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Is There an Edge to Evolution? Part 6: The Cathedral of Life

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December 4, 2010 Tags: Design

Today's entry was written by David Ussery and Darrel Falk. You can read more about what we believe here.

Is There an Edge to Evolution? Part 6: The Cathedral of Life

An Evaluation of Behe’s Edge of Evolution, Chapter 9 – The Cathedral and The Spandrels

This series of posts has been going through Michael Behe’s book, The Edge of Evolution, chapter by chapter. This penultimate chapter focuses on the findings of one of the most fascinating new topics in biology today, evolutionary developmental biology (evo-devo). In essence this is a field that couples two sub-disciplines, evolutionary biology and developmental biology using the tools of molecular biology. Chapter 9 is moving on to "higher levels of biological organization", and Behe readily admits that things are now a bit less well-defined, and "the arguments in this chapter will necessarily be more tentative and speculative than for previous chapters" because now the subject will be dealing with more complicated things - plants and animals, and "much less is known about what it takes to build an animal than to build a protein machine" (pages 172-173).

As often happens in science when one examines a phenomenon through a different window, many new and often surprising insights come into view. In 1940, for example, few people studying genetics imagined that DNA would be the genetic material; most everyone thought it would be proteins. However, soon afterwards the tools of microbiology began to reshape how biologists viewed the genetic material, and that in turn opened the window for Watson and Crick to see the gene’s true molecular nature. With that, the now-famous double helix came into view for the first time.

Examining the surprises that appear when one looks at a phenomenon from a new vantage point is what makes science so engaging. Scientists love surprises. In this chapter, Behe focuses on one of the most exciting scientific discoveries of the past thirty years, and implies that because evolutionary biologists were surprised, that evolutionary theory had reached the edge of its scientific limits. Let’s examine the basis of the surprise and then explore whether Behe is justified in concluding that the scientific surprises discussed in Chapter Nine correspond to a cliff-edge. Is Behe correct in concluding that going beyond that edge, one enters into territory that can only be explored by inserting a [supernatural] Intelligent Designer into the scientific “equations?” Is Behe’s edge simply a window of opportunity to see where mainstream biological tools will take us, or is it a blank wall? Behe believes it is a blank wall. Why?

In an earlier post our colleague, David Kerk, described the tinman gene, the gene required for making a heart. It is one of the many conserved “master” genes whose functions are now understood, through the new perspectives afforded by evo-devo. These genes serve as genetic switches that have the capability of activating particular developmental programs. A given switch (i.e. a master gene) is often structured quite similarly throughout the animal world even when comparing widely disparate species like flies and frogs. This high degree of conservation shocked evolutionary biologists. It was startling, for example, to realize that the same gene that served as a switch to turn on eye development in flies was found in humans, because if you think about it, the eyes of flies are a lot different than human eyes! Indeed, the mouse master gene for making eyes has been transplanted into fruit flies where it still works. Fly cells respond to the mouse switch by making eyes—fly eyes, not mouse-like eyes—but eye tissue nonetheless. Biologists didn’t expect genes to be conserved through the greater than 550 million years since mice and flies had a common ancestor. However, even though it was a surprise, it is extremely consistent with evolutionary theory. Despite the surprise, the finding is completely consistent with natural selection and common descent. Master genes are conserved through the parade of life. Like the hour hand on a ticking clock, they change, but only at a crawl.

Actually, the surprise comes from just how beautifully consistent the view is from this vantage point. Scientists were expecting consistency, but certainly not in such an eye-popping, mind-boggling manner.

Behe chooses to view things differently. This is evidence, he says on page 190, that:

... the best minds in science have been misled. They justifiably expected randomness and simplicity…

These scientists were NOT expecting randomness and they were most certainly NOT expecting simplicity. What they were expecting was greater complexity—not the degree of simplicity they found. The same genes are being used to build insects as what are used to build mammals. What could be simpler than that? So from this perspective, it is difficult to even begin to grasp Behe’s point about expected simplicity.

