiae in this latter family had originally existed as organs for preventing the ova from being washed out of the sack?
-- Charles Darwin, "On the Origin of Species", 1859
Darwin makes two critical points here:
1. A modern organ need not have evolved into its present form and function from a precursor which had always performed the same function. Evolution is quite capable of evolving a structure to perform one function, and then turning it to some other "purpose".
2. Organs/structures can reach their present form through a *loss* of function or parts, not just through *addition* of function or parts.
Despite the fact that these observations were laid out in 1859, Behe's version of "Irreducible Complexity" pretends they are not factors, and defines "IC" as something which could not have arisen through stepwise *ADDITIONS* (only) while performing the same function *THROUGHOUT ITS EXISTENCE*.
It's hard to tell whether Behe does this through ignorance or willful dishonesty, but the fact remains that *his* definition and analysis of "IC" is too restrictive. He places too many "rules" on how he will "allow" evolution to reach his examples of "Behe-style IC" structures, while evolution itself *IS NOT RESTRICTED TO THOSE RULES* when it operates. Thus Behe's conclusion that "Behe-style evolution" can not reach "Behe-style IC" hardly tells us anything about whether *real-world* evolution could or could not have produced them.
For specific examples, Behe's example of the "Behe-style IC" flagellum is flawed because flagella are composed of components that bacteria use FOR OTHER PURPOSES and were evolved for those purposes then co-opted (1, 2), and Behe's example of the "Behe-style IC" blood-clotting process is flawed because the biochemistry of blood-clotting is easily reached by adding several steps on top of a more primitive biochemical sequence, *and then REMOVING earlier portions which had become redundant* (1, 2).
Even Behe's trivial mousetrap example turns out to not actually be "IC".
The usual qualitative formulation is: "An irreducibly complex system cannot be produced...by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system, that is missing a part is by definition nonfunctional..."
Note the key error: By saying that it "breaks" if any part is "missing" (i.e. taken away), it is only saying that evolution could not have reached that endpoint by successively only ADDING parts. True enough, but Behe misses the fact that you can also reach the same state by, say, adding 5 parts one at a time, and then taking away 2 which have become redundant. Let's say that part "A" does the job, but not well. But starting with just "A" serves the need. Then add "B", which improves the function of "A". Add "C" which helps A+B do their job, and so on until you have ABCDE, which does the job very well. Now, however, it may turn out that CDE alone does just fine (conceivably, even better than ABCDE does with A+B getting in the way of CDE's operation). So A and B fade away, leaving CDE. Note that CDE was built in "one change at a time" fashion, with each new change improving the operation. HOWEVER, by Behe's definition CDE is "Irreducibly Complex" and "could not have evolved (been built by single steps)" because removing C or D or E from CDE will "break" it. Note that Behe's conclusion is wrong. His logic is faulty.
The other error in Behe's definition lies in this part: "...any precursor to an irreducibly complex system, that is missing a part is by definition nonfunctional". The problem here is that it may be "nonfunctional" for its *current* function, but perfectly functional for some *other* function helpful for survival (and therefore selected by evolution). Behe implicitly claims that if it's not useful for its *current* function, it's useless for *any* function. The flaw in this should be obvious.
"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."
True as far as it goes, but but this is hardly the same as Behe's sleight-of-hand in the first part of his statement, which relies on the false premise that a precursor to a structure is 100% useless for *any* purpose if *taking away* (but not adding) one part from the current purpose makes it unsuitable for the current purpose. Two gaping holes in that one...
Behe (an anathematized name)
For reasons I've outlined above.
talks of the bacterial flagellum, which contains an acid-powered rotary engine, a stator, O-rings, bushings, and a drive shaft. The machinery of this motor requires approximately fifty proteins.
Except that it doesn't. As many biochemists have pointed out, other organisms have function flagella (even *as* flagella) with fewer proteins (and/or different proteins). That flagellum isn't even "IC" by Behe's own definition since you *can* remove proteins and have it still work as a flagellum. [...]

For a far more realistic look at the evolutionary "invention" of the flagellum, see Evolution in (Brownian) space: a model for the origin of the bacterial flagellum , which I linked earlier in this post. From the abstract:
The model consists of six major stages: export apparatus, secretion system, adhesion system, pilus, undirected motility, and taxis-enabled motility. The selectability of each stage is documented using analogies with present-day systems. Conclusions include: (1) There is a strong possibility, previously unrecognized, of further homologies between the type III export apparatus and F1F0-ATP synthetase. (2) Much of the flagellum’s complexity evolved after crude motility was in place, via internal gene duplications and subfunctionalization. (3) Only one major system-level change of function, and four minor shifts of function, need be invoked to explain the origin of the flagellum; this involves five subsystem-level cooption events. (4) The transition between each stage is bridgeable by the evolution of a single new binding site, coupling two pre-existing subsystems, followed by coevolutionary optimization of components. Therefore, like the eye contemplated by Darwin, careful analysis shows that there are no major obstacles to gradual evolution of the flagellum.

