Copyright © 1996
A Touchstone Book, Simon & Schuster
In this book, Dr. Behe argues that the biochemistry of living cells is so unbelievably complex that some aspects could not have evolved.
To categorize him: Dr. Behe believes in "intelligent design", a recent flavor of creationism. He accepts an old age for the earth, and "has no particular reason to doubt" common descent. However, he argues that science's insistence on naturalistic explanations must be abandoned.
The scientific community has published a number of angry rebuttals, accusing Behe of:
"By Irreducibly Complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts cause the system to effectively cease functioning." [Page 39]Behe asserts that such systems cannot evolve "directly" by a series of small modifications, each of which is a slight improvement to some initial system. He briefly mentions that "indirect" circuitous development is possible. However, he asserts that this is tremendously unlikely. Also, it would be tremendously unlikely for any complex system to arise naturally in one fell swoop by mutation.
The book gives some details of several complex biochemical systems. He claims these are Irreducibly Complex, and that the scientific community has no Darwinian explanation for them, and isn't even looking for explanations. He concludes that these aspects of life did not evolve. Therefore by default these are the result of Intelligent Design.
There are a whole bunch of things in this category. I'll start with the big stuff, and then just list the rest.
For one, Behe thought he had invented Irreducibly Complexity. On pages 203-204, he wonders if some unknown mechanism could generate I.C.-ness. He dismisses the possibility. On page 233 he compares his great discovery to those of Newton, Einstein, Pasteur and Darwin. He should instead have compared himself to Nobel Prize winner H. J. Muller , who invented irreducible complexity in 1939. Muller argued in some detail that evolution would routinely cause such systems. That conclusion is today a common wisdom of evolutionary biology. Behe didn't rebut Muller's argument because he didn't even know it existed. He says on page 187 that evolution always progresses by addition, but any evolutionist knows that it often happens by subtraction.
His examples - cilia, clotting, the immune system and the bombardier beetle have failed to impress experts on these specific topics. Behe doesn't seem to be up to date. Although he implies on page 114 that he is expert at computer searches for scientific articles, he somehow managed to not find pretty well the entire literature on biochemical evolution. I personally own a textbook entitled Molecular Evolution, despite his claim that no such book exists.
Behe also doesn't seem to be aware of the basic way that the history of a molecule can be studied: namely, by examining its variation across a set of living species. If the tree of descent (phylogeny) of the creatures is known from other data, then it is sometimes possible to deduce a great deal. He dismisses this on page 175, apparently in total ignorance of the successes of the method.
Behe argues that many biochemical systems would cease to function if various crucial elements were missing. However, there are many examples  of biochemical systems that continued to function when put to just such a test. As that article says,
"It is a hallmark characteristic of evolved biochemical systems that there are typically multiple causal routes to a given functional end, and where one route fails, another can take over."In particular, Behe spent Chapter 4 saying that the clotting cascade couldn't be reduced. But there are lab mice from which we have removed several parts of the clotting cascade, and they seem quite normal. Behe did not mention any of these experimental results, presumably because he didn't know about them.
Behe argues strongly for "intelligent design". So, just exactly when did this designer operate? From Behe's examples, He can't have just created each species - Behe says on page 5 that he "has no particular reason to doubt" common descent. On page 227 Behe throws out the suggestion that the original cell contained all of the design information used later. He suggests on page 231 that scientists do research to check if it could be true.
It's really puzzling that Behe thinks research is needed. We already know facts proving that theory wrong. For one thing, at least billions of species have existed. It's quite out of the question to store that much information in one cell. Next, there's no mechanism for making the stored information come out at the right time. We've studied the genes of many species, and found no such stored information in any of them. A simple calculation shows that mutation would have scrambled the information long before it was time to use it. And why do different groups of species do the same thing in different ways? Eyes seem to have arisen independently at least 40 times, and we say that because the eyes work in unnecessarily different ways. Clotting and cilia are different in different creatures, too. In short, how come he didn't know that his suggestion is already disproven?
There are a whole bunch of lesser issues. In page order:
On page 38, Behe complains that Dawkins doesn't give much detail. But Behe is quoting from a book which he describes on page 33 as "accessible to the interested layman" and "entertaining". And he expects detail, too ???
On pages 93 to 96, Behe has fun at Doolittle's expense, pointing out imprecise language, and complaining that Doolittle didn't give numbers. However, Behe is attacking a talk given to some clinicians. Of course it was casual. It was trying to be casual! If this was the only article in the world on blood clotting, the situation would be as bad as Behe claims. But it isn't.
On page 220, Behe correctly points out that the "Methinks it is a weasel" analogy is goal directed, whereas science says that evolution is not goal directed.
First, this is an attack on an extraneous factor. By definition, an analogy is imperfect. The whole point of teaching by analogy is to keep complications and distractions at bay while one explains one single point. Dawkins's point was that search under a selection pressure is utterly incomparable to a random search. He was right. I wrote a weasel program, and it is about 1045 times more efficient than a random search. People with other weasel programs ( Ian Musgrave, WikiPedia, ISCID) report much the same.
