The Skeptical Biochemist: Is There an Edge to Evolution? Part 1

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October 16, 2010 Tags: Design

Today's entry was written by David Ussery. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

The Skeptical Biochemist: Is There an Edge to Evolution? Part 1

An Analysis of Michael Behe’s book, The Edge of Evolution

In the 12th century, the Danish king set aside a large area of forest along the eastern coast of the island of Zealand, as a Royal Hunting grounds. The area was fenced-off a few hundred years later, and is now open to the public. Fortunately for me, I live close to the “Deer Park,” and early in the morning, before many people get out of bed, I go for a run there. I am often truly impressed by what I see in nature, such as the majestic stare of a stag looking at me, as I go by, or the noise and sight of a flock of geese flying overhead. As an individual, I have no problem saying that what we see around us can point towards transcendence – there is grandeur and beauty. When discussing the Intelligent Design movement with my oldest brother, Steve, he asked me what was wrong with the idea that we can see God in nature—that is, that the goodness and design we see around us is surely an argument pointing towards God. I told him I don't have problems with this line of thinking. Having thought about this some, I realized that this idea is very common in the Bible, and for example Jesus often seemed to point to this in parables. However, as a scientist, I am deeply skeptical of claims that one can use science to somehow ‘prove’ God exists (or to ‘prove’ there is no God, for that matter). In 1661, around the same time the Danish king fenced-off the area around the “Deer Park,” one of the first chemists, Robert Boyle, wrote a book called The Sceptical Chemist. (Hence the title of this review.) Boyle was a devout Christian as well as a very good scientist; I will come back to Boyle later.

This brings me to mention the target audience of this review. Of course anyone can read this, but it is intended mainly for educated readers who are interested in the science/religion dialogue, and in particular are interested in Intelligent Design, and either have read or want to read The Edge of Evolution: The Search for the Limits of Darwinism, by Michael Behe (Free Press, New York, 2007). I have heard from some of my friends and family that they find this book “convincing” from a scientific point of view. Before I go into a discussion of the book, I want to give the reader a bit more perspective about myself. I grew up in Springdale, Arkansas, and am the youngest of five children. Some (not all) of the members of my family are “young earth creationists,” that is, they think that the world is less than 10,000 years old. I first heard of Mike Behe about 25 years ago, when I was a Ph.D. student, working on showing that alternative DNA helical structures could exist inside of living cells. Behe had published a paper with Gary Felsenfeld, showing that methylation of certain DNA sequences could greatly facilitate the formation of left-handed Z-DNA, and that Z-DNA did not like to be wrapped around the nucleosome. Probably for most people, that last sentence doesn't make much sense, but for me, this was a paper that I was very fond of, as these results pointed in the direction of perhaps some sort of biological meaning. I eventually got my Ph.D. (in biochemistry/molecular biology from the University of Cincinnati College of Medicine), did a post-doc at the Institute of Molecular Medicine, Oxford University, and about 12 years ago moved to Denmark, where I have been the leader of the comparative microbial genomics group at CBS (the Center for Biological Sequence analysis, a bioinformatics center in the Department of Systems Biology, at the Technical University of Denmark).

Now that I've laid down my philosophical and personal perspective I can get on with the review. I feel that this is a necessary background as, after I reviewed Darwin's Black Box more than 10 years ago, I was accused by several readers of being critical of Behe not based on the science, but because I “wanted to promote atheism,” which is certainly not the case. I will struggle to give what is written in Edge of Evolution a fair hearing - let's see how well the scientific evidence supports what is written in the book.

First, I want to start on a positive note - there are (at least) two things that I liked about the book:

  1. Behe does a good job of describing the logical outcome of thinking in contemporary molecular biology. For example, IF in fact DNA is really some sort of computer code, where did this information come from, how is it maintained, and Who wrote it? IF in fact the mutational frequency of DNA is in the range of 1 change per hundred million base-pairs (that is, the DNA polymerase incorporates the “wrong” base about once ever hundred million times), then how can we explain the incredible diversity we see around us?

