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 The BioLogos Foundation. He transitioned into Christian higher education 25 years ago and has given numerous talks about the relationship between science and faith at many universities and seminaries. He is the author of Coming to Peace with Science.

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gingoro - #44836

December 24th 2010

Larry@44814
I’m sure there are clearer posts from Rich that he accepts common descent but these are indicative.

http://biologos.org/blog/francisco-ayala-responds-to-signature-of-controversy/#comment-16013

http://biologos.org/blog/francisco-ayala-responds-to-signature-of-controversy/#comment-16011

A search on the Biologos site probably would yield more.
Dave


Rich - #44837

December 24th 2010

Larry:

Merry Christmas to you, too. 

Larry, the reason that my answers, and the answers of thoughtful ID and ID-related people like Behe, Dembski, Meyer, Sternberg, Berlinski, etc., don’t satisfy you, is that you are looking for a yes or no answer to questions for which the best answer is “maybe” or “yes, but with qualifications.” 

I acknowledge the data which is put forward as evidence for macroevolution.  I understand perfectly the reasoning by which this data is turned into an argument—I was a hard-core Darwinian for many years before moving (due to philosophical and scientific considerations, not religious ones) toward an ID position.  But unlike yourself, I see both logical and evidentiary weaknesses in standard evolutionary theory.  And unlike yourself, I acknowledge the data that seem to point to design.  My inclination is toward a teleological, designed process of evolution.  But I don’t offer teleological evolution as a hard scientific theory, merely as a speculation.  There I differ from the Darwinists here, who pretend that their speculations about random mutation and natural selection are hard science.  “Hardly science” would be more like it.

Good-bye, Larry.


Gregory - #44859

December 24th 2010

“Why didn’t you answer?”

B/c I asked you first & you didn’t answer. I told you this. So I wait.

John wrote: “The key here is that for me, doing biology brings me closer to God.”

I asked twice, once in bold: *How* does biology bring you closer, John, to God? & I even said: This is what people who visit BioLogos want to know, John! So?

If you have no explanation for *how* but you still believe it, then people would also like to know that! That is what BioLogos list is for, John, stories like yours. Why not tell it? Most people at BioLogos are not IDists, so arguing against ID here is misguided. Go elsewhere to do that.

Honestly, John, I know far too many biologists who make NO difference to people, just beaker carriers working in a lab for someone else’s plans, that to pretend you make a difference is not possible for me. The BioSphere, I do *not* worship it; only the Creator (quick, slow, staggered, orderly, etc.) of the BioSphere.

You will not be forgiven for not admitting your errors if you don’t ask Rich for forgiveness. Everybody who reads BioLogos, or who has followed the public documentation of you not admitting your obvious errors sees this. What’s it gonna be, John?


Gregory - #44860

December 24th 2010

Guess what, Larry. I am an anti-evolutionist, let’s qualify that, in the human-social sciences. I think evolution is an over-stretched ideology that needs to be ‘put in its place.’

Yes, indeed I will help to destroy, to dislocate, to convince people to stop using evolution in the human-social sciences, with the help of two former Field presidents & the current one. These are big-name anti-evolutionists in Europe. Not just biologists with no taste for theory. Who really cares if there is not a USAmerican on the front line to help us!

Do that mean anything to you?

‘anti-evolutionist’ - this is a credible & praiseworthy title in some academic fields where the ideology of ‘evolution-ISM’ has reared its ugly head.

Don’t believe evolution is an ‘over-stretched’ term in the Academy? Think again, harder. Open your eyes. It is easy to see.

Biologism & scientism are two popular ideologies in contemporary USA. They are both HIGHLY problematic & biologists are among the least capable to recognize this & among the most LIKELY to actually be committed ideologically to scientism, eVo biologists especially, than most other natural scientists. Why?


Larry - #44874

December 24th 2010

Gregory,

I only commented because I saw a very specific statement made here, that ““Rich has confirmed at BioLogos on many occasions that he ´accepts common descent.´” Having seen a great deal of Rich’s comments here, this took my by surprise, and so I wanted to be provided with a link. No more, no less. I am simply not interested in discussing the extension of evolution into the human-social sciences, and you might even find that I agree with what you have to say on the subject. All I am asking is that you provide me with the link I requested, or you can retract the original statement. I have no problem either way


Gingoro,

All I can say is that if you think those comments by Rich indicate his acceptance of common descent then you and I must have a very different understanding of the English language.


Rich,

I have wasted more than enough time with you on here and so, even though my comments concerned you, I most certainly did not direct them towards you. Merry Christmas to you but please do not attempt to engage me further, unless you want to provide me a link to these comments of yours which I am assured exist somewhere, but which nobody has yet been able to provide.


John - #45194

December 28th 2010

Gregory:
“*How* does biology bring you closer, John, to God? You said it. This is what people who visit BioLogos want to know, John!”