Let’s go back though to his statement regarding the notion that the scientists’ “expected randomness.” Why would he tell a general audience that? Natural selection is the very converse of a random process with an unanticipated outcome. They knew it would be non-random—natural selection is by definition non-random. What surprised them—what shocked them actually—was just how foundationally simple and non-random evolutionary mechanisms turn out to be. Evo-devo is not inconsistent with the core of evolutionary theory. Quite the opposite actually—natural selection is by definition a non-random process.

It is important to be fair to Behe here. He has stated clearly that the data as a whole are consistent with common descent. This is not in question for him. Indeed, it would probably have been good for him to emphasize in this chapter that these data are beautifully consistent with his own premise—common descent. One can track the lineage of the “genetic toolkits.” The toolkits get modified slightly and one can trace their modifications as one examines the tree of life. But there is a tree—one tree—Mike agrees with this! Indeed his entire approach to intelligent design is grounded in common descent. So in that regard Behe is in total alignment with mainstream biology. In that regard BioLogos and Behe are truly at one. We wish he would say that more often. There is a sense in which Mike Behe is more closely aligned with BioLogos than with many of his colleagues at the Discovery Institute including Bill Dembski and Stephen Meyer, who, although they waffle on occasion, have come out against common descent. Neither Bill nor Steve are biologists. It would be great if they would listen to their own biochemist. If they would, then perhaps Mike Behe’s statement on page 191 would take us to a whole new day:

Let’s acknowledge that genetics has yielded yet more terrific (and totally unanticipated) evidence for common descent.

Do you hear that, members of the ID Movement? Perhaps the single most important figure in the ID movement over the past fifteen years has called for an acknowledgement that common descent has occurred. Implied in this statement is evidence for common descent all the way from single cells to human beings. If the leaders and followers who do not have credentials in biology and biochemistry would get on board with their expert who does, then half of the concerns with the ID movement would be over.

Behe goes on from there to demonstrate the complexity of the genetic circuitry needed to build various cell types. Vertebrates, for example have B lymphocytes to help fight off infections; invertebrates, he says, do not. The genetic circuitry to build any cell type is exceedingly complex. Organisms are placed into classification groupings, based on somewhat subjective human ideas. Vertebrates are member of the phylum, Chordata. Invertebrates are members of other phyla. Behe proposes that the differences between phyla are so large, that they require the invention of whole new cell types. Since new cell types require new protein interactions and since he believes he has already shown that new substantive protein interactions won’t occur without intervention, new phyla as he sees it cannot arise without intelligence.

Let’s be clear, there is an Intelligence behind all of life. So, even here we don’t disagree. The question is why Behe wants to draw a line (an edge) between presence of God and absence of God in life’s history—presence of intelligence and absence of intelligence. Perhaps it is because of the necessary “absence of intelligence” to serve as an experimental control for “presence of intelligence?” If so, this sounds as though his theology is flying free. It is not grounded in Scripture. The Bible asserts that “by him all things were created…He is before all things and in him all things hold together.” (Colossians 1:16, 17). It also says, “Through him all things were made, without him nothing has been made that has been made” (John 1:3).

Further, one could build a case that he has now floated free of his scientific roots as well. Based on the data available so far, Behe may be correct that we cannot successfully trace the step-by-step lineage of new particular cell types in certain phyla. Behe’s assertion that for scientific reasons, however, we must now insert an Outside Architect is deeply flawed. The only scientific evidence he lays out to support the scientific hypothesis of the need for this architect harbors back to the same sort of calculations on the probability of new protein/protein interactions. We have already demonstrated that those calculations are off by many orders of magnitude.

What are those calculations that show no new protein/protein interactions have occurred? What is the data he analyzes? On page 200 Behe suggests that out of a billion rats subjected to warfarin in the past 50 years, we might have expected “many new regulatory regions; none seemed to have helped against warfarin.” Did anyone check these billion rats to see if some had undergone changes in regulatory regions? It seems that this is really a premature conclusion to put forward to the public without vetting it before the scientific community first. From there he goes on to fruit flies that have been studied in the lab for 100 years. During this time “no new, helpful, developmental-control programs have appeared.” Is there some reason why we might have expected some new “helpful” program in flies? What sort of “new help” would Behe have envisaged for fruit fly development? How would it have been detected? Was anyone actually looking for such a thing?

