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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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pds - #35874

October 22nd 2010

Sad to report:

The Debate Is Off: Is There a “No Debating ID” Policy at Biologos?

Can a Biologos person comment on this?


Gregory - #35879

October 22nd 2010

Yes, can I BioLogos person please comment on this.

Though I didn’t respond, I read your news item, pds. Must say I was quite looking forward to hearing about Meyer and Axe vs. Falk and Isaac (though Isaac is not ‘officially’ a BioLogos person - at least I haven’t seen him officially listed here).

Indeed, it may be that meaning of ‘BioLogos’ has little to no positive content, other than “God created/evolved the biosphere.” So, perhaps the two positions couldn’t agree on a topic that would be satisfactory to both ‘sides.’ If Falk and Isaac thought they could go to a ‘debate’ to merely criticize the alternative position (i.e. as anti-IDists) and not have to defend their own position (as theistic evolutionists/BioLogicists), that of course would rig the results unfairly.

As it is, I’ve not yet read a BioLogos ‘proponent’ even recognize the question that Behe raises in the subtitle to his book and in the title itself: Can there *possibly* be an ‘edge’ to ‘evolution’ or a ‘limit’ to Darwinism? WIthout yet dignifying the question, BioLogos does injustice to the science, philosophy and/or theology that is being applied in the discussion.


pds - #35880

October 22nd 2010

According to the Conference web site, the topic was going to be “Origin of Life.”:

“26.  Darrel Falk and Stephen Meyer with Randy Isaac and Doug Axe. Walter Bradley, moderator. Origin of Life.”

Maybe Biologos did not want to take a public position against ID on this topic.


John - #35903

October 22nd 2010

Gregory wrote:
“As it is, I’ve not yet read a BioLogos ‘proponent’ even recognize the question that Behe raises in the subtitle to his book and in the title itself: Can there *possibly* be an ‘edge’ to ‘evolution’ or a ‘limit’ to Darwinism?”

Instead of loading it with the confusing term “Darwinism,” why don’t you simply ask if there can possibly be a limit to rates of evolutionary change caused by a lack of genetic polymorphism, which is Behe’s assertion in less-loaded terms?

The answer is yes, but Behe’s desperate quote mining in a few cases doesn’t show us one, particularly when his factual claim—on which one of the cases Behe himself chose was based—was wrong by a factor of infinity.

There’s a reason why his empirical productivity has been zero for a long time, and there’s a reason why he no longer reads the primary literature.


Rich - #35906

October 22nd 2010

pds:

Re R Hampton’s suggestion—for which I’m grateful—if you have a gmail account or any other account with an email address with a phoney name, that would be my preferred means of contact.


Rich - #35909

October 22nd 2010

John (35903):

You don’t have a clue what Behe reads.  You don’t know him personally.  You don’t follow him around 24 hours a day and view what he’s reading at the library or on his computer.  Don’t make statements you can’t prove.

In any case, whatever he reads, he’s contributed something to human thought.  You haven’t contributed a single useful piece of scientific information even to this blog site, let alone two books that have stimulated worldwide debate by raising significant questions about evolutionary theory.  All you’ve done is carp and throw out ad hominem remarks.

If you know as much as you claim to know (which I doubt), why don’t you have the courage to reveal yourself, and challenge Behe to a public debate?  If he’s as incompetent as you claim, you should be able to thrash him.  But you can’t, can you?  So rather than stand up in public in a contest in which you would come off much the worse, you snipe from the shadows.

You may have a science degree, but you don’t conduct yourself like a scientist.  All my science professors were gentlemen who argued against the point, never against the man.  Your tactics bring science into disrepute.  You should be ashamed of them.


beaglelady - #35912

October 22nd 2010

Rich and PDS,

You can also contact BioLogos privately and ask to be put in touch with each other.


John - #35913

October 22nd 2010

Rich went for the all-out ad hominem attack:
“You don’t have a clue what Behe reads.”

We all do. Read his testimony from the afternoon of Day 12 of the Kitzmiller vs. Dover trial. Are you claiming that Behe was lying under oath?