  2. Behe is writing from the point of view of a non-materialist. Thus, he seems to think that there is more to the world than what we see around us, and this is in contrast to many other vocal atheistic scientists

I will now make my way through the text, in order of the chapters. In my opinion, the book starts well, and then begins to veer off in strange directions - but I'm getting ahead of myself.

Chapter 1 - The Elements of Darwinism

I agree with Behe when he says that “Darwin's theory has to be sifted carefully, because it's actually a mixture of several, unrelated, entirely separate ideas”: random mutation, natural selection, and common descent. He then goes on to say that of the latter, “in brief, the evidence for common descent seems compelling,” but that he feels “random mutation is extremely limited.” Later in this chapter, he states “Evolution from a common ancestor, via changes in DNA, is VERY well supported. It may or may not be random.” [page 12, emphasis in the original] This will in fact be the main focus of the rest of the book - whether “random mutation” alone can generate enough diversity on which natural selection can work , in order for evolution to occur. So just to flesh this out a bit—in Behe's defense, clearly he is not a “young earth” creationist, who thinks that the world is less than 10,000 years old. He has no problem with the world being about 4.5 billion years old, and life slowly evolving from the first single-cell bacteria appearing almost as soon as fossils could form, through another 4 billion years as mostly single-celled or tiny microscopic organisms, and the very recent appearance of larger plants and animals a bit less than a half-billion years ago. This is all fine and accepted to be true—it is just the MECHANISM for how this might have happened that is being considered. Just as a minor point, one thing in this chapter that is stated as fact, isn't quite right in my opinion—“By far the most critical aspect of Darwin's multifaceted theory is the role of random mutation. Almost all of what is novel and important in Darwinian thought is concentrated in this third concept.” Perhaps this is true today, but certainly when Darwin published his Origin of Species, the critical novel, important and new idea, in contrast to the current thought, was that of common descent—in fact Darwin hadn't a clue about HOW diversity was generated, but the whole point of his book was to demonstrate the evidence for natural selection and change of species (common descent) over time, in contrast to the idea that each individual species had been recently created by God, a few thousand years ago. And common descent, Behe admits, is supported by “compelling evidence”—so we are in agreement here. Evolution has happened over billions of years, and there is “compelling evidence” for evolution by common descent.

In my next post we will examine where Behe and I part company.


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.

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Gregory - #35508

October 20th 2010

And thus, it is also quite clear that BioLogos’ definition of ‘neo-Darwinism’ is wrong because it confuses neo-Darwinism with “the scientific theory of evolution by natural selection.”

Will BioLogos admit its error and change the definition of ‘Darwinism’ in its question section?


R Hampton - #35520

October 20th 2010

Lateral (or Horizontal) Gene Transfer is an uncontroversial and accepted part of modern Evolutionary Theory and I don’t see how “symbiogenesis” is any different.


Rich - #35523

October 20th 2010

R Hampton:

“Modern evolutionary theory” is too vague a term.  There are many different versions of modern evolutionary theory.  That is why evolutionary biologists debate endlessly with each other.

All kinds of things are put forward as “mechanisms” of evolution:  random mutations, symbiogenesis, “genetic drift,” “natural selection,” etc.  Depending on which of these mechanisms are included or excluded, and on their relative weight as causes, you can get many different evolutionary theories, just as you can get many different theories in modern cosmology or many different systems of bidding in contract bridge.

The predominant evolutionary theory in the 20th century was neo-Darwinism, also called The Modern Synthesis.  It emphasized “random mutation” and “natural selection” as the overwhelmingly predominant factors.  It could be “touched up” with some other putative mechanisms of change, of course, but those two elements were central.

Margulis says that neo-Darwinism was fundamentallly wrong.  Not about common descent (which is implied in *any* theory of evolution), and not about natural selection, but about the creative power of “random mutations.”  She says it’s close to zilch.  You have the quotations.


