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Behe’s B-Cell Bravado, Part 3: Failure to Engage the Evidence

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July 7, 2010 Tags: Genetics
Behe’s B-Cell Bravado, Part 3: Failure to Engage the Evidence

Today's entry was written by Kathryn Applegate. You can read more about what we believe here.

Many non-scientists are unaware of the importance or extent of “the scientific literature.” In the geeky world of science, success doesn’t depend on social prowess or earning power (thankfully!), but on one’s publication record. It’s hard to get published—to do so means making a significant contribution to the field, as judged by a panel of anonymous reviewers. Most people have nightmares about being chased or drowning. Scientists have nightmares about their papers getting rejected.

The main database for accessing the biomedical research papers, called PubMed, contains over 19 million articles. If you search PubMed for irreducible complexity, you’ll get 11 hits, none of which represents a peer-reviewed piece of work showing evidence of an Intelligent Designer. Most of the hits are commentaries on the Intelligent Design (ID) movement itself or attempts to “reduce” irreducible complexity. A couple of them are totally irrelevant.

Could this mysterious absence from the literature be a result of a conspiracy by Big Science to deliberately marginalize the work of people like Michael Behe? Though ID proponents often try to make this case (just watch Ben Stein’s Expelled), I think it’s very, very unlikely. But let’s give them the benefit of the doubt. If ID theory is scientific in nature, we can expect its leaders to engage scrupulously—as all scientists must—with the literature.

Unfortunately, Michael Behe does not have a great track record in this department. Consider his 1996 book Darwin’s Black Box. When reading the chapter on the immune system, for example, I kept expecting him to interact with the evidence for the gradual development of the antibody recombination system. The transposon hypothesis, which we examined in detail in Part 2, is a well-tested model for how this system could have originated. I couldn’t wait to see what Behe would say about it! His response was more than a little disappointing. He does refer to the model, at least indirectly, but only by discounting a two-page commentary—the purported “best efforts” in the field—as mere speculation:

[The authors] make a valiant stab at accounting for the components [of the antibody diversity generation system], but in the end, it is a hop in the box with Calvin and Hobbes. The authors speculate that a gene from a bacterium might have luckily been transferred to an animal. Luckily, the protein coded by the gene could itself rearrange genes; and luckily, in the animal’s DNA there were signals that were near antibody genes; and so on. In the final analysis the authors identify key problems with gradualistic evolution of the immune system, but their proffered solutions are really just a disguised shrug of their shoulders (137).

Seriously, a hop in the box with Calvin and Hobbes? If you search Pubmed for RAG transposon, you’ll get 18 hits, and they’re all relevant to the evolution of the immune system. More papers deal directly with the data for the transposon hypothesis than for the much broader topic of irreducible complexity! The top two hits are recent reviews, each of which cites dozens of papers. And the first paper ever to propose the transposon hypothesis (Sakano et al. Nature 1979, which doesn’t even appear in this narrow search) has been cited hundreds of times in peer-reviewed publications.

Questions certainly remain about the details of the transposon model, but Behe makes it sound like a pie in the sky idea with no supporting data. He writes, “We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system” (138). This is patently false. Behe may not like the answers, but he misleads the public when he suggests they don’t exist.

Nearly 15 years have passed since Darwin’s Black Box first came out. During that time, scientists have collected some of the most compelling evidence for the transposon hypothesis (see Part 2). What has Behe said about this new data?

In 2005, he testified in a now-famous Dover, Pennsylvania, courtroom in favor of teaching ID alongside evolution in public schools. Behe maintained his previous position: “The scientific literature has no detailed testable answers on how the immune system could have arisen by random mutation and natural selection.”

The judge, John E. Jones, wrote in his decision that Behe “was presented with 58 peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution…” Jones ultimately ruled against teaching ID in classrooms, in part because of the impossibly high burden of proof Behe demanded. In 2006, the 10th anniversary edition of Darwin’s Black Box appeared, featuring a new afterword. While Behe cleared up a few apparent misconceptions about irreducible complexity, he stood by the original text as a whole:

Despite the enormous progress of biochemistry in the intervening years, despite hundreds of probing commentaries…,despite implacable opposition from some scientists at the highest levels, the book’s argument for design stands. Other than updating the list of my children in the Acknowledgements…there is very little of the original text I would change if I wrote it today (255).