Secondly, this attack misses the point that Dawkins chose a problem which could be studied by writing a small computer program. Just exactly how does Behe propose to write a small program that demonstrates selection pressure and is not goal directed?
Third, Dawkins himself explained (on page 50) that weasel had that exact deficiency. He then explained a more realistic program. It was much more complicated.
A large problem with Irreducible Complexity is that it's ill-defined. Words like "function" and "system" may seem clear, but in practice there are problems. A given chemical may have several uses. Which one is its function?
Behe deals with this on page 196, and gets it wrong. If a computer is used as a paper weight, then yes, that is its function. That may not be its intended function, but intentions don't count.
It gets worse. In biochemistry, it is pretty normal for both chemicals and systems to have multiple functions, in different places, or at different times. For example, the protein crystallin is transparent and is used in your eyes. Crystallin is also an enzyme which acts on the stress proteins used in coping with heat shock or osmotic shock. (It is thought that the enzyme function came first, and the first eye just co-opted this useful stuff that was lying around.)
So how are we to draw boundaries around systems? Behe is not very helpful about how to do that. And if you can't find the system, how can you decide if you have an Irreducibly Complex system? Suppose one possible boundary gives you an I.C. system, and another boundary doesn't? How are we to know his examples don't suffer from this? How are we to identify "crucial" components, when biochemical systems with important pieces removed sometimes continue to work well? 
Behe also doesn't define "indirect" when he says on page 40 that evolution could indirectly produce Irreducible Complexity. Just what is an indirect route, and why is it unlikely?
On page 223, Behe argues that Intelligent Design does not mean good design. Throughout his book he emphasizes the Rube Goldberg nature of life. That is, most of his examples of Irreducible Complexity seem to be poor designs. He excuses this by saying that perhaps we don't know the intentions of the designer. But an evolutionist could equally say that perhaps these things evolved in a way we haven't thought of. Why does Behe think that the first is a good excuse, and the second is a bad excuse?
It's also strange that he didn't notice the Irreducible Complexity of many other biological things, like the four chambered heart, or the bolas spider. Why aren't they in his book? Of course, we know how they evolved, but I don't suspect Behe of leaving them out for that reason. I suspect he simply didn't think to look outside his specialty.
On page 190, Behe makes the incorrect statement that the proponents of self-organizing complexity "have not yet succeeded in connecting it to real life." . But on page 273, we discover that "under the right conditions the components will spontaneously reform ribosomes." This contradicts the first quote.
Basically, Behe is saying that if he personally doesn't know a naturalistic explanation, today, it must be because the explanation is non-naturalistic. But since his only evidence is his lack of knowledge, he's not actually drawing a logical conclusion. He's merely stating his willingness to give up.
In Boston Review, Behe stated:
"To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved."to which Orr replied:
"I find this statement extremely curious as, in his book, Behe plainly admits that some cellular processes could have evolved by natural selection. If all those other cases didn't cause Behe to surrender his pet theory, why should one more?"In short, Orr asks why we should believe that Behe won't move the goalposts. Whenever some evolutionary explanation is offered to him, he can simply say that he has some other problem that's even harder, so the solved problem wasn't hard enough to qualify. And, of course, after you've been told the answer to a problem, it's easy to think that it wasn't very hard.
The above exchange happened in 1997. As of 1999, Behe has simply avoided the goalposts. I do not know of a public acknowledgement that some of his examples, such as clotting have been convincingly explained. Instead, in September 1999 he said "The point in dispute is whether natural selection can produce major innovations." But surely his book holds up the immune system as a major innovation, and as of 1998 it was no longer disputable that evolution could have caused that.
Although Behe describes these on pages 59-72, it isn't clear exactly what the irreducible systems are, and why they can't be reduced.
Suppose we took flagellin, which in E. coli K-12 is a chain of 497 amino acids. What if we chop out a third of those? If the "system" is irreducible then removing these parts should make it stop functioning. But that has been done, and the flagellum still worked fine . So is this reduced system Irreducible? Apparently we don't have a good way to know, since the method applied to the original system gave a wrong answer.
Flagellin is also used for "active transport" inside cells, but a cutdown version with 183 aminos will do that . This implies that there was some earlier molecule that was only used for transportation. Evolution replaced that molecule with flagellin, and flagellin was then co-opted into its flagella role because it was lying around.
So, there is evidence suggesting evolutionary scenarios leading to a flagella. Behe tries to ridicule these on page 66, but the best he can do is demand detail. As Behe points out on page 62, microtubules are involved in transport, and in simpler ways than their use in flagella. Just from his description, one would guess that transport came first, and in fact we're quite sure that flagella were not present in the original ancestral cell. Since this is an area of ongoing research, there is every reason to believe that further evidence will be found that suggest or constrain the sequence of events. Here is one guess, based on current knowledge:
Let us imagine a bundle of tubulins serving a structural function at the cell membrane, sticking out and causing a projection (but a static one) from the cell surface. Let's call such a projection a microvillus (to choose a name at random :-)). One of the consequences of these microvilli would be an increase in the surface to volume ratio of the cell. Surely, even Behe might be able to come up with a reasonable selective environment where such microvilli might be favored, even if they could not move at all. Now one, as Behe points out, might envision motor molecules involved in transport along the axis of these fiber bundles (for precisely the reasons one might expect microvilli to form in the first place). Linking some of the bundles might allow some minor movement of the microvilli at levels that would be insufficient to cause cell motility. But movement, by creating microcurrents, might have uses without being sufficient to move the organism. Under conditions that select for more vigorous movement, you might well get the emergent property of motility.