Why not be honest and say that this is what YOU want to know? It brings me closer to God because the mechanisms I find in biology are totally alien relative to the machines I know that are designed by humans. I know that metaphors are useful, but they always fail as one digs deeper for knowledge.

Therefore, I know full well that “it looks designed” is a lie, as those who use it are afraid to look and lie with impunity about the actual data. The ribosome is a fine example of this.

“Your soft-defined ‘edge of evolution,’ John - how many biologists (e.g. field, laboratory, theoretical, computer, etc.) out of 100 do you think would agree with you about it?”

100. There might be a few hardheaded developmental biologists who might not; “evo-devo” just represents their late arrival at the realization that much of the developmental circuitry (a metaphor) they’ve touted is illusory.

I’ve answered many of your questions and asked you if you accept common ancestry. Why didn’t you answer?


John - #45195

December 28th 2010

Gregory:
“You will not be forgiven for not admitting your errors if you don’t ask Rich for forgiveness.”

Now that is an amazing position to take! If Rich takes Christianity seriously, he would forgive me anyway. But I’m not interested in Rich’s forgiveness—I’m interested in exposing lies, pseudoscience and revolting theology that turns God into a cockroach to be stuffed into the gaps in our knowledge. Rich is the last person I want to represent the message of Jesus Christ in the eyes of others. He employs it as a weapon to promote authoritarian politics.

In the post on which you are commenting, Dave Ussery points out that Behe not only fudges the data, he completely misrepresents the predictions of modern evolutionary theory. Do you agree?

“Guess what, Larry. I am an anti-evolutionist, let’s qualify that, in the human-social sciences. I think evolution is an over-stretched ideology that needs to be ‘put in its place.’”

Guess what, Gregory—the post on which you are commenting has nothing to do with the human-social sciences.

“Do that mean anything to you?”

It do mean that you aren’t interested in coherent theology or reason if you think it’s relevant to Dave Ussery’s post here.


John - #45196

December 28th 2010

Gingoro,

I don’t see acceptance of common descent in either of those two comments. I see evasiveness.

Behe accepts common descent, full stop. Rich claims Behe to be an Einsteinian figure, but clearly won’t get in the same boat.


Dave Ussery - #45272

December 29th 2010

I’ve been away for awhile, but saw this article in today’s PNAS - I think it goes to the root of some of Mike Behe’s objections about whether the probability of two beneficial mutations occurring…..

There’s plenty of time for evolution

It is pretty mathematical, but here’s the first paragraph of the paper:

The 2009 “Year of Darwin” has seen many welcome tributes to this great scientist, and reaffirmations of the validity of his theory of evolution by natural selection, though this validity is not universally accepted. One of the main objections that have been raised holds that there has not been enough time for all of the species complexity that we see to have evolved by random mutations. Our purpose here is to analyze this process, and our conclusion is that when one takes account of the role of natural selection in a reasonable way, there has been ample time for the evolution that we observe to have taken place.

I can email anyone a copy of the pdf - just drop me a line…


gingoro - #45498

December 31st 2010

Dave Ussery
Please send me the pdf as I have wondered how we know that 4.7 billion years is enough time for evolution to work. 

Tak Gott Nytt Ar
Dave W

detdaba at primus dot ca


Dave Ussery - #47002

January 12th 2011

dunno why there’s such a delay in my next section (part VII) being posted (probably the Christmas break).

In the meantime, here’s the abstract for another article about mechanisms of evolution that could explain Behe’s observations…

The joys and terrors of fast adaptation: new findings elucidate antibiotic resistance and natural selection

John Roth

Molecular Microbiology, 79:279-282 (2011)

Summary

Experiments of Pränting and Andersson demonstrate how bacteria adapt to the growth limitation caused by antibiotic resistance mutations. The process of adaptation relies on gene copy number changes that arise at high rates, including duplications (10−4 per cell per generation), amplifications (10−2 per cell per generation) and mutant copy loss (10−2 per cell per division). Reversible increases in copy number improve growth by small steps and provide more targets for rare sequence alterations (10−9 per cell per division) that can stably improve growth. After sequence alteration, selection favours loss of the still mutant gene copies that accelerated adaptation. The results strongly support the amplification-reversion model for fast adaptation and argue against the alternative idea of ‘stress-induced mutagenesis’.


Rich - #50246

February 5th 2011

gingoro (45498) and Dr. Ussery (45272):

I’m not taking sides regarding the paper mentioned above.  But just as a public service announcement, for anyone interested in reading a critique after reading the paper, here are some informal comments on it by Doug Axe:

http://biologicinstitute.org/2011/01/14/breaking-news-from-the-academy-there’s-plenty-of-time-for-evolution/


gingoro - #50278

February 6th 2011

Thank you Rich.
Dave W


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