In the chapter, Behe then goes on to report that the malaria parasite has evolved no new reported “cell forms or regulatory systems” in a hundred billion billion chances. How does he know this? It is true that no one reported new regulatory systems. But was anyone looking for them? For all we know the parasite might have been evolving and even changing elements of its regulatory system. A careful analysis might even have been able to show this.

Based on analyses like these, Behe ends his chapter by discussing spandrels, the space between the arches that hold up a great cathedral. The arches, he says are clearly designed by a great architect. The artwork that decorates the spandrels were added after the fact—after the architect had left the scene. Now moving towards a metaphor, he states that science, his science, has now shown that the major classification groups of animals are like the arches of a great cathedral—they have been designed by God, the Greatest Architect. Darwinian evolution comes in and decorates the spandrels with all sorts of species and maybe genera and families--but the existence of phyla requires an Architect. This is Professor Behe’s cathedral and although one has to give him credit for being creative, this is based on his claim that rats that don’t evolve new systems (for which no one was carefully looking, to be honest). It is based upon fruit flies that don’t seem to be developing new and better body plans than they already have, and it is based on billions of billions of malaria parasites that are not being analyzed for changes at the molecular level. Surely ID is now floating free of scientific data. A theology based on a God whose Presence in creation comes and goes is equally problematic. Is not ID also floating free of Scripture?

It doesn’t have to be this way. Professor Behe, since he accepts common descent, is already half way home towards accommodating the scientific community. As imperfect human beings, we are all wrong on occasion. As mentioned early on in the chapter, "the arguments are more tentative and speculative" here. But there's also a danger that perhaps the arguments have strayed far from solid science as well as sound theology. It doesn’t have to be this way.


David Ussery is an associate professor of comparative microbial genomics at the Center for Biological Sequence Analysis at the Technical University of Denmark and on the faculty at the University in Oslo, Norway. Ussery is the co-author of Computing for Comparative Microbial Genomics and has authored or co-authored 130 articles for science and professional journals. He is also a frequent public speaker on the topic of bacterial genomics.
Darrel Falk is former president of BioLogos and currently serves as BioLogos' Senior Advisor for Dialog. He is Professor of Biology, Emeritus at Point Loma Nazarene University and serves as Senior Fellow at The Colossian Forum. Falk is the author of Coming to Peace with Science.

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John - #43336

December 10th 2010

Mike:
“Bottom line here is that given Volvox and humans last shared a common ancestor a billion plus years ago, and the sequence outside the repeats is not strongly conserved, I’m not sure a negative result here means all that much.”

It means that both beta-catenin and the hypothetical Volvox protein are both members of a superfamily of proteins that contain ARM repeats.

“However, I do think your concern is indeed legitimate, as you may be right.  But I would maintain the Volvox protein can be scored as putative homolog of beta-catenin (more than “just a protein with Arm repeats”) and this scoring is supported by some circumstantial evidence (after all, I would further argue that beta-catenin and alpha-importins are also homologs, yet there the evidence is even more qualitative).”

I think you’re just fudging on the term “homolog” instead of following the data.

“However, right now, this is mostly a testable hypothesis.  What is needed are functional assays with this protein to seal the deal.”

Why? When sequence identity poops out, the most reliable indicator is structure.


Bilbo - #43439

December 11th 2010

@John - #43330

Really? Then you won’t hesitate to answer a simple question: what proportion of genes with roles in eye morphogenesis (morphogenesis, not merely physiology) play roles ONLY in eye morphogenesis?

I don’t know.  Are you saying that there are no genes with roles in eye morphogenesis in most phyla, which is what I meant by “toolkits”?


John - #43469

December 12th 2010

Bilbo:
“I don’t know.”

Then why not be bold and make a prediction based on your favorite ID hypothesis?

“Are you saying that there are no genes with roles in eye morphogenesis in most phyla, which is what I meant by “toolkits”?”

My question isn’t about phyla, it’s about “toolkits” involved in the morphogenesis of different structures in a single organism. What does your ID view of frontloaded development predict?

And if you’re shy about predicting, why weren’t you shy about using the toolkit metaphor?