“Don’t make statements you can’t prove.”

The proof is in Behe’s own sworn testimony. He makes categorical public pronouncements on subjects in which he can’t be bothered to read the primary literature.

“In any case, whatever he reads, he’s contributed something to human thought.”

Nothing useful wrt ID, because he’s unwilling to test his hypotheses—see the same testimony, given under oath.

“All you’ve done is carp and throw out ad hominem remarks.”

I’ve argued from evidence, something that strikes fear in you.

“If you know as much as you claim to know (which I doubt), why don’t you have the courage to reveal yourself, and challenge Behe to a public debate?”

Science is settled by data, by people who work in the lab or in the field, something Behe is too lazy and faithless to do. You’re still trying to sell the desperate lie that science is just like high-school debates. You lack the faith to test an ID hypothesis.


John - #35914

October 22nd 2010

“If he’s as incompetent as you claim, you should be able to thrash him.  But you can’t, can you?  So rather than stand up in public in a contest in which you would come off much the worse, you snipe from the shadows.”

You’re projecting, Rich. If ID is as wonderful as you claim it to be, you and Behe would be excited about working at the bench or in the field to test an ID hypothesis and show the results to peers and the public, like real scientists do.

“You may have a science degree, but you don’t conduct yourself like a scientist.”

This just shows how far from real science you are, Rich. One’s degree doesn’t make one a scientist. Doing science makes one a scientist, and Behe quit doing that 15 years ago. I suspect you’ve never done any science.


John - #35915

October 22nd 2010

Rich:
“All my science professors were gentlemen…”

I’ve found that among real working scientists, tact is not common.

“... who argued against the point, never against the man.”

So what do your ad hominem attacks say about you? Particularly when you ignore all substance in favor of them.

Here’s some substance for you and pds to run from.

Do the studies cited in the reviews cited by Dave Ussery contradict Behe’s claims?  Here’s a specific one cited:

Sekita Y, et al. 2008. Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta.
Nat Genet 40: 243–248.

How did pds (or you, since you are defending pds with your ad hominem attacks) determine that the data from this study:
1) are not a specific example, and
2) do not directly contradict Behe’s assertion?

“Your tactics bring science into disrepute.  You should be ashamed of them.”

Your buddy pds has yet to respond to the point above, and I predict that you won’t either. You don’t know, you don’t care, and you are afraid to even look for anything but quotes to pull out of context because you have no faith.


Gregory - #35922

October 22nd 2010

I asked: Can there *possibly* be an ‘edge’ to ‘evolution’ or a ‘limit’ to Darwinism?”

John replied (in the midst of relentless attacks on Behe and his character): “The answer is yes.”

Well, why don’t you offer us your ‘scientific’ opinion then, John. What do you think the ‘edge(s)’ of ‘evolution’ is/are and/or the ‘limits’ to Darwinism?

Have you identified *any* limits? Or do you just have mere speculations of them?


Rich - #35926

October 23rd 2010

John:

You made a sweeping statement about what Behe reads *now*.  You can’t base that on a statement he made *five years ago*, even supposing that you have not misinterpreted that statement.  But you know, it’s funny; I’ve read every single reply that Behe has published to critics of *The Edge of Evolution*.  In those replies he cites dozens of scientific articles.  Have you read every single one of those replies, and checked every single article he cites?  Is not a single one of those articles from “the primary literature”?  When you’ve checked them all, one by one, get back to us and report.

In any case, what you still cannot see, because you don’t understand the meaning of “ad hominem” (it doesn’t mean just personal insults), is that 95% of your arguments on this blog against ID have been ad hominem.  Ad hominem arguments are directed against the person rather than the point.  References to how much someone has read, how many experiments he has done, whether or not his colleagues respect him, whether or not he has “faith” and so on, are not pertinent to demonstrating the truth of falsity of the statements a person makes.  If Behe is wrong, show that his *statements* are wrong.  Don’t talk about *Behe* at all.


pds - #35978

October 23rd 2010

Rich,

“Re R Hampton’s suggestion—for which I’m grateful—if you have a gmail account or any other account with an email address with a phoney name, that would be my preferred means of contact.”

