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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

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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David vun Kannon - #22059

July 16th 2010

With respect to Rich’s comment @ 21297,

If you are counting people, not handles, then you should do the same for number of messages. Comparing ‘people banned per month” to “messages per month” is disingenuous. My rough estimate is that UD runs about 2-3,000 comments a month, but most are by the same small core of posters. If bans run at one a month, it is one compared to forty or fewer regulars. Perhaps twenty.


Reciprocating Bill - #22079

July 16th 2010

Clive -

What is apparent in your moderation decisions is that moderation at UD serves to limit or end discussions involving valued regulars when that regular’s argument is going badly. Don’t bother denying this.

But it’s all good. It is “your” blog, and you are free to moderate it as you wish - including the enunciation of moderation policies that you subsequently ignore or contradict by your actions, and/or apply in a biased and transparently self-serving manner.

By moderating in this way you cement UD’s reputation, already indelible, as unable to mount a defense of its core positions that stands up to critical scrutiny. As this characterizes ID generally, there is little to be done about that.

RB


David vun Kannon - #22082

July 16th 2010

Clive,

As RB says @22079, it is obvious that your moderation extends special protection to Stephen Bussel and Denyse O’Leary. In the interest of the whole truth, why is that?

You are correct that I would enjoy returning to UD, preferably as Nakashima or myself. I ask the above question from a desire to conform my behavior to your policies.


Clive Hayden - #22101

July 16th 2010

I see that all the usual suspects have come out of the woodwork. Notice how all of you have been banned, with the exception of Arthur Hunt.

Seversky,

You were banned for calling for the Discovery Institute’s destruction, an institute made up of people, one of which is William Dembski, the founder of the blog on which you called for destruction. If that isn’t incivility, I don’t know what is. You may as well call for the destruction of the church that members who own this blog attend. I’m sure you wouldn’t mind that actually. 

Nakashima,

Why can’t you be honest about how many times you’ve been banned without me having to come to this thread and correct you?

Here’s a gem from After the Asylum Closes from you:

“It is a good thing that you can’t rearrange the letters of my username here to spell “D*ckless Pinhead”, you might accuse me of being the entire cast of UD.” 

Yeah sure thing David, you’re only interested in honest dialogue to further the discussion and have only mutual respect in mind, right? I mean, that’s obvious.


David vun Kannon - #22110

July 16th 2010

Hi Clive,

The number of times I’ve been banned wasn’t particularly germane to the topic of why I was banned most recently, a topic you’ve failed to address. Rich’s comment above was that Seversky and Nakashima know why they’ve been banned, and that is what I’ve been reacting to.

“I’ll answer that. If PZ — or anyone else — came here and minded his manners, he would be more than welcome. I’m not holding my breath though, because PZ does not appear to be able to rise above adolescent name calling.” - BarryA, as quoted above.

Nakashima’s comments on UD have been consistently clean and civil, and while I’ve had the privilege of posting on UD, I’ve kept my comments on AtBC to a minimum, out of respect for the desire to continue posting clean and civil comments on UD. Now that you’ve banned me, I admit to being freer in my criticism and language.

What of it, Clive? Was it said on UD?  Was it uncivil? More uncivil than fart noises for a Federal judge? Was it more uncivil than calling Jews psychotic and Christ killers?

If you want the status quo ante, unban Nakashima. Medecins Sans Frontiers will thank you.


gingoro - #22113

July 16th 2010

Clive Hayden @22101

Clive IMO part of the problem at UcD is the combativeness of some of the writers of the main posts, especially when they start responding to comments.

Take Ms O’Leary for example:

http://www.uncommondescent.com/evolution/coffee-which-of-these-theories-is-not-like-the-others/

I have been described as a friendly critic of ID and if you look at my comments I did not come across as a strong supported of neo Darwinism.  Yet Denyse called me anathema.  I suggest UcD clean up it’s own act and that doing so might yield more polite commentators.  When I read her comments my initial reaction was to come back very strongly, fortunately by grace I was able to stifle that to a large extent. 