Rich - #43840

December 15th 2010

Since the article above is about Behe’s *Edge of Evolution*, I don’t think it would be off-topic to mention that Behe has followed up on the themes of that book in a new peer-reviewed article.  The article is called, “EXPERIMENTAL EVOLUTION, LOSS-OF-FUNCTION MUTATIONS,
AND “THE FIRST RULE OF ADAPTIVE EVOLUTION,” and it can be found in *The Quarterly Review of Biology*, Vol. 85, No. 4 (Dec. 2010).  It is available at:

http://www.lehigh.edu/~inbios/pdf/Behe/QRB_paper.pdf

It is interesting that this article is acknowledged to have some merit (albeit grudgingly) by Jerry Coyne, a major evolutionary biologist and Darwinian with no love for Behe’s ideas.  No doubt many commenters here will decide before reading Behe’s article that it must be rubbish, and will read it with closed minds, and will proceed to savagely attack it afterward, finding nothing but falsehood in it—that’s par for the course here.  But since Coyne, who is a hostile witness, finds the article to have some pertinence, I do not think that this usual purely reflexive reaction to Behe will come across to impartial observers as reasonable or fair.


John - #43854

December 15th 2010

Rich:
“I don’t think it would be off-topic to mention that Behe has followed up on the themes of that book in a new peer-reviewed article.”

How did you determine that it was peer-reviewed, Rich?


Rich - #43859

December 15th 2010

From the website of *The Quarterly Review of Biology*:

“Submitted manuscripts typically are vetted by an Editor and an Associate Editor and are peer-reviewed by two or three referees.”

Of course, whether or not the article was peer-reviewed is irrelevant to the question:  does it have anything important to say?  Jerry Coyne, a world-class evolutionary biologist, chose to focus on the latter question.  Maybe that focus on substance rather than professional formalities explains why Jerry holds an important chair at Chicago whereas so many of the anonymous Behe critics here are relegated to positions at minor universities, if indeed they have academic positions at all.


John - #43875

December 15th 2010

Rich quoted:
“Submitted manuscripts typically are vetted…”

You’re not answering my question. How did you determine that Behe’s particular ms was sumbitted and not invited?


Rich - #43878

December 15th 2010

“You’re not answering my question. How did you determine that Behe’s particular ms was sumbitted and not invited?”

That wasn’t the precise question asked.  The question asked could be interpreted as:  “Did you check to make sure that that journal is a peer-reviewed journal?”  But now that the precise emphasis of the question is known:  the majority of articles in any journal are peer-reviewed, not invited.  The onus is on the person who thinks it was invited to prove it.  But even if it was invited, that shows that the editors of a mainstream biological journal thought that Behe was particularly competent in the subject-area of the article, which hardly fits in with the line that certain commenters are pushing around here, i.e., that Behe is a poor scientist.  Poor scientists aren’t generally invited to write articles for mainstream biology journals, are they?

Of course, people desperate to deny Behe a legitimate recent publication will grasp at straws.  If it turns out the article was submitted, the next straw grasped will be that it is only “secondary” and not “primary” literature, won’t it?  Lesser men will always try to drag down greater ones, on any pretext.  And the least of them will do it anonymously.


John - #43881

December 15th 2010

Rich wrote:
“That wasn’t the precise question asked.”

I know. I made it more specific.

“The question asked could be interpreted as:  “Did you check to make sure that that journal is a peer-reviewed journal?””

Not by a knowledgable academic, because journals tend to be mixtures of peer-reviewed primary literature and invited reviews.

“But now that the precise emphasis of the question is known:  the majority of articles in any journal are peer-reviewed, not invited.”

No, RIch. You’re generalizing to avoid addressing the question. Behe’s ms is not primary literature, therefore it is likely that it was not peer-reviewed.


John - #43882

December 15th 2010

Rich:
“The onus is on the person who thinks it was invited to prove it.”

Given the fact that most of the secondary literature is not peer reviewed and the fact that this is secondary literature, the onus is on you to demonstrate that your claim was not simply wishful thinking, like your false claim about deleting flagellar proteins. If Scott Minnich had made your claim while testifying at Dover, he would have committed perjury.