R Hampton - #35526

October 20th 2010

You are getting hung up on “neo-Darwinism.” As I said before, LGT/HGT is uncontroversial and accepted even by Richard Dawkins:

(8/7/07) “The rest of [Freeman] Dyson’s piece is interesting, as you’d expect, and there really is an interesting sense in which there is an interlude between two periods of horizontal transfer (and we mustn’t forget that bacteria still practise horizontal transfer and have done throughout the time when eucaryotes have been in the ‘Interlude’). But the interlude in the middle is not the Darwinian Interlude, it is the Meiosis / Sex / Gene-Pool / Species Interlude. Darwinian selection between genes still goes on during eras of horizontal transfer, just as it does during the Interlude. What happened during the 3-billion-year Interlude is that genes were confined to gene pools and limited to competing with other genes within the same species. Previously (and still in bacteria) they were free to compete with other genes more widely (there was no such thing as a species outside the ‘Interlude’). If a new period of horizontal transfer is indeed now dawning through technology, genes may become free to compete with other genes more widely yet again.”
http://www.edge.org/discourse/dawkins_dyson.html


Rich - #35527

October 20th 2010

R Hampton:

I am not getting “hung up” on neo-Darwinism.  You are not following the conversation.  Let me put it in point form for you:

1.  Bilbo said that Margulis rejected neo-Darwinism.
2.  Arthur Hunt implied that Bilbo misinterpreted Margulis.
3.  Bilbo and I provided decisive quotations to show that Margulis rejects neo-Darwinism.
4.  Arthur will not concede that he made a mis-statement about Margulis’s view, even in fhe face of documentary evidence.

We are not arguing here about how evolution works, what mechanisms there might be, whether horizontal gene transfer can be combined with neo-Darwinism (I’d guess that it can).  We are arguing about what Margulis said.  If you don’t find that an interesting argument, don’t join in. 

The reason it’s relevant is that we are discussing Behe on this thread, and Behe self-consciously opposes “neo-Darwinism.”  (No, I am *not* saying he agrees overall with Margulis about evolution, so don’t even go there.  If you do, you’re not paying attention.)  Behe and Margulis have different views of how evolution works, but they agree that neo-Darwinism is a very inadequate account.  That’s all Bilbo meant.  And he’s right.  Arthur should concede the point and move on.


R Hampton - #35563

October 20th 2010

horizontal gene transfer can be combined with neo-Darwinism (I’d guess that it can).

That was my point and thank you for acknowledging it. Do you think Behe and Margulis agree that neo-Darwinism includes LGT/HGT?


Arthur Hunt - #35570

October 20th 2010

Rich’s claim:

2.  Arthur Hunt implied that Bilbo misinterpreted Margulis.

What I said:

Bilbo,  if you take the time to understand Margulis’ ideas more completely, you will realize that her criticisms have little to do with “neo-Darwinism”  and much more to do with the definition of a species, an organism, even a genome.

Rich, your reading skills are as lacking as your knowledge of biology.  I made a recommendation to Bilbo (one he seems to have taken somewhat to heart, based on later comments), not an accusation.

My opinions of Margulis’ ideas are pretty defensible.  As one would find out, if one were to pose my “rats vs. mice” example to her.

I’m going to leave this subject with one last note.  Darrel’s original intent was to find a biologist who might not agree with Ussery and would instead defend Behe.  Anyone who reads Margulis’ works would realize that she isn’t this person.  She may or may not agree with Ussery, but it is not likely that she would agree with Behe’s ideas, that still posit critical roles for genetic changes in evolution.


Arthur Hunt - #35572

October 20th 2010

Gregory @ 35437:

I have no idea where you get your odd notions.  “Darwinism” is shorthand for a biological theory, and my summation in 35430 is a good accounting of it.  When you add such bizarre notions as you do to what is a theory of biology, and then begin to rant and rave against your fictional constructs, I quickly lose interest in the discussion.  I am not inclined to waste my time entertaining your strawmen and then making sense of your objections to them.

I apologize for being blunt about this, by the obsession with ideology and the like really destroys what could be a fun discussion.


Gregory - #35582

October 20th 2010

Arthur Hunt wrote:
“her [Lynn Margulis’] criticisms have little to do with “neo-Darwinism”...”

