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Behe’s B Cell Bravado, Part 1

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June 11, 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 1

In my last couple of posts, we examined a classic example of evolution in action—the production and selection of antibodies. Evolution in the body is a documented reality, but how did the process for generating antibodies come about in the first place?

Intelligent Design proponent Michael Behe says scientists don’t have the faintest idea. In his 1996 book Darwin’s Black Box, he laments, “Although great strides have been made in understanding how the immune system works, we remain ignorant of how it came to be” (136). As evidence, he cites two brief articles (in his view, the field’s “best efforts”) before dismissing their conclusions out of hand. He continues, “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).

But is science really silent on this topic? So much blood, sweat, tears, and NIH money have been spent on the study of the immune system that a complete lack of answers about its beginnings would, as Behe suggests, mean doom for evolutionary theory. The truth is, according to Web of Science, even by 1996 hundreds of peer-reviewed papers had been published on the subject, each contributing a tiny piece to the overall puzzle.

Quick review: components of the antibody diversity system

Behe argues that three aspects of the immune system—clonal selection, antibody diversity, and the complement system—are irreducibly complex and pose “massive challenges to a putative step-by-step evolution” (138).

Because we have already examined how antibody diversity is generated, we will limit our discussion to the evidence for how this ingenious system might have arisen. Much more could be said about other aspects of the innate and adaptive immune responses.

Recall that the genome contains several clusters of gene segments (red and green in the figure below), each of which has tens to hundreds of members. In B cells, proteins encoded by two Recombination Activating Genes (RAGs; blue) join together one member from each of the clusters by excising the DNA between them. The genome of each B cell is thus irreversibly altered in a unique way, depending on which segments are joined, such that the recombined gene segments code for the antigen-binding site of that B cell’s antibody.

RAG1 and RAG2 can’t bind just anywhere on the DNA; they recognize special sequences called Recombination Signal Sequences (RSSs; orange and yellow). RSSs are found flanking each gene segment, similar to special cues we use in grammar like capitalized words at the start of sentences and punctuation marks at the end. The RAG proteins home in on two randomly-chosen RSSs, bring them physically close to one another, and cleave the double-stranded DNA at both gene-RSS junctions. DNA repair machinery then repairs the break, joining the two gene segments together and the two RSSs together. The closed loop of DNA containing the RSSs gets removed, while the recombined gene is now ready to code for an antibody..

Behe’s mistaken assumptions

Behe argues that a minimally functional antibody diversity system needs three components: the antibody genes themselves, start and stop signals (like RSSs), and machinery to cleave and rejoin the DNA at the signals (like RAG and the DNA repair proteins). He can’t imagine how a multi-component system could have arisen by a gradual process, because each component is dependent on the other two for the whole shebang to work.

From the start, Behe makes the faulty assumption that antibody receptors incapable of recombination would be useless. He writes:

A primitive system with only one or a few antibody molecules would be like the propeller turning at one revolution per day: not sufficient to make a difference... Because the likelihood is so small for the shape of one antibody being complementary to the shape of a threatening bacterium—perhaps one in a hundred thousand or so—an animal that spent energy making five or ten antibody genes would be wasting resources..." (130-1).

What Behe fails to recognize is that many, many receptors in the immune system do their jobs without gene arrangements. These receptors bind to molecules commonly found on the surface of harmful microbes. In fact, some 90% of animal species on the planet don’t even have adaptive immunity, so antibody production by a gene rearrangement mechanism cannot be imperative for life (though humans and other vertebrates are quite dependent on it now). Contrary to Behe’s assumption, the first antibody genes could easily have had useful functions without RSSs and RAGs.

A family of molecules called the Toll-like receptors (TLRs) demonstrates the utility of having an all-purpose microbe detector that does not require millions of randomly-generated variants. TLRs, located on the surface of special immune cells in the blood, recognize bacterial cell walls and virus-specific DNA sequences, causing an all-out attack by the body on the foreign invader. In the process, some of the host tissue gets destroyed, but this collateral damage is a necessary cost to slow down the infection.