Dave W (wdwllace @ sympatico ca)

ps It appears that one is supposed to be able to subscribe to comments on UcD via RSS.  I have devoted some time and have never been able to get it to work even in Google Reader under IE or Firefox.  I subscribe to BioLogos comments in Postbox my email reader which also serves as an RSS reader.  Very useful in that if I prefer not to see Seversky’s or Nakashima’s comments I can filter them out even before you as moderator do.  Never have been able to find an email for the UcD webmaster.


Clive Hayden - #22119

July 16th 2010

David,

Correction, you’ve been banned four times, not three, and the list may continue to grow. It is enough to ban a sock puppet for the sole purpose that they are a sock puppet and have been banned before. You were banned by Dave Scot and Dr. Dembski. You ought to be thanking me for giving you the opportunity to post under your Nakashima moniker, given that I knew who you were the entire time, and I let you comment nevertheless, even after you had insulted Denyse O’Leary.


“What of it, Clive? Was it said on UD?  Was it uncivil? “

Did you just ask “was it uncivil”? Is that a serious question? You cannot be serious. This dialogue will go no where unless you come to realize what constitutes civility and incivility. If you don’t “see” proper conduct from the outset, no argument can bring you to it. Morality is always the premise.

Your argument against StephenB is historically inaccurate. But you probably don’t believe that there was a man named Jesus, who was tried at night and sentenced to death in a travesty of justice by the Jewish leadership; you probably believe He didn’t exist at all, yet you claim to school others on the events surrounding His death and the Jewish role in it? Very consistent.


Clive Hayden - #22123

July 16th 2010

David,

Rich’s comment above was in reaction to Alan Fox’s assertion that there is rampant banning occurring at UD, which is simply not true. And now you and Seversky know why you’ve been banned. You would have to ask Dave Scot and Dr. Dembski why they banned you. I reckon if you don’t actually do my job, you can make a lot of wild speculations about what I do, but you should be leery of making them dogmatically.


Reciprocating Bill - #22125

July 16th 2010

Clive:

If you don’t “see” proper conduct from the outset, no argument can bring you to it. Morality is always the premise.

BarryA clearly, unequivocally articulated the principle that conduct elsewhere has no bearing upon one’s posting privileges at UD, so long as one “minded one’s manners” on UD. He cited PZ Myers as a possible example.

Now you state the opposite: “uncivil” language directed at UD on blogs other than UD is grounds for exclusion from UD.

Indeed, you banned me (as Reciprocating_Bill) from the very thread on which Barry articulated that policy, citing my posts elsewhere as justification. There I was quite up front that one purpose of my posts was to test the accuracy of BarryA’s newly articulated policy. UD failed the test: you were unable to sustain the policy he articulated for even a single thread.

For the original policy see:

http://www.uncommondescent.com/intelligent-design/a-word-about-our-moderation-policy/#comment-307882

My subsequent banning in direct contradiction to that policy:

http://www.uncommondescent.com/intelligent-design/a-word-about-our-moderation-policy/#comment-309298

Which is it? Are you guided by a principle vis this issue, or aren’t you?


David vun Kannon - #22128

July 16th 2010

Clive,
In what way do I now know why Nakashima was banned? For a remark I made after I was banned? For not being Asian? For reminding readers of UD that StephenB can be casually anti-Semitic and get away with it? I’m afraid your remarks here have not clarified your reasoning.

I don’t believe that I have made any speculations, wild or dogmatic, about how you do your job. I’ve asked you to clarify how you do your job, and I hope that by asking civily and getting a civil answer, I might be able to participate in the UD discussions in the future.


David vun Kannon - #22130

July 16th 2010

Hi Clive,
Sorry I missed your earlier post. Yes, I agree that I’ve been banned four times in toto at UD, once as DvK, Pendulum, and twice as Nakashima. I’m glad that is clear. I’ve also been unbanned once, and would like to make that twice.

I agree that someone using a new username, and all posters in general, do post at the whim of the moderators. I am grateful, and I believe I have said so on UD, quite sincerely. I’ve also apologised publically on UD to Mrs O’Leary.