It’s obvious that there is something fishy going on here.

Quotes from L. Margulis (linked in this thread):
“The real disagreement about what the neo-Darwinists tout, for which there’s very little evidence, if any, is that random mutations accumulate and when they accumulate enough, new species originate.”

“neo-Darwinists are a minor twentieth-century religious sect within the sprawling religious persuasion of Anglo-Saxon Biology.”

“Neo-Darwinism is very bad; it is reductionistic…& took the life out of biology.”

“You neo-Darwinists - Use your heads!”

On top of this she even calls herself a ‘POST-DARWINIST.’

Yet Arthur Hunt, soil & plant scientist, perhaps in an attempt to protect, obviously not science, but rather his personal worldview, i.e. that DarwinISM could possibly make him an ‘intellectually fulfilled atheist’,  thinks her criticisms have “little to do with neo-Darwinism”!?!

This is just plain astonishing!

Next Arthur will perhaps say that Margulis *totally* agrees with neo-Darwinism! B/c the truth doesn’t seem to matter to this ‘scientist.’ Humility out the window.


Rich - #35604

October 21st 2010

Arthur Hunt:

I’m sorry, but it is your reading skills that are defective.  Neither Bilbo nor I ever said that Margulis agreed with Behe—in fact, we stressed she didn’t—yet in your last paragraph you “correct” us on this, as if you haven’t paid any attention to what we said.

And I already said (twice, I believe) that I was not applying Margulis’s statements to David Ussery’s challenge, but you keep “correcting” me on that point.

I focused on a misleading statement you made about Margulis.  That statement was: “her criticisms have little to do with ‘neo-Darwinism.’”  That statement was false.  Bilbo and I have shown this with passages from Margulis, passages on which you refuse to comment.

Pulling rank about your superior knowledge of biology is pointless.  I was challenging your interpretation of Margulis’s prose, not your biological views.  I was clarifying the way she uses the term “neo-Darwinism” and the way she characterizes her relationship with neo-Darwinism.  My exegesis is correct (and don’t overlook the possibiity that I know more about the *history* of biology than you do).

If you can’t bring yourself to say to a non-biologist, “I stand corrected,” that’s your problem.


Rich - #35605

October 21st 2010

R Hampton:

Please make a distinction:

One can construct a hybrid evolutionary theory in which neo-Darwinism (RM + NS) is the backbone, and other mechanisms (horizontal gene transfer, etc.) play an ancillary role.  If that is what you are saying, of course you are right and I agree.  Most evolutionary biologists of the past few decades have done exactly that, maintained the basic neo-Darwinian claim as the main explanation for evolution, while allowing that random mutation may need to be supplemented by other genome-altering events.

*But that is not Margulis’s position*.  She says that mainstream evolutionary biology has been wrong to make random mutations the primary driver of the creation of new forms.  In fact, as you can see from her remarks which I quoted, she thinks that random mutations have contributed at most a small part of biological novelty.  She is therefore not a neo-Darwinian, by definition.  *And she says so*.  For you or Arthur to argue that she does not mean what she says is sheer stubbornness.  If we cannot agree on the meaning of simple, blunt, clear statements such as hers, there is no hope of any serious discussion of much more complex biological matters.


Trevor K. - #35616

October 21st 2010

Since I’m half-way around the world, any meaningful participation in the lively discussions is out of the question. Hence the interjecting comments here and there.

In my opinion, “the theory of evolution” is a collection of ad-hoc beliefs that cannot be falsified [because they will always be supplanted by more ad-hoc assumptions] and hence the “theory of evolution” does not exist.
Like someone already mentioned, the ABILITY of random mutations and natural selection to create completely positive, functionally uplifting new genetic information [that does not already exists within the genome]  simply doesn’t exist.