Specifically about the immune system, Behe mentioned one new paper from 2005, but only to reemphasize that nothing in his thinking had changed:

Whatever interesting things [the 2005 paper] speculated about gradual evolution, however, it had nothing to say about Darwinian evolution. In fact neither Darwin’s name nor any derivative word appeared in the paper. Nor did the phrase “natural selection” appear; “selection” is used once.” “Mutation” appears twice, but the envisioned mutations are not specified (269).

This sort of defense is peculiar. Behe counts words when he should be grappling with the data. Interestingly, he implicitly admits that a gradual evolutionary process may be sufficient to explain the origin of the irreducibly complex immune system, but he contrasts such a process with Darwinian evolution, by which he means mutation and natural selection.

Recall the quote I referenced in my last post, in which Behe lays out the criteria for detecting design:

The laws of nature can organize matter…The most relevant laws are those of biological reproduction, mutation, and natural selection. If a biological structure can be explained in terms of those natural laws, then we cannot conclude that it was designed. Throughout this book, however, I have shown why many biochemical systems cannot be built up by natural selection working on mutations: no direct, gradual route exists to these irreducibly complex systems… (203).

The transposon hypothesis outlines a possible gradual route to an irreducibly complex system, and it relies entirely on the laws of reproduction, mutation, and natural selection. Nevertheless, Behe remains unconvinced. In his mind, to explain the origin of an irreducibly complex system entirely in terms of natural laws, one would have to show that the steps were in fact unguided.

Such a requirement can be seen more clearly in his 2009 letter to the editor at Science, written in response to a news focus article about the origins of the immune system. Science chose not to publish the letter, so Behe posted it on the ID blog Uncommon Descent. He wrote:

Darwin’s chief contribution was not the simple idea of common descent, but the hypothesis that evolution is driven completely by ateleological mechanisms, prominently including random variation and natural selection. Intelligent design has no proper argument with the bare idea of common descent; rather, it disputes the sufficiency of ateleological mechanisms to explain all facets of biology…

Many scientists agree with Behe that evolution may have been guided in some mysterious way by a Mind. But whether or not the methods of science could ever rigorously detect teleology—mindful purpose—by studying the physical world is hotly debated. Most working scientists I know do not believe science is equipped for such a task.

Questions about teleology are fascinating, but today I’m concerned with just one thing: whether or not Behe has sufficiently engaged with the scientific literature. If I had read his book without any prior knowledge of immunology (or the other topics he covers), I’m pretty sure I would be left with a deep distrust of scientists and the scientific process. I think that’s a pity.

Kathryn Applegate is Program Director at The BioLogos Foundation. She received her PhD in computational cell biology at The Scripps Research Institute in La Jolla, Calif. At Scripps, she developed computer vision software tools for analyzing the cell's infrastructure, the cytoskeleton.

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Reciprocating Bill - #22844

July 21st 2010


Like I said, you were banned for being banned before.

It’s banning all the way down. And that’s your defense!

Carry on, Clive.

Clive Hayden - #22846

July 21st 2010

Reciprocating Bill,

It’s absolutely true, if you would like to take up why you were banned in the first place, take it up with the person who banned you in the first place.

Yours Truly,


Reciprocating Bill - #22847

July 21st 2010


It’s absolutely true, if you would like to take up why you were banned in the first place, take it up with the person who banned you in the first place.

So, if DaveScot, himself banned from UD, recants my banning, you’ll reinstate me?



unapologetic catholic - #22848

July 21st 2010

The discussion of UD bannings distracts from the main point of the thread.

A review of Behe’s two publsihed books shows a failure to engage the evidence.

Relying on argument by analogy is simply not the way that science is done.

Dover was the ID’ poponents’ best opportunity to present pisitive ID evidence—a failure for ID.

Seversky - #22874

July 22nd 2010

Clive Hayden - #22484

July 19th 2010

I banned Nakashima for being banned before, same with Reciprocating Bill. Seversky did call for the destruction of the Discovery Institute, plainly, by agreeing with Matheson’s call for it’s destruction. I do not defend Seversky’s “right to free speech” for calling for it’s destruction on UD, but do in general, on his own blog or wherever else Seversky would like to say it

Again, while I sympathized with Matheson’s feeling towards the Discovery Institute, I did not agree with or support his call for its destruction.