I don’t, but you could set one up pretty quickly.  If you do, I would be happy to email you.


John - #36655

October 26th 2010

Rich wrote:
“You made a sweeping statement about what Behe reads *now*.”

Yes, and I stand by that.

“You can’t base that on a statement he made *five years ago*, even supposing that you have not misinterpreted that statement.”

I’m not basing it only on that statement.

“...I’ve read every single reply that Behe has published to critics of *The Edge of Evolution*.  In those replies he cites dozens of scientific articles.”

That’s nice. Surely, given your training, you know that the set of “scientific articles” is not synonymous with the set “primary scientific literature,” and that citing an article is in no way synonymous with having read the article cited?

Rich, it’s not about what he does cite, it’s about what he fails to cite.


John - #36657

October 26th 2010

Gregory wrote:
“Well, why don’t you offer us your ‘scientific’ opinion then, John. What do you think the ‘edge(s)’ of ‘evolution’ is/are and/or the ‘limits’ to Darwinism?”

Ribosomal structure shows the edges of evolutionary mechanisms. This evidence is so powerful and convincing that Meyer grossly misleads his audience about it in Signature of the Cell.

Are you familiar with this beautiful work?

As for “limits to Darwinism,” the phrase is gibberish.


Gregory - #36666

October 26th 2010

“Ribosomal structure shows the edges of evolutionary mechanisms.” - John

Sorry, not sure what that means. What does ribosomal structure show about ‘edge of evolution’? What are the ‘edges of evolutionary mechanisms’? Does this mean that those ‘mechanisms’ are somehow limited?

Thanks,
G.

p.s. no, i haven’t read Meyer’s “Signature IN THE Cell” and don’t plan to
p.p.s. so you don’t consider yourself a ‘Darwinist’ then, right?
p.p.p.s. in a recent interview with Behe and Fox, Behe indicated that he *did* read two recent papers (2007 and ?) that Fox cited - http://www.premierradio.org.uk/listen/ondemand.aspx?mediaid={A942B34A-2BF8-482C-BA7C-61F3C95DC77A}


John - #36674

October 26th 2010

Gregory wrote:
“Sorry, not sure what that means. What does ribosomal structure show about ‘edge of evolution’?”

It demonstrates its inability to replace important, ancient structures for which there is no clear pathway to replacement.

“What are the ‘edges of evolutionary mechanisms’? Does this mean that those ‘mechanisms’ are somehow limited?”

See above and absolutely, respectively.

“p.s. no, i haven’t read Meyer’s “Signature IN THE Cell” and don’t plan to”

Just read pp. 304-306 on Amazon, then.

“p.p.s. so you don’t consider yourself a ‘Darwinist’ then, right?”

It’s a term of obfuscation with multiple definitions. When did you stop beating your wife?

“p.p.p.s. in a recent interview with Behe and Fox, Behe indicated that he *did* read two recent papers (2007 and ?) that Fox cited”

That’s nice. Do you not realize that “the primary literature” is a collective term?

Before or after Fox cited them? Were they from the primary literature?


Upright BiPed - #39751

November 13th 2010

Ussery states: “If I did not agree with Darwinian evolutionary theory, AND I COULD SCIENTIFICALLY offer a valid, alternative - I would probably be promoted, as well as get a paper published in Science or Nature.  Good science is in a sense bucking the system, proving someone else is wrong.  It is much much easier to prove someone (or something) is NOT true, than to prove that it IS true.”

This could not be more disinginuous - divorced from the facts within the academy. These are the kinds of comments meant to have an impact on those who really haven’t spent any time with the issues. They are ridiculous to those of us who have followed the arguments for years.


Rich - #40593

November 18th 2010

For those interested, Behe has responded to this column (and Part II) here:

http://www.evolutionnews.org/2010/11/dave_ussery_ruminates_about_th040631.html#more


John - #40710

November 19th 2010

Behe’s “response” makes no sense, just as it makes no sense not to respond here if he’s an honest guy trying to enlighten instead of fool his audience.


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