“If you don’t “see” proper conduct from the outset, no argument can bring you to it. Morality is always the premise. “

And yet, like fart noises in a Flash animation, incivility sometimes escapes. No, the question was not serious, it was rhetorical.

My argument against StephenB is that he used the terms ‘psychotic’ and ‘neurotic’ in an indiscriminate way against Jewish groups, and repeated the slander that together they killed Christ. There is no Gospel story that justifies labelling an entire Jewish sect psychotic.

I accepted Christ at 15 and converted to Orthodox Judaism at 25. I’ve looked at the life and death of Jesus from several perspectives. Don’t speculate about my beliefs, they are irrelevant to what StephenB said.


Alan Fox - #22133

July 16th 2010

Clive Hayden:

Rich’s comment above was in reaction to Alan Fox’s assertion that there is rampant banning occurring at UD, which is simply not true.

Wow, Clive! I think anyone who has nothing better to do can read UD and the thread dedicated to it at “After the Bar Close” and make their own assessment as to your integrity, especially with respect to leaving comments in perpetual moderation. Banning getting on for 2 commenters a week this year is pretty fair going considering the rapid wane in interest in"Intelligent Design”.

But as others have said UD can operate however it wishes. Please feel free to carry on.


Rich - #22135

July 16th 2010

David vun Kannon/Nakashima:

I wish you had mentioned your Christian and Jewish history on Uncommon Descent.  As either a Christian or an orthodox Jew, you would be required to affirm the doctrine of Creation, which implies acceptance of at least a degree of design in nature (even if it doesn’t imply that the design is scientifically detectable).  I never got a sense of sympathy for design from any of your posts at UD.  Why hide your candle under a bushel, when letting it shine could facilitate friendlier discussion and prevent misunderstandings?

In any case, if you and Clive can come to some kind of agreement, and if you are allowed to return to UD as Nakashima, I would be most interested in hearing how your thoughts about design and evolution connect with your orthodox Judaism.  There are not nearly enough Jews posting on UD (or for that matter here).  I think that much religion-science discussion these days suffers from lack of Jewish input.


Clive Hayden - #22140

July 16th 2010

David,

“In what way do I now know why Nakashima was banned?”

Because Nakashima is you, old friend, and you had been banned three times before. You act like Nakashima is a separate person. I can’t take your reasons for wanting to post at UD seriously David, I would like to, but I just can’t, given what I’ve read when you’re free to say what you really think on After the Asylum Closes, and what you say there is the opposite of your stated reasons for posting at UD here.

Alan,

After the Asylum Closes can say whatever they like, individual ignorance of my moderating does not become knowledge by virtue of being in a group of other individuals ignorant of my moderating.

Reciprocating Bill,

You had already been banned you as well.


David vun Kannon - #22144

July 16th 2010

Hi Rich,
My interest at UD is in discussing the science of evolution and the possibility of a science of intelligent design. I’m not there for the culture war, and I’m not there to encourage ID to stay in the nest of its religious origins. That means helping people move down the path to rigor and precision in their thinking, and avoiding the cheap rhetoric. I’ve mentioned some aspects of my own religious journey a few times on UD, but I’ve never seen it move the conversation in a very positive direction.

Sure, I’d like to post again as the wily Nakashima. I haven’t given up my goal of becoming the first “loyal opposition” white box poster there. It’s totally up to Clive, though.

I agree that BioLogos, to the extent that it wants to explore theistic, rather than explicitly Christian, perspectives, could benefit greatly from interaction with the Torah U’Madda philosophy of Modern Orthodoxy.


Reciprocating Bill - #22145

July 16th 2010

Clive:

You had already been banned you as well.

You twice explicitly cited posts at AtBC as your reason for banning me at that time. Now you are stating that there was another reason? This sort of back fill is why you have no credibility, Clive.

But here is your chance to do right. I was banned in October 2006 (IIRC) by DaveScot for no other reason than I pressed a point regarding ID and an equivocal definition of irreducible complexity. There was absolutely nothing personal in any of my posts. Nor was the banning justified by my posting at AtBC - for the simple reason that, at the time, I was unaware of AtBC. Like many at the time, I discovered and began contributing to AtBC only after my entirely reasonable and cordial attempts to participate at UD resulted in my banning. I made no attempts to return to UD until BarryA’s announcement of a new moderation policy, at which time I returned as “myself,” e.g. Reciprocating_Bill.

