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

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July 7, 2010 Tags: Genetics

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

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

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 - #22700

July 20th 2010


I’m sure there is another side the the coin from previous moderators that would tell a different story

My contribution to that thread, as well as similar contributions to prior threads, is the only data. There is no other data. There is no other story, or “side to the coin.” (To be honest, I can’t imagine what you mean by that in this instance.)

I fully understand that you would want to be the judge in your own case.

No, I asked YOU to express YOUR judgment in this case. Strictly as an illustration. If you support and embrace DaveScot’s action, then explain to us why you find it reasonable. State the principles illustrated therein that will assist other new participants in avoiding being banned at UD in the first place, as you advised above.

Persistent cuss that I am, I remain hopeful that you will answer my above questions, summarized in #22499.


Reciprocating Bill - #22703

July 20th 2010

BTW, Clive, I don’t see how an account of why you find DaveScot’s actions reasonable, and what principles illustrated by his actions you embrace, “undermines” him.


Clive Hayden - #22717

July 20th 2010

Let me clarify. When I’m aware that someone is a sock puppet, I have, in the past, allowed them to continue posting, granted that they are sincerely there for a sincere discussion. Which, it should be noted and remembered, I do not have to allow even for this leniency.  So when I check elsewhere and see that they are not, I use my discretion and ban them again. The ban is fully justified by the fact that they’ve been banned before; I need no other justification. I have allowed sock puppets such as Reciprocating Bill and Nakashima to post comments, though I knew they were sock puppets, in hopes that they would be sincere about their motives, which is, in my opinion, pretty considerate of me, so when I see the way they mock and chide UD and it’s participants at After the Asylum Closes, even though their posting is a privilege considering they’ve been banned before, I ban them for being a sock puppet that should’ve stayed banned in the first place. My justification is that they have already been banned; I don’t need any other justification. If anything I ought to be thanked by you who’ve been banned for allowing a known banned person to continue to post. I am under no obligation to do that.

jerry - #22725

July 20th 2010

Clive:  You said “This is absolutely not true, and if it were true, then there would be no need to create a sock puppet, because all sock puppets would disagree with UD/ID and get banned. Look at the site, you’ll see plenty of dissenting views. “

The only dissenting views you allow are Colbert-like!  Such as “ID:  Great Science, or The Greatest Science?”.  You actually only allow the IDBelievers to disagree about How Many Designers Can Dance On The Head Of A Flagellum…. so don’t pretend that you encourage dissenting viewpoints!

Jesus… I mean The Designer - will send you to hell for lying like that you know.

Reciprocating Bill - #22726

July 20th 2010


Let me clarify…

Clive, we’ve been begging you to clarify.

It would follow from the above that a participant who had never before been banned from UD, and who “minded his manners” while posting at UD, may post whatever he pleases elsewhere (say, at AtBC), however derogatory of UD or it’s participants those external posts may be, and however “insincere” those posts reveal him or her to be. Because they had never before been banned, and their posts at UD conform to requested standards, their posting behavior elsewhere can never constitute justification for banning. 

Is that correct?

CeilingCat - #22782

July 21st 2010

Clive, please don’t let this bunch of Freethinking So and Sos intimidate you into changing Uncommon Descent in any way whatsoever.  UD is a perfect gem!  You are carrying on a proud tradition.  Don’t let anybody stop you.

Always remember that you represent UD’s founder, a proud profesional student (about 19 years of college!), the man who got Robert Sloan fired from Baylor after Sloan rescued him from teaching at a summer camp, the man who personally put the fart noises into a cartoon criticizing Judge Jones, the man who called Homeland Security when Professor Eric Pianka started talking like an Old Testament prophet while accepting the Texas Academy of Sciences Distinguished Scientist of the Year award, the man who invented the Explanitory Filter which proves that God was designed, the man who personally printed the names, home addresses, home phone numbers and personal email addresses of the entire Baylor Board of Regents, who aroused his wrath, the man who personally removed the audio from a video copyrighted by Harvard and substituted his own, the man who believes in the Bible Code, faith healing and that vaccines cause autism.

You have a proud tradition to uphold.  Please don’t let those scoffers stop you!

Dave - #22784

July 21st 2010

Clive wrote:
——“but seeing as how ID is a worthless philosophy designed by charletons to mislead the masses…”

The above statement would get you banned, and you wonder why you’re banned…....
And yet that statement, substituting “Darwinism” or “evolution” for ID, would not get you banned at PT or AtBC. In one place dissenting views, even uncivil ones, are tolerated because they are laughable and easily rebutted. In the other place dissenting views, even civil ones, are not tolerated because they cause panty-twisting and cannot be rebutted. See the difference, Clive?