This so-called innate immune response—the first line of defense—occurs immediately upon infection, while antibodies take several days to produce. Without innate immunity, the animal might die before antibodies even have a chance to work. The fact that virtually all multi-cellular organisms have TLRs indicates how critical they are to survival.

If innate immunity is so effective that 90% of animals live just fine without adaptive immunity, it’s natural to wonder why some animals do have it. A major advantage it provides is an immunological “memory” of past infections, making it easier to fight off similar pathogens in the future. (Vaccines work on this principle—by exposing the body to inactivated or dead viruses, we give B cells a “heads up” so they can make and store antibodies before the real thing hits.) Antibodies also enable targeted killing of the pathogen, preventing further damage to the host by the non-specific innate immune response.

There’s another way to ask why some animals have an adaptive immune response: rather than seek to explain what added function or advantage it serves, we can ask about the mechanism by which it came to be in the first place. That will be our topic in my next post

References:

Bottaro, Andrea, Inlay, Matt A., and Matzke, Nicholas J. “Immunology in the spotlight at the Dover 'Intelligent Design' trial.” Nature Immunology. 7(5), 433-435. May 2005.

Inlay, Matt. "Evolving Immunity: A Response to Chapter 6 of ". http://www.talkdesign.org/faqs/Evolving_Immunity.html

Travis, John. “On the Origin of the Immune System.” Science. 324(5927), 580-582. May 2009.


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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Nick Matzke - #17338

June 13th 2010

“As a matter of practice, it is actually not that hard for a science to achieve a state where we think that it is unlikely that supernatural intervention would ever be needed to explain an event.  Many fields of chemistry and physics are already there.”

What?  Why is that, exactly?  I demand that you give me a molecule-by-molecule explanation for the production of every single individual photon that has struck the Earth over the last 4 billion years, or else I’m going to say it’s reasonable to think that supernatural intervention is still in play as a serious explanation.


Rich - #17339

June 13th 2010

Larry:

When did I ever deny that human beings and chimpanzees are related by common descent?  I made no claim one way or the other regarding common descent.  I indicated clearly, here and on other threads, that there is a range of circumstantial evidence for it—fossils, markers in the genome, etc.—and that I have no objection to the inference, as a tentative, revisable inference, like all scientific inferences.  But the fact that I can find your notch in various trees in New York, Ohio, Missouri, etc., all the way to California, does not tell me whether you got to each destination by car, motorcycle, bicycle, bus, train, or on foot.  For that matter, it cannot guarantee me that you weren’t whisked from location to location by an angel or a demon.  All I can be sure of is that you passed that way.  And that’s all we can say, at the moment, about whale evolution, even if the entire hypothetical fossil sequence is granted without qualification or cavil.

You don’t have to write to Sternberg to find out his position.  There’s a wealth of material on his site, if you take the time to read it.  You should also read his recent series on the Discovery web site, with comments pertinent to Biologos.


Rich - #17340

June 13th 2010

Nick M:

You’re being silly.  I’ve never suggested that nature, as we experience it, doesn’t work by what are called natural laws.  Nor have I ever suggested that we need a 100% detailed causal history to be pragmatically sure that only natural causes are involved.  There is no difference between a TE, and IDer or an atheist regarding our confidence in the basic rules of electromagnetism or celestial mechanics, or photosynthesis or embryonic development.  Nobody expects to find an anomaly in the orbit of a planet that can be explained only by the push of an angel, and nobody is arguing that cell division in embryonic development is caused by a special action of God.

We’re talking about origins here.  There’s no reason to assume that the origin of all the natural systems that we know of can be explained in terms of wholly unguided natural processes.  That’s something to be demonstrated, not assumed.  The first cell may have originated due purely to accident and the laws of chemistry, but that has not been proved or even nearly proved.  Land mammals may have become whales via neo-Darwinian processes, but we have no demonstration or near-demonstration of that fact.  Why is this so hard to admit?  (continued)


Rich - #17342

June 13th 2010

Nick M:

Notice that I have not argued that neo-Darwinian processes *can’t* explain the origin of whales; I’ve argued only that they have not yet come anywhere near to explaining the origin of whales.  I’ve not dogmatized.  But no matter how non-dogmatic I try to be, it never calls forth a corresponding non-dogmatism from the Darwinian side (atheist or TE).  I still get the same rage as if I had argued “Darwinian processes can’t produce complex systems, therefore God did it.”  It seems clear to me that the devotees of neo-Darwinism aren’t interested in moderate, cautious scientific statements, but in extracting a confession of faith in Darwinian mechanisms from all dissenters.  That’s not science, that’s ideology.