“But even if it was invited, that shows that the editors of a mainstream biological journal thought that Behe was particularly competent in the subject-area of the article…”

Or they wanted to increase revenues.

“... which hardly fits in with the line that certain commenters are pushing around here, i.e., that Behe is a poor scientist.”

Behe stopped being a scientist 15 years ago.


John - #43883

December 15th 2010

Rich:
“Poor scientists aren’t generally invited to write articles for mainstream biology journals, are they?”

Poor scientists are generally invited to write secondary literature for mainstream biology journals that have a low impact factor, absolutely.

“Of course, people desperate to deny Behe a legitimate recent publication will grasp at straws.”

People desperate to tout the secondary literature as evidence of scientific productivity grasp at straws, Rich.

“If it turns out the article was submitted, the next straw grasped will be that it is only “secondary” and not “primary” literature, won’t it?”

It’s secondary either way. “Primary” doesn’t mean “peer reviewed,” it means “containing new data.”

“Lesser men will always try to drag down greater ones, on any pretext.  And the least of them will do it anonymously.”

And Dave Ussery is criticizing Behe’s gross misrepresentations here. Behe won’t appear here, and you will neither address Dave’s posts nor comment under your full name.

What did Jesus Christ say about hypocrisy? A lot more than He did about evolution, IIRC.


Rich - #43889

December 15th 2010

Re 43883:

If anyone has proof that Behe’s article was invited rather than submitted, they can trot it out.  Otherwise it’s just speculation.  And in any case, “invited article” doesn’t mean “poor article.”  Generally speaking a journal invites an article which it expects will be a good one.

Competent evolutionary biologists, like Coyne, don’t dwell on the question whether an article was invited or submitted.  They are more interested in its contents.

To the best of my knowledge, Behe has not been invited to appear here—at least, not to write an extended series of columns through which he could properly reply to Dr. Ussery’s comments.

I find it morally acceptable for those who are vulnerable to academic or economic reprisal to write under pseudonyms.  I don’t find it acceptable for tenured professors to do so.  Tenure exists to protect professors from being fired for holding unpopular opinions.  And in the case of ID such protection is unnecessary, since anti-ID is the popular stance among faculty.  Anyone who has tenure and who disagrees with Behe should do so under his real name.  I cannot think of a noble motive for attacking Behe from concealment, whereas I can think of many ignoble ones.


John - #43918

December 16th 2010

Rich scrambled:
“If anyone has proof that Behe’s article was invited rather than submitted, they can trot it out. “

Why not just admit that you had no basis for claiming that Behe’s ms was peer reviewed?

“Otherwise it’s just speculation.”

My point was that your claim was mere speculation.

“And in any case, “invited article” doesn’t mean “poor article.” “

I’m simply challenging your claim that it was peer reviewed. You clearly had no basis for such a claim, just as you have no basis for claiming that deleting any bacterial flagellar component prevents flagellar function.

“Competent evolutionary biologists, like Coyne, don’t dwell on the question whether an article was invited or submitted.  They are more interested in its contents.”

Why are you making completely unsupported claims about whether the article was peer reviewed? Obviously, making the claim was very important to you.

BTW, when are you going to produce an on-topic comment that addresses the evidence presented by Dave Ussery?


John - #43919

December 16th 2010

Rich:
“Competent evolutionary biologists, like Coyne, don’t dwell on the question whether an article was invited or submitted.  They are more interested in its contents.”

Why are you making completely unsupported claims about whether the article was peer reviewed? Obviously, making the claim was far more important to you than the contents.

BTW, when are you going to produce an on-topic comment that addresses the evidence presented by Dave Ussery?

“To the best of my knowledge, Behe has not been invited to appear here—at least, not to write an extended series of columns through which he could properly reply to Dr. Ussery’s comments.”

So what? Behe hasn’t appeared here. If you want to claim that he is unwelcome here, please present evidence.


John - #43921

December 16th 2010

Rich:
“I find it morally acceptable for those who are vulnerable to academic or economic reprisal to write under pseudonyms.  I don’t find it acceptable for tenured professors to do so.”