And:

For an analysis of numerous errors and such in Dembski's Design arguments/examples, see Not a Free Lunch But a Box of Chocolates: A critique of William Dembski's book No Free Lunch. It also contains material on the flagella issue you raise next.
As for Behe (the other author):
One small example is the flagella on a paramecium. They need four distinct proteins to work.
Actually they need a lot more than that. And as far as I know, Behe never used the cilia on paramecia as his example, he has primarily concentrated on bacterial flagella.
They cannot have evolved from a flagella that need three.
Contrary to creationist claims (or Behe's) that flagella are Irreducibly Complex and can not function at all if any part or protein is removed, in fact a) there are many, many varieties of flagella on various species of single-celled organisms, some with more or fewer parts/proteins than others. So it's clearly inaccurate to make a blanket claim that "flagella" in general contain no irreplacable parts. Even Behe admits that a working flagella can be reduced to a working cilia, which undercuts his entire "Irreducibly Complex" example/claim right off the bat.
For a semi-technical discussion of how flagella are *not* IC, because many of their parts can be eliminated without totally breaking their locomotive ability, see Evolution of the Bacterial Flagella
But even if one could identify, say, four specific proteins (or other components) which were critically necessary for the functioning of all flagellar structures (and good luck: there are three unrelated classes of organisms with flagella built on three independent methods: eubacterial flagella, archebacterial flagella, and eukaryote flagella -- see Faugy DM and Farrel K, (1999 Feb) A twisted tale: the origin and evolution of motility and chemotaxis in prokaryotes. Microbiology, 145, 279-280), Behe makes a fatal (and laughably elementary) error when he states that therefore they could not have arisen by evolution. Even first-year students of evolutionary biology know that quite often evolved structures are built from parts that WERE NOT ORIGINALLY EVOLVED FOR THEIR CURRENT APPLICATION, as Behe naively assumes (or tries to imply).
Okay, fine, so even if you can prove that a flagellum needs 4 certain proteins to function, and would not function AS A FLAGELLUM with only 3, that's absolutely no problem for evolutionary biology, since it may well have evolved from *something else* which used those 3 proteins to successfully function, and only became useful as a method of locomotion when evolution chanced upon the addition of the 4th protein. Biology is chock-full of systems cobbled together from combinations of other components, or made via one addition to an existing system which then fortuitously allows it to perform a new function.
And, lo and behold, it turns out that the "base and pivot" of the bacterial flagella, along with part of the "stalk", is virtually identical to the bacterial Type III Secretory Structure (TTSS). So despite Behe's claim that flagella must be IC because (he says) there's no use for half a flagella, in fact there is indeed such a use. And this utterly devastates Behe's argument, in several different ways. Explaining way in detail would take quite some time, but it turns out that someone has already written an excellent essay on that exact thing, which I strongly encourage you to read: The Flagellum Unspun: The Collapse of "Irreducible Complexity" .
(Note: Several times that essay makes a reference to the "argument from ignorance", with the assumption that the reader is already familiar with it. I'd like to point out that contrary to the way it sounds, Miller is *not* accusing Behe et all of being ignorant. Instead, he's referring to this family of logical fallacies, also known as the "argument from incredulity".)
That is called irreducible complexity.
That's what Behe likes to call it, yes. But the flagella is provably *not* IC. Oops for Behe. Furthermore, while it's certainly easy to *call* something or another "Irreducibly Complex", proving that it actually *is* is another matter entirely.
As the "Flagellum Unspun" article above states:
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)).
For more bodyblows against the notion of Irreducible Complexity, see:
Bacterial Flagella and Irreducible Complexity
Irreducible Complexity Demystified
Irreducible Complexity
Review: Michael Behe's "Darwin's Black Box"
The fatal flaws in Behe's argument were recognized as soon as his book was published, and countless reviewers pointed them out. And yet, creationists and IDers, who seem to rely mostly on the echo-chamber of their own clique and appear to seldom read much *actual* scientific sources, still seem blissfully unaware of the problems with Behe's thesis, and keep popping in on a regular basis to wave the book around and smugly yell something like, "See, evolution has already been disproven!"
What's funny is that by Behe's own argument, a stone arch is "irreducibly complex" because it could not have formed by nature *adding* sections of stone at a time (it would have fallen down unless the entire span was already in place -- and indeed will fall down if you take part of the span away):
Needless to say, what Behe's argument is missing in the case of the stone arch is that such arches form easily by natural means when successive layers of sedimentary rock added on top of each other, and *then* erosion carves a hole out from *under* the arch by *removing* material after the "bridge" of the arch itself *was already there*.
Similarly, Behe's arguments about why certain types of biological structures "could not" have evolved fall flat because he doesn't realize that evolution does not only craft features by *adding* components, it also does so by *lateral alteration*, and by *removing* components.
Behe's "irreducible complexity" argument is fatally flawed. It only "proves" that a *simplified* version of evolution (as envisioned by Behe) couldn't give rise to certain structures -- not that the *actual* processes of evolution could not.

And:

[Behe:] An example of an irreducibly complex cellular system is the bacterial flagellum: a rotary propeller, powered by a flow of acid, that bacteria use to swim. The flagellum requires a number of parts before it works - a rotor, stator and motor. Furthermore, genetic studies have shown that about 40 different kinds of proteins are needed to produce a working flagellum.
Behe's either a liar or an idiot on this point. Far from being "irreducibly complex", many simpler versions of working flagella get along just fine, as do several subcomponents of the particular flagellum which Behe uses as his poster-child. And *both* points violate the requirements which Behe states are necessary conditions for a system to be "irredicubly complex". Oops!