Rich - #17343

June 13th 2010

Larry:

I’m not asking for impossibly high levels of certainty.  Why is it asking for “impossibly high levels of certainty” to ask for *some* evidence that neo-Darwinian mechanisms can do the job?  If you were hiring someone to build you a house, wouldn’t you try to obtain evidence that he had built a house before?  Or at least a little shed, or a bathroom, or a tree fort?  Or would you just trust any stranger who said he would build you a house if you handed him half a million dollars?  Why should I believe Mayr or Gould or Dawkins when they say that neo-Darwinian processes produced the whale, when they can’t even explain how they could have produced *part* of a whale?  I’m not questioning the fact of evolution, I’m questioning the adequacy of the mechanism.  And I’m not demanding 100% of the pathways, but we don’t even know 1% of them.  I don’t have an unreasonably high standard of proof; you have an abysmally low standard of proof.


Rich - #17346

June 13th 2010

Larry:

You belittled Sternberg’s institutional affiliations, without conducting a level-playing-field comparison.  You didn’t answer my question about the scientific reputation of the institutions that Biologos columnists teach or do research at.  Are they major research institutions?  Are they religiously neutral institutions?  I haven’t conducted a systematic survey myself, so let me know what you find.


unapologetic catholic - #17349

June 13th 2010

“You belittled Sternberg’s institutional affiliations, without conducting a level-playing-field comparison. “
The Biologic Institute is not a research laboratory or any research facility.

It is “sciency” just pretending to do science without actually doing any.

It has zero research projects, zero equipment and is located at 16310 NE 80TH ST Suite 102
REDMOND, WA in a business park office building.  No science being performed here, I’m afraid.


unapologetic catholic - #17351

June 13th 2010

The Biologic Institute is its smoke and mirrors website with no physical address, locations or genuine contact information.  The Biologic Institute in short, is a blog.

In sharp contrast is the Thewissen Laboratory [with cetacean evolution informaiton that Rich denies exists]  where you can get the geographic location, the university affiliations and the phone number and email address of Dr. Thewissen himself. 

http://www.neoucom.edu/DEPTS/ANAT/Thewissen/

http://www.neoucom.edu/audience/about/departments/anatneuro/faculty 

The Thewissen Lab is the source of an abundant collection of information that “supports” the evolution of whales” from land mammal, in Rich’s words.  Does the evidence “prove it?”  NO, because science doesn’t deal with logical proofs as any rookie philosopher would know. 

But, the “support” for whale evolution from land mammals is very well established.  It’s a combination of paleontological, geological, morphology and genetic evidence.  All fields of study independently lead to the same result.  None of the separate fields of study lead to a different result although nothing prevents diverging results that would cast doubt on the conclusion.


Rich - #17352

June 13th 2010

Un. Catholic:

All the members of the Biologic Institute have doctorates in the life sciences, and all the members of the Biologic Institute have published peer-reviewed papers in standard scientific journals.  I wouldn’t be running them down, until you have accomplishments on that level yourself.

The notion of “proof” in this discussion didn’t originally come from me.  It was others who insisted that genomic evidence proved beyond a doubt chimp-human common ancestry, etc.  If you want to lambaste someone for introducing the “proof” notion, don’t look at me.  My job here is merely to puncture Darwinian overconfidence.  No one here has the slightest clue what genetic changes are necessary to go from land lactation to marine lactation, yet *everyone* here is *utterly confident* that Darwinian mechanisms could have done the trick.  And no one seems to understand the elementary logical problem:  one has no right to be confident that Mechanism X could have accomplished Task Y if one has *no idea* how mechanism X actually works in detail.  Basically the logic here is:  “We have a plausible fossil sequence, therefore neo-Darwinian mechanisms can build a whale.”  That’s a failure in Logic 100.