So you just invalidated your entire attack against my use of my first name alone.

Thanks! So we won’t be treated to any more of your tired ad hominem hooey?

Again, I note that Dave Ussery uses his entire name, but you have yet to engage him on any of the content in any of his posts, despite your posting of dozens of comments to them. Why is that?


Rich - #43949

December 16th 2010

Re 43918:

John:  “Why not just admit that you had no basis for claiming that Behe’s ms was peer reviewed?”

Because it’s not true.  I did have a basis.  That particular journal is a peer-reviewed journal, and most articles in peer-reviewed journals are peer-reviewed.  It was a reasonable inference.  True, I did not write to the editors of the journal to check.  So I have no proof.  If you want an admission that I have no proof, you’ve got it.  Now address the point of substance.  Why did the editors of a mainstream journal assign Behe the job if he is such a lousy scientist as you and many others claim?

Re: 43919

“Behe hasn’t appeared here. If you want to claim that he is unwelcome here, please present evidence.”

I made no such claim.  I was responding to your claim “Behe won’t appear here,” which carried the implication (given what you’ve said elsewhere) that he fears to appear here.  You have no proof that his failure to engage in bickering with the likes of you springs from cowardice.  You have no proof that if offered a chance for a full-length rebuttal, he would not appear here.  Has he been invited to do this, and refused?  Until then, charges of cowardice should not even be entertained.


Rich - #43951

December 16th 2010

Re: 43921:

Rich:  “I find it morally acceptable for those who are vulnerable to academic or economic reprisal to write under pseudonyms.  I don’t find it acceptable for tenured professors to do so.”

John:  “So you just invalidated your entire attack against my use of my first name alone.”

No tenured professor is vulnerable to academic or economic reprisal for criticizing Behe.  Thus, the logical implication of the rebuttal is that John is not a tenured professor.  Yet just the other day John said that he was on a sabbatical.  In the context of academic biology which John continually invokes here, that implies that John is a tenured professor.  Either John is leading the reader to a false inference now, or he was leading the reader to a false inference then.  Which is it?

Horns of a dilemma:  John is either misrepresenting himself as an academic when he’s not, or he is an academic but lacks the courage to identify himself to Behe.  An unenviable choice.


John - #44607

December 21st 2010

Rich wrote:

“That particular journal is a peer-reviewed journal,…”

Rich, no biologist is likely to refer to any journal with “Review” in its title as a peer-reviewed journal, as most of us know that the vast majority of reviews are invited and not peer-reviewed.

I’m sorry that your PhD was the pinnacle of your academic career, but you should get over it.

“...and most articles in peer-reviewed journals are peer-reviewed. “

Most reviews are not peer-reviewed.

“It was a reasonable inference.”

Yet you stated it as a fact.

“Now address the point of substance.  Why did the editors of a mainstream journal assign Behe the job if he is such a lousy scientist as you and many others claim?”

Behe ceased being a scientist 15 years ago. I claim that he’s not a scientist at all because he is clearly afraid to test the hypothesis he champions. Before that, he was a mediocre scientist.


John - #44608

December 21st 2010

Rich:
“...which carried the implication…Thus, the logical implication of the rebuttal…that implies…”

One would think that someone with a PhD in philosophy would not conflate implication with inference, but Rich’s ego is leading him to do exactly that.

“Either John is leading the reader to a false inference now, or he was leading the reader to a false inference then.  Which is it?”

Neither, because I’m not leading anyone to anything as you are trying to do. I’m simply telling the truth. Shall we bet $10,000 that I am?

Again, I note that Dave Ussery uses his entire name, but you have yet to engage him on any of the content in any of his excellent posts, despite your appending of dozens of comments, most ad hominem attacks on other commenters, to them.

Why is that? What should we infer from your failure to engage on matters of substance?


Rich - #44610

December 21st 2010

John wrote:

“Behe ceased being a scientist 15 years ago. I claim that he’s not a scientist at all because he is clearly afraid to test the hypothesis he champions. Before that, he was a mediocre scientist.”

Coming from one whose claim to be a scientist of any kind, mediocre or otherwise, is seriously in doubt, this remark is of no value to the ongoing discussion.


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