That said, perhaps a little new spam is in order:
http://creation.com/james-s-allan-genetics-in-six-days —- the story of an evolutionist’s journey into 6-day creation belief.

http://creation.com/can-christians-believe-evolution  —- something to consider.


gingoro - #35643

October 21st 2010

Since the comments on this thread seem to have degenerated from looking at objective problems with ID to general bashing of ID I thought a list of how to’s would be appropriate.
http://satirizingscientism.blogspot.com/2009/07/presenting-op-ed-piece-from-dr.html

Dave W
(ps for those who don’t get it, I am being sarcastic!)


Arthur Hunt - #35644

October 21st 2010

Rich:

Pulling rank about your superior knowledge of biology is pointless.  I was challenging your interpretation of Margulis’s prose, not your biological views.

LOL.  In other words, don’t try to confuse the issue with biology.

My bad.

I’ve given readers here a clear and easy thought experiment that makes my case.  I’ll repeat it - given Margulis’ prose (quoted here, or anything else one might be aware of), how might she explain the differences between mice and rats?  Then ask yourself - is she talking about “neo-Darwinism” or is the real issue/complaint/point/revelation the definition of a species.  If you cannot bring yourself to try this, then you might want to find another discussion, since you have no interest in understanding anything I am saying.  And if you are not going to think about my “prose”, then you are wasting everyone’s time.

The point of what was an innocent aside was to get some here to look more closely into Margulis’ ideas, and especially to explore things with the veils of ideology removed.  It would seem as if I ask for way too much.


Rich - #35650

October 21st 2010

Arthur Hunt:

I really tire of the territorial pride of the life scientists on this site.  And as someone with a Ph.D. in a deep and serious academic subject which requires scrupulous honesty about what texts say,  I’m appalled at the level of intellectual dishonesty that Ph.D.s in Biology allow themselves to get away with, when they will not yield to direct quotations from an author.

Margulis is a world-famous specialist in evolutionary biology.  As far as I know, your field is not evolutionary biology.  Who is more likely to have a firm grasp on what the term “neo-Darwinist” means?  If you are too proud to learn from a non-biologist, learn from your senior in the biological sciences.  I’m done.


Arthur Hunt - #35660

October 21st 2010

Shorter Rich:

“Art, I don’t understand what you are saying, and I am not interested in understanding what you are saying.  I just don’t like that you are saying it.”

Fair enough.  Perplexing, but entirely your prerogative.


Rich - #35661

October 21st 2010

Arthur:

And shorter:

“Rich, your quotations from Margulis are irrefutable, but I’ll be d——-d if I take any correction from from a non-biologist, even when he’s right.”


pds - #35664

October 21st 2010

Arthur Hunt,

We all understand your point about Margulis.  We are just more interested in the question raised by Darrel Falk and Bilbo’s response.  Rich has made that very clear.  It amazes me how often I encounter scientists who don’t seem able to follow a line of discussion in a logical manner.

Darrel:

“We make this point, because some have proposed there is controversy within the discipline of biology about evolution—i.e.some think that Behe’s ideas may well be held by other reputable biologists.”

Bilbo:

“Would Lynn Margulis and James Shapiro count?  Neither one of them thinks neo-Darwinism can account for most of evolution.  And though their arguments are not as detailed and specific as Behe’s, it is clear that their rejection of neo-Darwinism is for the same reasons.”

**********

What seems clear to me is that many biologists and other scientists share some of Behe’s views about how much random mutation and natural selection can explain.  Far fewer would endorse all of Behe’s views.


pds - #35665

October 21st 2010

Falk’s standard strikes me as a unrealistic. 

Falk:

(“Shapiro and Margulis would count if they would publicly endorse the science presented by Michael B in “Edge of Evolution,”  and point out where they think David Ussery has it wrong.”)


Arthur Hunt - #35676

October 21st 2010

pds, Margulis rejects neo-Darwinism for reasons very, VERY different than those Behe offers.  Margulis very likely does not give any credence to Behe’s thoughts about evolutionary change, since Behe thinks of organisms much as do most biologists.  In other words, Behe’s emphasis on protein evolution (front-loaded, intelligently-designed evolution, but still evolution driven by mutational change in an organism’s genome) flies in the face of everything that Margulis is asserting.


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