Gregory - #17353

June 13th 2010

unapologetic catholic,

Just one question: do you consider yourself a ‘Darwinist’?

If so, I wonder why. The Roman Catholic Church, via the Pontifical Academy of Sciences, Pope John Paul II and Pope Benedict XVI, has made it clear that *some* aspects of ‘Darwinian evolution’ are unacceptable for a Christian worldview.

I can sense your frustration with Rich. But why take an extreme position that is inconsistent with your Church?

Neo-Darwinism and evolutionary biology are *not* synonyms; the post-Darwinians have shown that quite clearly.

Why accept the label ‘Darwinian’, if that’s what you do? Do you call yourself EInsteinian, Maxwellian or Heisenbergian also?


Rich - #17355

June 14th 2010

To Those Who Keep Touting Thewissen:

From http://bing.search.sympatico.ca/?q=thewissen + whale&mkt=en-ca&setLang=en-CA:

“Scientists have long known that cetaceans (whales, dolphins, and porpoises) descended from four-footed land mammals.”

The word “known” implies that Thewissen regards this as *proved* (whether he uses the word “proved” or not).  Yet people here insist on telling me that science does not claim to “prove” things.  Well, if it doesn’t, then Thewissen should have written “Scientists have long surmised that cetaceans…” or “Scientists have long hypothesized that cetaceans…” or “Evidence has long been accumulating which suggests that cetaceans…”

So people here are going to have to make up their minds:  Is the common descent of chiimpanzees and man “proved” (even though science can’t prove things), or is common descent merely highly likely?  Is whale evolution “proved”, or only highly likely?  If it’s the latter, then no one should have complained (as one angrily did) when I spoke of “circumstantial evidence” for common descent; if it’s the former, then the recent lectures I’ve received about science not being able to prove anything should be retracted.


unapologetic catholic - #17356

June 14th 2010

“The word “known” implies that Thewissen regards this as *proved* (whether he uses the word “proved” or not). “

No,  “known” does not imply “proved”  You’re putting words in their mouths.  “Know” means “know, not “proof.” 

“So people here are going to have to make up their minds:  Is the common descent of chiimpanzees and man “proved” (even though science can’t prove things), or is common descent merely highly likely?  Is whale evolution “proved”, or only highly likely?”

Very highly likely. 

On a scale of 1 to 100 with 100 being “nearly certain” and 1 being “extremely unlikely”
where do you put cetacean evolution from land animals?  1?  10?  40?  80?

Same question for human/primate common ancestry?  1?  10?  40?  80?


unapologetic catholic - #17357

June 14th 2010

“Just one question: do you consider yourself a ‘Darwinist’?”

No, the term is meaningless.

The Catholic Church does teach that (1) the earth is very old about 4.5 billion years old, (2) that evolution is generally correct, (3) that common descent is probably correct and (4) common ancestry is probably correct.


unapologetic catholic - #17358

June 14th 2010

“If it’s the latter, then no one should have complained (as one angrily did) when I spoke of “circumstantial evidence” for common descent;”

Probably because you don’t seem to understand how powerful circumstantial evidence is.  Circumstantial evidence is not “merely circumstantial evidence” as if there was some form of evidence that is somehow superior to circumstantial evidence.  It is, quite often, the very best evidence in support of a fact. 

There was a recent sinking of a South Korean Naval vessel.  The evidence for the cause of the sinking is entirely circumstantial.  But it is extremely powerful evidence.

http://www.spiegel.de/fotostrecke/fotostrecke-55107-6.html


Rich - #17359

June 14th 2010

Un. Catholic:

Whatever may be the case in religion, art, literature, or personal life, in philosophy, mathematics, and science, you cannot “know” what has not been demonstrated, i.e., proved.  It is wrong to claim that scientists “know” anything that they have not proved.  Otherwise the word “know” is meaningless in a scientific context. 

