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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Rich - #17382

June 14th 2010

Arthur Hunt:

Have you or have you not published anything on the specific evolutionary mechanisms which could have produced marine lactation, a reshaped and relocated blowhole, and all the other morphological modifications noted by Sternberg?  Has Larry Moran or has he not published anything on the subject?  Has Steve Matheson or has he not published anything on the subject?  Can you cite me literature which *has* been published on the subject?  I’ve already shown that Thewissen doesn’t address the question at all, at least not on the web site which has been touted here as answering all of Sternberg’s questions.  Why do you neo-Darwinists not have the sheer intellectual integrity to admit what you don’t know?  Why can’t you confess, here in front of Biologos supporters:  “The best biologists in the world have very little idea of the specific mechanisms by which the necessary morphological changes were produced?”  Is this your idea of Christian scientific honesty, to bluff about what is known and to conceal what is unknown?

For those interested in a judicious summary of the Matheson-Sternberg-Moran-Hunt debate, I recommend them to:  http://www.evolutionnews.org/2010/06/


unapologetic catholic - #17396

June 14th 2010

“Can you cite me literature which *has* been published on the subject?”

Blowholes:

http://books.google.com/books?hl=en&lr;=&id=WI3cNUItCJMC&oi=fnd&pg=PA67&dq=evolution+of+cetacean+blowholes&ots=11Sojg277G&sig=nU7nfxk-kpr5ISijuzHIZgm33Zs#v=onepage&q=evolution of cetacean blowholes&f=false

http://pandasthumb.org/archives/2008/03/whale-evolution.html

Read the second article if you don’t have much time.  It’s a good overview and demonstrates that the claim that ther is no literature is a claim of willful ignorance.


RBH - #17400

June 14th 2010

Rich wrote

For those interested in a judicious summary of the Matheson-Sternberg-Moran-Hunt debate, I recommend them to:  http://www.evolutionnews.org/2010/06/

Judicious?  That’s beyond laughable.


Rich - #17401

June 14th 2010

Un. Catholic:

First, I’ll never check any of your references again, because I’ve checked them before and they’re always either bluffs or partisan rubbish.

Second, Panda’s Thumb is not a refereed scientific journal, but a culture war web site for anti-YEC and anti-ID polemics, plus superficial propaganda for neo-Darwinism.  Most of the material on it is written by internet hobbyists, and what isn’t is written by scientists who are taking a moral holiday from cautious and dignified academic debate and stooping to polemics and invective.  There are also frequently some nasty anti-Christian remarks made there, but of course, unholy alliances with atheist evolutionary biologists have never been objectionable to TEs, so it doesn’t surprise me that Christians here frequently cite Panda’s Thumb without any sense of shame.  I expect you’ll be citing Pharyngula and Dawkins’s web site next.

Maybe some day you’ll cite an article by an orthodox Roman Catholic writer who understands Catholic theology well enough to be critical of neo-Darwinism, but I’m not holding my breath.


Arthur Hunt - #17402

June 14th 2010

“For those interested in a judicious summary of the Matheson-Sternberg-Moran-Hunt debate, I recommend them to:  http://www.evolutionnews.org/2010/06/”

Judicious?

The best that can be said for Wells’ piece is that he has gotten whole hog into the World Cup spirit, what with his rather embarrassing own goal and all.  I explain this in the first comment at of this discussion:

http://sandwalk.blogspot.com/2010/06/jonathan-wells-weighs-in-on-alternative.html

Wells is even less informed than Sternberg (if that’s possible).


Rich - #17407

June 14th 2010

Arthur:

Who are you to talk about how informed Sternberg is?

He has two Ph.D. in the life sciences.  That’s one more than you have, and as many as you and Larry Moran have put together.  His *special field* within the life sciences is *evolutionary biology*, unlike yours or Moran’s.  He has an impressive track record of publications, which can be found on his web site.

I notice you haven’t answered my previous question.  What are your publications regarding whale evolution?  Which of Sternberg’s questions about whale evolution can you, Moran or Matheson answer?  If you can’t answer them, have the intellectual honesty, required by both science and Christian faith (though perhaps you’re not a Christian, since you post supportively on the atheist blog Sandwalk) to state that *evolutionary biologists know very little about the mechanisms of whale evolution*.  Why can’t you get those true words out of your throat?  Why can’t *anyone* here do that?  Any good scientist admits freely what he doesn’t know.  I can only infer that what I’m up against here is not open-minded scientists but ideologues committed to neo-Darwinism at all costs.


Mike Gene - #17415

June 14th 2010

Argon:

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

Are you saying that as long as you can see a Duck, there is no Rabbit?  Are you demanding a gap?


Arthur Hunt - #17425

June 14th 2010

“Arthur:

Who are you to talk about how informed Sternberg is?”

Um, maybe because I know what I’m talking about and Sternberg doesn’t?

I don’t care if he has 10 Ph.D.‘s.  His statements tell me that he doesn’t know this material.  And that he is a poor source of information for anything that relates to genetics, genes, and molecular biology.

Ya see, Rich, I’m not relying on the letters after his name or any other of the trappings of authority.  I’m going by what Sternberg says.  He’s wrong and unwilling to learn from his mistakes.  That’s the story, cut and dried.


Rich - #17436

June 14th 2010

Arthur:

Good.  I’m glad you are arguing from your knowledge and not based on authority.  So take it up with Sternberg, and may the best thinker win.

Only instead of taking it up on an odious blog run by an odious atheist, why don’t you publish your objections someplace respectable?  Why don’t you write a column here on Biologos, for example?  If you are a Christian scientist who believes in neo-Darwinism, they will welcome you with open arms and sign you up right away to attack anyone associated in any way with ID.

If you do this, Sternberg will doubtless reply, and I will read the back-and-forth with great interest.  But I can’t bring myself to read anything posted on Matheson’s or Moran’s blogs.  The tone in both places is arrogant and chippy, sometimes descending to vulgar, and the atmosphere is not scientific but pure culture-war, which interferes with the dispassionate discussion of the truth.


Argon - #17582

June 16th 2010

Mike Gene: “Are you saying that as long as you can see a Duck, there is no Rabbit?  Are you demanding a gap?”

For expectations from different explanations, yes; at least somewhere. For example, Newtonian and Relativistic physics yield different expectations and therefore can be differentiated.


Nick Matzke - #17627

June 16th 2010

“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. “

There is the minor problem that anything more than a fraction of a light-year away from the Earth must be orbiting the Earth at a velocity faster than the speed of light in order to get around the Earth every 24 hours.  It’s not all relative in relativity…


Bilbo - #17705

June 17th 2010

Hi Argon,

First you insist that ID present positive case for ID.  Then when Mike Gene says he’s been doing that for years, you switch and demand negative evidence—a gap.  We could send you back to Dembski and Behe, but then you will just demand positive evidence, again.  There’s just no pleasing some people.


Argon - #17717

June 17th 2010

Biblo, I ask for positive discernability. A difference *between* explanations.

Newtonian physics makes positive predictions as does Relativistic physics. The relative merits of the theories can be determined because their predictions differ.

Similarly, the idea that the Earth is young also makes positive predictions about geology, chemistry, physics and astronomy. These differ from predictions related to the idea that the Earth is billions of years old.

Here’s the problem: Assume Theory-Y is a combination of Theory-X (e.g. current evolutionary theory) and Mechanism-Z (e.g. design). If one can’t empirically differentiate between Theory-Y and Theory-X, what does the addition of Mechanism-Z get you, scientifically? It may have use in apologetic arguments but not science.


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