I’m glad to read that you would support my right to free speech in fora other than UD.  In spite of my little jibe, for which David vun Kannon has rebuked me, I never thought otherwise.

As for UD moderation, if a major criterion is civility then, in my view, a number of people have been banned unfairly.  Not only were they civil by any reasonable meaning f the word but they behaved with exemplary restraint in the face of considerable provocation from ID supporters who were not held to the same standards.  While it is your right, it is hardly to your credit.

CeilingCat - #22889

July 22nd 2010

Clive: “Anyone not previously banned can disagree and critique ID in any way, granting the moderation policy, at UD.

I am done with this discussion.”

Please don’t run away just yet Clive.  I was silently banninated under my real name some time ago.  I’m not sure exactly why because nothing was said to me or anybody else, my login just stopped working.  I had the password and login in my browser and also written down and I’m very sure I didn’t just forget the password or something.

My best guess is that I was banned because I had (politely) corrected one of Denyse O’Leary’s more egregious mistakes the previous day.  The message correcting her disappeared too, although it was there right after I wrote it because I wasn’t on moderation.

Which brings me to my main point: You can command civility and I was always civil.  (Very unlike most of your regular pro-ID posters.)  But you can’t command respect, you have to earn it.  And that collection of ignoramuses and yahoos you’ve collected at UD are never going to earn respect from anybody who knows anything about science.  Just read some of the .sigs on Uncommonly Dense for examples why.

CeilingCat - #22891

July 22nd 2010

Having criticized Uncommon Descent and the people behind it a couple of times, let me now sing their praises. 

Back around 2001, William Dembski started the International Society For Complexity and Design. 

This society is so august and factual and its journal, Progress in Complexity, Information and Design, is so well edited that it has not had to retract or modify one single paper since November, 2005.

Not even the Very Prestigious Journal Nature can beat that record!

Reciprocating Bill - #22907

July 22nd 2010

Clive, I puzzle over your use of “sincere.”

I assure you that my disdain of UD and ID are quite sincere, as I believe ID to be a contemptible sham. My posts (say, as Diffaxial) directly conveyed that attitude in the form of arguments that, while NEVER personal, sometimes relentlessly demolished (I think) those arguments for ID I disdain. I never feigned admiration or respect, although I felt more of both for some regulars than others (e.g., Joe G. deserves nothing but contempt, while I appreciated Vjtorely and said so).

There was no question of “mutual respect”, as I was repeatedly called a liar and a coward by regulars such as UB and StephenB, and generally experienced a drizzle of insults. I never responded in kind. You, in your advocacy of civility, said nothing - then invoked your above described Orwellian moderation philosophy to ban me given the slightest pretext.

Of course, because I wished to post at UD, and was quite aware of your propensity to ban effective critics given the slight pretext, I scrupulously followed the moderations rules.

For that I am “insincere.”

Apparently, you wish that I become even less sincere, and refrain from expressing my disdain for ID in other places and in other ways.

Reciprocating Bill - #22922

July 22nd 2010

“Is quite sincere.”  Victim of editing needed to get inside the restrictive character limitations of this forum.

Stephen Matheson - #22961

July 22nd 2010

Clive, a cursory examination of your site reveals that the moderation policy has little to do with “civility.” This should be obvious, but let me explain.

Others have noted the transparently capricious nature of bannings, which were best explained by Seversky @ 21346:
...the history of banning at UD suggests that it is applied mostly to protect the sensibilities and the theological and philosophical positions of the regulars.  It is evidence that ID is unable to hold its own in open debate…
The regular silencing of critics would be enough to discredit your community with regard to intellectual honesty.

But much more damaging to your credibility is the fact that you proudly proclaim your fealty to civility while ignoring behavior that is anything but. (To borrow your phrase, “If that isn’t incivility, I don’t know what is.”) The sole reasonable conclusion is this: you ban to protect your community, and you cover it with an indefensibly disingenuous appeal to “civility,” a pretense that could fool only the truly blind.

I wish I could offer a suggestion for how you could fix that. My only suggestion is this: stop pretending that your policy advances or values civility.

Clive Hayden - #22963

July 22nd 2010

Reciprocating Bill,

——-“So, if DaveScot, himself banned from UD, recants my banning, you’ll reinstate me?”