No, I thought not. Carry on.

DNA_Jock - #22785

July 21st 2010

Clive, if you wish to claim that UD does not ban posters for mere dissent, then either Barry Arrington or yourself need to explain why he banned BGOG, todd, God’s iPod, quaggy and DNA_Jock (and hdx??) in the space of only three hours! see :
for the carnage
Because Barry deletes the ‘offending’ post, it can be tough to tell how ‘offensive’ each final post was. Sometimes, though, a UD regular considers the post is response-worthy, and quotes from the soon-to-be-deleted post (See for example post 31)
Even more insulting to free speech is Barry’s *editing* of posts he disagrees with. Luckily, thanks again to Clive’s quoting, we can learn that Barry’s edit
“Indeed, [SNIP], I do not find organized religion or its written guides in any way uniquely authoritative.” was originally
“Indeed, as hdx demonstrated in his now purged post, I do not find organized religion or its written guides in any way uniquely authoritative”
Here we have a lawyer, of all people, deleting the evidence of his own intolerance.
Earlier, he deleted a reference to a previous BarryA thread, simply because it made him look bad. I wonder why UD has a reputation…

Clive Hayden - #22791

July 21st 2010

Reciprocating Bill,

That is correct. I have never banned a new commenter for the sake of anything written outside of UD. That is absolutely true.

For the rest of you who believe that incivility ought to be allowed, I disagree. There is a morbid internet culture, especially in this debate, that abounds, and is not constructive to a real discussion. If you think it is constructive, then I question your definition of constructive. But I also think constructive discussions are not the intended goal for folks who want incivility. 

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

I am done with this discussion.

Dave - #22794

July 21st 2010

Comment removed by moderator.

Clive Hayden - #22795

July 21st 2010


You’d have to ask Barry about that.

jerry - #22798

July 21st 2010

Clive - re:  “You’d have to ask Barry about that”...

So, when will noted creo-coward Barry A come out from behind the skirts of UD, so that we might actually have an open dialogue with him?

Yeah… I thought so. 


Reciprocating Bill - #22804

July 21st 2010

So, what have we learned?

We learned that Clive has invented a status of Double Secret Probation for people who create new identities at UD after having been banned at any time in the history of UD (this is his invention; UD moderation guidelines are silent on this). Those on Double Secret Probation post only at Clive’s pleasure.

There are no moderation guidelines for those on Double Secret Probation other than those Clive invents. For example, Clive’s whims determine who he will permit to post in a second or third incarnation and who he will not. Further, he invented the requirement that one be “sincere” to post at UD, as evidenced by posting behavior on other sites. Not merely civil, or in conformance to UD moderation rules, but “pure of heart.” Those he deems insincere will be banned again. When they are, Clive will tell himself that the rebanning is justified by their prior banning, however arbitrary or unfounded that prior banning was. Of course, this reasoning permits Clive to ban those on Double Secret Probation for any reason he pleases. Providing StephenB with cover appears to be an oft-repeated example. Clive then cites the prior banning as his justification.

We knew it was something like this.


Reciprocating Bill - #22806

July 21st 2010

Clive worked hard to hide Double Secret Probation. Above we learned from Clive that Reciprocating_Bill was on DSP and THAT is why he was banned.


RB, You had already been banned you as well…I banned Nakashima for being banned before, same with Reciprocating Bill.

But Clive announced RB’s banning with this:

[RB]: “Given that my participation has been serious and respectful…”


You said this yourself:

[Quotes RB from AtBC.]

Bye Bill.

Next post:

And, lest we forget, this gem from Reciprocating Bill…

[Quote from AtBC]


You have banned RB for remarks made on a completely different forum?


JayM…Barry’s moderation policy was one of no name calling and no disrespect, both of which RB was guilty, by his own admission [in a quote on AtBC]


Yes, RB has been banned for discourtesy, you are right. No insulting behavior is allowed by anyone, on either side of the debate.

The astute reader will note that Clive made no mention of prior banning in 4 explanatory statements.

Then he suggests that others have been dishonest.

David vun Kannon - #22815

July 21st 2010


For the rest of you who believe that incivility ought to be allowed, I disagree.

I see that a judgement must be called down upon the poster on UD who called his opponents ‘Darwinitwits’. Onlookers! Clive ‘Ko-Ko’ Hayden, the Lord High Banninator will execute the sentence.

What’s that you say, Bunky? It cuts its own throat? Uncommon Descent doesn’t have a second trombone? Your whale doesn’t speak Chinese?