I have previously given a highly speculative, but similar, possible pathway to produce flagella via non-motile, but still functional intermediates.
Can I prove these scenarios? Nope. Are they totally out of line? Well, if you look for evidence of these intermediate states, you need to ask whether tubulins are involved in maintaining cell structure in microvilli, whether pilins have utility, whether there are protein transport pores, etc in current organisms. This, of course, is not direct evidence. It is evidence like that that Darwin presented for the eye. It is evocative, possible, and is congruent with natural law mechanisms. But it is the only type of evidence that anyone has in these cases.
Posted 1 Sep 1997 on Usenet's talk.origins by Howard Hershey
It is also difficult to accept that a flagella represents Intelligent Design, when it is so different from a cilia or an undulopodia. And why do archae and bacteria use a very different flagellin? What kind of intelligent designer doesn't re-use designs, or even components?
In my ignorance section, I pointed out some problems with Behe's attack on the article by Russell Doolittle. Doolittle has written his own response which points out that there are animals with simpler molecules, as you'd expect if the molecular evolution happened in one line of descent but not in another. Doolittle ends by showing that lab animals can get along fine without parts of this "irreducible" system.
George Acton wrote a slightly more technical response and says that it's "like reading a discussion of the Shroud of Turin that totally omits any mention of the radiocarbon dating studies."
Behe spends Chapter 6 on the immune system, and on page 137 he talks about scientists who have "gamely" tried to explain the system. The scientific efforts have paid off. There is now a detailed theory as to how the system could have been started. And, there is now experimental evidence that the theory is correct. Work continues, demonstrating that the theory of evolution is fertile, and not (as Behe put it) "sterile".
There is a good analysis of the bombardier beetle at the talk.origins archive.
The main problem with Behe's analysis is that he doesn't seem to know what data to look for. Any evolutionist would have immediately proposed a whole list of things to be investigated. Do we have a tree of descent of related species? Which of them secrete what chemicals? Which ones have specialized bladders? - and so on. All of these would be useful as raw material for constructing hypotheses and for ruling hypotheses out. But Behe just cries out for more detail of the final answer. It's as if he doesn't know how to attack these problems.
This is partly science, and partly not science.
The science part is wrong.
The not-science part surprises me. Dr. Behe is a working scientist, but chose to announce his idea in a popularized work. Subsequently, he has toured, speaking to church groups. He's said that scientists don't accept his views because scientists are anti-religious. Since there are scientists of all religious persuasions, that's lame.
I could guess that he is religiously motivated. On the other hand, he may really know that little about evolution. He has spoken highly of Denton's book, which strongly implies that he didn't notice its many major scientific flaws. And of course, he didn't notice the major flaws in his own ideas.
He certainly doesn't know much about the history of science, to claim on page 243 that the Scientific Method is a prescription for timidity. Historically, a great many people have tried his alternative. They are not much remembered, because the people who used the Scientific Method made all the progress. Notice, please, that I am not saying that atheism is a good idea. I'm saying that if you ascribe some part of nature to intervention by God, you have given up on trying for a more specific explanation. Behe is asking the winning team to steal strategy from the losing team.
Box by John Catalano
Irreducible Complexity and Michael Behe
Molecular evolution and scientific inquiry, misperceived by Robert Dorit
A Biochemist's Response by David Ussery
A Rebuttal of Behe by Clare Stevens
Darwin v. Intelligent Design (Again) by H. Allen Orr
Behe's response to Orr. Notice he says "The concept of irreducible complexity is new", when it was Orr's point that Muller invented it in 1939. The response completely fails to mention Muller, or address Muller's ideas about how evolution creates Irreducible Complexity.
Other responses to Orr's article, including Jerry Coyne documenting how Behe committed "deliberate distortion" when quoting Coyne. Russell Doolittle complains about how he was quoted, and shows that mice with part of the clotting cascade missing were perfectly normal.
Karen Bartelt head Behe speak, and wasn't impressed.
Behe has provided us with an anonymous review he received from a scientific journal.
 Construction of a minimum-size functional flagellin of Escherichia coli, G. Kuwajima, Journal of Bacteriology 170: 3305-3309 (1988)
 Export of an N-terminal fragment of E. coli flagellin by a flagellum-specific pathway, Kuwajima et al, Proceedings of the National Academy of Sciences 86:4953-4957 (1989)
 Reversibility in Evolution Considered from the Standpoint of Genetics, H. J. Muller, Biological Reviews 14 (1939): 261-80. See commentary.
 Redundant Complexity: A Critical Analysis of Intelligent Design in Biochemistry, Niall Shanks, Karl H. Joplin, Philosophy of Science 66 (June 1999), pp. 268-298