As this original banning was unjustified under any version of UD’s policy, nor any current version, you should rescind your decision and restore my posting privileges as Reciprocating_Bill.

Incidentally, you evade answering my question vis this policy, above.


David vun Kannon - #22147

July 16th 2010

Clive,

So you’re saying that at the precise moment we start to discuss StephenB’s casually anti-Semitic remarks, an amazing coincidence takes place and you can no longer tolerate the presence of the thrice banned? Thanks for clearing that up. The unaware might have thought you were simply trying to protect one of your favorites.

Since that conversation was so unfortunately cut short, why not continue it here? I once heard a man say, morality is always the premise. So Clive,what was the morality of calling the entire sect of Pharisees psychotic? What was StephenB’s ‘moral premise’?


Seversky - #22180

July 17th 2010

Clive Hayden - #22101

July 16th 2010

Seversky,

You were banned for calling for the Discovery Institute’s destruction, an institute made up of people, one of which is William Dembski, the founder of the blog on which you called for destruction. If that isn’t incivility, I don’t know what is. You may as well call for the destruction of the church that members who own this blog attend. I’m sure you wouldn’t mind that actually. 

As I suspected, Clive, you tend to see what you want to see rather than what is there.  What I actually wrote on June 19 was:

I share Matheson’s opinion of the Discovery Institute but he should have remembered Voltaire’s dictum: “I disagree with what you say but I will defend to the death your right to say it”

In other words, while I sympathized with Steve Matheson’s opinion of the Discovery Institute I most certainly did not call for its destruction, nor any other church for that matter.  Quite the opposite in fact.  I was arguing that, however offensive we might find its views and propagandizing, we were bound to defend its right to behave that way if we believed in the right to free speech - a view of the right not shared by the moderators at UD, apparently.


Reciprocating Bill - #22191

July 17th 2010

Clive, 3/13/09:

From reading the comments by Bob O’H on the other thread, he should not be re-instated. This should be obvious to anyone with a modicum of decency…

David Kellogg (also now banned) asked:

A person’s behavior on every forum must match their expected behavior on this forum?

Clive:

...if that person’s “behavior” on the other forum is directly insulting to those on this forum–yes.

BarryA 1 1/2 hours later:

CannuckianYankee writes: 
“I’m just wondering Clive, Let’s say a person such as, oh, PZ Meyers wanted to post here and he kept his language cordial and non-insulting, would he be welcome to post? ...I might enjoy seeing how others here would challenge him.”

I’ll answer that. If PZ — or anyone else — came here and minded his manners, he would be more than welcome. I’m not holding my breath though, because PZ does not appear to be able to rise above adolescent name calling.

Come on, Clive, which is it?

http://www.uncommondescent.com/intelligent-design/a-word-about-our-moderation-policy/#comment-307692


Reciprocating Bill - #22192

July 17th 2010

Retry, formatting intact:


Clive, 3/13/09:

From reading the comments by Bob O’H on the other thread, he should not be re-instated. This should be obvious to anyone with a modicum of decency…

David Kellogg (also now banned):

A person’s behavior on every forum must match their expected behavior on this forum?

Clive:

...if that person’s “behavior” on the other forum is directly insulting to those on this forum–yes. I won’t re-instate Bob O’H, he’s insulting. This is obvious. I don’t see why it needs to be defended.

BarryA 1 1/2 hours later:

CannuckianYankee writes: 
“I’m just wondering Clive, Let’s say a person such as, oh, PZ Meyers wanted to post here and he kept his language cordial and non-insulting, would he be welcome to post? ...I might enjoy seeing how others here would challenge him.”

I’ll answer that. If PZ — or anyone else — came here and minded his manners, he would be more than welcome. I’m not holding my breath though, because PZ does not appear to be able to rise above adolescent name calling.

Come on, Clive, which is it?


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