Don’t worry Bunky. Look at the bright side of UD. Godot will be there tomorrow. And if not, surely the day after. You wait. Just you wait. And see. I heard crowds yelling “Waterloo!” in the distance. I heard the fart noises of victory. Or perhaps it was the wind. He’ll be there tomorrow, just you wait and see.

Clive Hayden - #22817

July 21st 2010

Reciprocating Bill,

Like I said, you were banned for being banned before. I don’t have to make mention of anything to anyone except Barry. I allowed you to post, which I wasn’t under any obligation to do. I, in my vast benevolence, have allowed sock puppets to post, given that their intentions are valid for actual discussion, and not strictly a matter of mockery and fodder for those at After the Asylum Closes. This is, of course, never counted in my favor among folks like you.

As an aside, After the Asylum Closes amuses me to no end, for all that happens there, is talk about us. We, at UD, like Biologos, talk about IDEAS, SCIENCE, CULTURE, CURRENT EVENTS, BOOKS, ETC., After the Asylum Closes only talks about US. It’s bizarre, no doubt about it. If you don’t like reading something, then don’t read it. I can’t imagine eating food that disgusted me, and then expounding at length on how much I couldn’t stand to eat it, every single day.

Clive Hayden - #22819

July 21st 2010


I appreciate your honesty in the above comment. It tells me how you really feel and what you really think, and doesn’t hide behind a thinly veiled false veneer of civility. Guys like you will flatter only to get what you want, and when you see you’re not getting what you want, the hidden claws come out. It’s classic. Many times I’ve seen a thinly veiled disgust from you, I think you can’t really hide it because you can’t really help it. I’m glad you’re finally honest enough to step up. I respect you more now as a man.



Dave - #22840

July 21st 2010

Clive prevaricates:

We, at UD, like Biologos, talk about IDEAS, SCIENCE, CULTURE, CURRENT EVENTS, BOOKS, ETC.

Bwaahahhaha. In your dreams. The current top topic is PZ Myers and how you all hope he quits blogging. And anytime someone does try to discuss SCIENCE, it gets drowned out by Chesterton/Lewis, the Bible, Gordon Mullings’ logorrhea, or BA^77’s 27 million ways that materialism leads to YouTube videos.
Clive further prevaricates:

After the Asylum Closes only talks about US.
Au contraire. We also discuss other IDiot sites like Telic Thoughts, Corny Hunter, VoxDay, the DI Biologic Institute, The Design Matrix etc. Other discussions involve food, Wildlife, Evolutionary Computation, the Origin of Life, as well as general SCIENCE (Science Break is the current top topic). You’re invited to join in on any of those topics, and to bring Barry A if he promises not to try to ban anyone. It won’t work over there.

Maya - #22841

July 21st 2010

Clive Hayden writes (#22817):
“As an aside, After the Asylum Closes amuses me to no end, for all that happens there, is talk about us.”

Actually, what happens at AtBC is people mocking and laughing at UD, for very good reasons.

Dave at #22784 makes a very strong point:
—begin quote—
Clive wrote:
“but seeing as how ID is a worthless philosophy designed by charletons to mislead the masses…”

The above statement would get you banned, and you wonder why you’re banned…....

And yet that statement, substituting “Darwinism” or “evolution” for ID, would not get you banned at PT or AtBC.
—end quote—

Ponder the difference between the two venues, Clive.  Which demonstrates the most confidence in their arguments and greatest commitment to truly open discussion.

Your behavior at UD proves you to be an intellectual coward.  You have the right to censor your blog that way, of course.  Just don’t be surprised when people point out your cowardice and hypocrisy.

Maya - #22843

July 21st 2010

While I’m here, Clive, please explain why I was banned for the following:
—begin quote—
DaveScot wrote:
“ID predicts that no evolution of complex structures will occur by chance & necessity within the temporal and geographical constraints imposed by the earth due to the statistical improbabilities involved.”

What is the ID theory that predicts this?  The reason I ask is the following statement from a senior member of the Discovery Institute, Paul Nelson:

“Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem.”

DaveScot continues:
“ID can be falsified by the observation of a single complex structure built by mechanisms of chance & necessity.”

What, exactly, constitutes a “complex structure”?  Michael Behe has admitted that a new viral protein-viral protein binding site has evolved in HIV.  This resulted in new function (an ion channel), a form of complexity that Behe claimed was beyond the “Edge of Evolution”.  That falsifies your prediction.
—end quote—

This post got me banned by the censor Patrick.  Uncivil?  I think not.  Asking questions that ID proponents can’t answer?  Definitely.

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