I never said that, I said if you wanted a reason why you were banned take it up with the person who banned you. I cannot speak for him. It was before my time. Since I have started I have banned very, very few new commenters. I might moderate them, but I rarely ban anyone new. I would say that 95% of names banned are sock puppets, who, by this point, have signed up so often as sock puppets, they cannot help but say things like “the longstanding laughing stock of UD” or “this is why no one takes UD seriously, it is a joke”, etc. etc., and their disdain gets to the point where is can hardly be controlled. I doubt this will be remedied, for the more they are banned the more resentful they become, the more chagrined and disenfranchised, and all the more mocking will be their underlying tone, as I see instances of all the time. It is all the more telling when I read the absurdity at After the Asylum Closes, which is not very often, only when I want a good reminder of what certain folks really think. This is the real world, with real people, not abstract insults at abstract screen names.


Clive Hayden - #22965

July 22nd 2010

The things said there are so adolescent and so juvenile, that I feel like an elementary teacher watching a school ground scuffle. But I wouldn’t even insult children with the comparison.

I see such inconsistency from people who wish UD to allow for insults and incivility and those who agree that there shouldn’t be incivility but cannot agree as to what is civil. One thing I would hope we can all agree on, that After the Asylum Closes, and many of the posts on this thread, are not civil. Claiming that UD contributors handle snakes and writhe around on the floor is so ridiculous as to merit a big belly laugh. They never would’ve never made it past my moderation, not because they are making an argument, but because they are not making an argument and are intentionally vile and spiteful, in spite of an argument being made by our side. Do I really have to explain that arguments get derailed when this behaviour begins? 

We can hash out only my reasons for moderation, not Dave Scots or anyone else’s, which is what most of the complaints boil down to. I’m willing to answer whatever questions you may have since I became moderator.

Clive Hayden - #22966

July 22nd 2010

Stephen Matheson,

———“The sole reasonable conclusion is this: you ban to protect your community, and you cover it with an indefensibly disingenuous appeal to “civility,” a pretense that could fool only the truly blind.”

I invited you through an email to come join us at UD and add your thoughts and comments. You declined. I am not protecting my regulars except as insofar that they are vilified and derided in general, but that protection is for everyone, you included. I have moderated some of the regulars that are on the side of ID, such as Bornagain, jerry, and joseph, to name a few. You really have no idea what you’re talking about Mr. Matheson, as you absolutely couldn’t without standing behind me watching over my shoulder every day I moderate. Who was the last person I put into moderation? Who was the last person I took out of moderation? How often are comments approved that are in moderation? How many contributors do we have in general, not just right now, but overall? How many are free to post that are purely ID critics? How many people have been banned in the last year? In the last month? I don’t want a lot of hand waving, I want answers from someone who claims to have them.

Clive Hayden - #22967

July 22nd 2010

Reciprocating Bill,

——“Here is an excerpt for 12 year olds:”

——“30 years later, StephenB alone on a park bench, clutching his cane, muttering.

——“Then I said, anything that begins to exist must have, uh…uh… a something. A cause! Ha! By cracky Diffaxitive I got you there, that’s what I said! I think that’s, I think that’s what I said. Heh. I said, heh heh. That Diffixative.”

——”(P, 132, Philosophy in Circles. See also p. 76-79, Philosophy by Definition.)”

That stuff is offensive, RB. I reject your above contention of scrupulously following all moderation policies for the sake of honest and sincere discussion. The above is a mockery, plain and simple. You might try to convince folks here otherwise, but I know better.

Stephen Matheson - #22972

July 22nd 2010

Clive, two simple questions. The prelude: I just read your excerpts of Reciprocating Bill’s misdeeds. I take it that he has been banned for them. If this is incorrect, let me know. Assuming I’m correct, then my first question: do you ban/moderate all commenters who type “offensive” comments like Bill’s?

Second question: would you like to discuss the environment into which you invited me (as you mention above)? Would you like to revisit that “discussion” and explain how your standards of “civility” were applied there?

Gregory - #22977

July 22nd 2010

In no way advocating UD as a place to discuss at a higher level than BioLogos or ASA, it is quite obvious S. Matheson is a hypocrite. He wrote: “you ban to protect your community.” Otoh, Matheson ‘goes silent to protect *his* community.’

Matheson is a ‘universal evolutionist.’ He simply cannot come up with “things that don’t evolve.” In so doing, he ‘privileges’ his own field at the cost of other fields.