Your question shows intellectual inaccuracy, in that you fail to distinguish between “evolution” as a process and particular causes of that process.  Since neo-Darwinists often blur the two together in their propaganda, it’s necessary to distinguish them.  If you are talking about “common descent”, I’d say that it’s reasonably likely.  If you are talking about neo-Darwinian mechanisms as the main driving force of whale evolution (or macroevolution in general), I’d say the likelihood is very small.  Such a chancey process could at best play an auxiliary role.  Sternberg’s argument is of course that neo-Darwinian mechanisms are seriously deficient as an explanation for whale evolution, and in fact he thinks that something other than neo-Darwinian mechanism is the primary driver of evolution.


Rich - #17360

June 14th 2010

For All Thewissen Fans:

I looked at the much-touted Thewissen web site, and discovered that its use in the debate here is another literature bluff, or at least, a semi-literature bluff.

Sternberg asks for two things:

1.  A list of morphological changes necessary to turn a land mammal into a cetacean;
2.  An explanation of how neo-Darwinian mechanisms could do the trick.

Thewissen *partly* answers the first, though he gives nowhere near a complete list.  He doesn’t touch at all on the second.  His discussion is all comparative anatomy; no genetic mechanisms are presented at all.  Plus, it’s clear that there isn’t even consensus (though Thewissen has an opinion) on what the hypothetical ancestor of the cetaceans is; and of course the hypothetical evolutionary pathways would be quite different depending on the starting point.  So Thewissen’s site does not answer any of the questions I asked, nor does it answer Sternberg’s challenge.  The people here who have averred or implied that it does either don’t comprehend what they have read on Thewissen’s site, or are literature bluffing again.


Rich - #17361

June 14th 2010

Un. Catholic:

I didn’t speak of “merely” circumstantial evidence.  Don’t put words in my mouth.

Regarding your answer to Gregory, on another thread, I already exposed your dangerous lack of knowledge regarding the official Catholic position on evolution.  Rather than repeat all the arguments here again, I’ll just warn everyone that your statements are not accurate, and that official Vatican documents should be consulted, minus your theologically untrained interpretive glosses.

As for whether the term “Darwinist” is meaningless, it isn’t to those of us who have actually read Darwin.  But not many TEs are in that position.


Gingoro - #17365

June 14th 2010

Larry - #17267

“Common descent between humans and chimps is beyond scientific dispute in the same way that an ancient earth and heliocentrism are. “

If I am in a nitpicking mood,  I would dispute heliocentrism as the earth’s course is not only affected by the sun but also by the center of mass of our galaxy as well as the center of mass of the universe.  The earth’s orbit is a kind of elliptical spiral that more or less centers on the sun’s center of mass. 

It seems to me that Einstein said in effect that there is no preferred set of coordinates so one could base one coordinates on the earth, however the math becomes highly complex and unwieldy. 

In general I don’t deny common descent although the shape is not a tree but a network of some type as there is horizontal gene exchange.  I don’t recall Rich denying common descent but maybe the mechanism that produced common descent.  In fact Rich does not deny the mechanism but wants more proof as do I.  Where by proof I mean that the mechanism’s capability is highly likely to be powerful enough to produce life as we know it. 

Dave W


Argon - #17371

June 14th 2010

Me: An alternate approach for IDists, and in my opinion a better way overall, would be to develop a positive theory of design.

Mike Gene: Been doing dat for years now.

A *differentiable* positive theory or postive attitude :^)? Post-abiogenesis, I think it’s pretty hard to tell.


Arthur Hunt - #17379

June 14th 2010

“Sternberg asks for two things:

1.  A list of morphological changes necessary to turn a land mammal into a cetacean;
2.  An explanation of how neo-Darwinian mechanisms could do the trick.”

As we have seen elsewhere in discussions about molecular mechanisms of splicing, Sternberg likely would not understand point one of any genetic or molecular or developmental mechanism that pertains to the evolution of whales. 

I think Richard needs to start at square 1.  A good start would be an understanding just what parts of your generic eukaryotic gene are actually functional.  Without a good understanding of this, he isn’t going to be able to begin to understand the answers to the question he purports to be asking.

see http://sandwalk.blogspot.com/2010/06/idiots-do-arithmetic-second-time-same.html for more on Sternberg’s whoppers.


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