This is a person who has shown that he *wants* an ‘unequal’ playing field; he doesn’t care *enough* @ human-social sciences to read their contributions to the study of ‘change’, or what he calls ‘evolution.’ To me, this is a sad state for the evangelical Christian church in America to have reached.

Folks like Venema, Applegate, Held, J. Martin, etc. Lost to the bigger picture! Mere specialists.

If you want to correct me, I invite Venema, Applegate, Held et al. to finally address questions I’ve asked them re: ‘evolutionISM’ as an IDEOLOGY. Silence! - where the story ends for most natural-physical scientists. They know almost NOTHING @ ideology.

K. Giberson could at least give these folks a lesson on this, if they would get off their empiricist horses & listen to him. That doesn’t seem likely.

Clive Hayden - #22982

July 22nd 2010

Stephen Matheson,

No, comments like that always alert me to the fact that the person may have been banned before, so I start to investigate, and sure enough, he/she had been banned before.

The atmosphere at UD was certainly critical, but not uncivil to anyone contributing. Had you commented, you would have been a contributor, but you wouldn’t. You’re still more than welcome to, I can start a new entry just for you in the context of the previous entry you alluded to. Does that sound like something that would interest you? I’ll even unban Seversky if you do, given that he agrees and disagrees with you.

Gregory - #22985

July 22nd 2010

Actually, Clive, I just returned to UD to make 2 posts this month after someone at BioLogos linked the thread there @ Dr. Applegate, whom I quite respect (though my thoughts @ ‘bigger picture’ above remain). I was banned before DScott by none other than Dembski himself because I questioned him @ his *revolutionary* credentials.

& for the record, Denyse O’Leary is a faithful quack, not worth much time other than journalistic sensationalism. I admire other Canadian Christian journalists much more genuinely. In fact, I have no admiration for O’Leary at all & think she is (xitri) fox-like in capitalising on the very real ‘desire to understand science’ among Christians.

There at UD this month, I was referred to as ‘gestapo police’ & other totally inappropriate things. You have a few people at UD who are quite obviously ‘sheltered’ from the global scientific community.

I have participated in scientific conferences in (still only) more than 5 countries & have published peer-reviewed articles in journals based in 3 countries. I am certainly not ‘Americo-centric’ as the IDM quite obviously & indisputibly is (though there are ‘sympathizers’ in several non-American countries). Why your self-justification?

Reciprocating Bill - #22986

July 22nd 2010


That stuff is offensive, RB.

Thank you for providing the opportunity for me to underscore your hypocrisy. The bit of snark you quote above was preceded by (in that thread and others) a very lengthy and intense discussion between myself, StephenB, and RoB. In a single thread StephenB and Upright Biped directed the following our way:

StephenB:  “Did you notice that Diffaxial just spent 633 words @180 responding to your comment without once addressing the question.”

Upright Biped: “It is a personal “skill” that Diffy excels at. Perhaps it is his only one. (It is certainly not logical consistency, nor is it intellectual courage)...”

UB: “I have little tolerance for people like Diffaxial who never allow themselves to be questioned. His state of mind is evident in the willfully incessant demands he places upon the conversation itself. It’s a coward’s weakness.”

StephenB: “I thought surely this would be the time when you would summon up the intellectual courage to take on the issue.”

“Why should I respect the intellectual timidity that will not keep its own implied promise?”

“Clearly, you are the one in need…of an injection of intellectual honesty.”

(continued below):

Reciprocating Bill - #22987

July 22nd 2010


(StephenB to RoB): “You are lying. I made no such statement”

“Personally, I think people should be banned for lying.”

“Forget about that last comment about banning. I am content to expose the lie.”

“I am not avoiding it. The premise is a lie.”

(StephenB to Diffaxial):  “All you can do it claim a contradiction, or rather join in on the lie.”

“Thus, you are lying. No surprise.”

“That makes both of you dishonest.”

“Diffaxial blathers on for hundreds of words ………”

“Like Diffaxial, you neither understand nor can apply the logic you claim to hold so dear.”

“Your ignorance is truly astounding.”

These remarks, and similar remarks elsewhere, were the context of the remark of mine you quote above.

Did you, Mr. Civility, step in? Did you ban StephenB or UB? Did you ask them to cease and desist with these personal attacks?

You did not. However, in response to my imagining StephenB muttering on a park bench, you banned me. Your actions (and lack thereof) speak for themselves.

For those interested, the thread is here:


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