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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 - #35677

October 21st 2010

Arthur,

“Margulis rejects neo-Darwinism for reasons very, VERY different than those Behe offers.”

They are different in some respects and they are similar in some respects.

Darrel Falk:

“Some have proposed there is controversy within the discipline of biology about evolution.”

This seems clearly to be the case.  And there is more controversy when biologists engage paleontologists.  Fossil evidence is at least as important as the evidence from biology.


Rich - #35679

October 21st 2010

Arthur:

Bilbo in 35104:

************************
”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***.”

It seems obvious that Margulis also ***rejects neo-Darwinism for the same reasons that Behe does***.  But instead of ID, she believes:

“The source of purposeful inherited novelty in evolution, the underlying reason the new species appear, is not random mutation rather it is symbiogenesis, the acquisition of foreign genomes.”

*******************
Bilbo is saying:  she *rejects* neo-Darwinism because there is very little evidence for the creative capacity of random mutations.  That’s not “very, VERY different” from Behe’s reason.  It’s *exactly* Behe’s reason.

Bilbo grants that Margulis’s *own* explanation of evolution is very different from Behe’s.  It’s what they *reject* that they have in common.  None of us claimed that Margulis would approve of Behe, so your comment lacks relevance.

pds:  I echo your frustration.  Darwinists have trouble following arguments, or even reading carefully.  Maybe biologists should be forced to take English electives.


Arthur Hunt - #35685

October 21st 2010

So, according to Rich and pds, Margulis believes that random mutations are exceedingly rare.  This is the bottom line of Behe’s book and the basis of Behe’s dispute with neo-Darwinism.  And apparently Margulis also thinks this way.

Simply unbelievable.


Steve - #35687

October 21st 2010

Well these speculations about Margulis’s views seem to have gone on too long. Her name was mentioned in response to a comment by Darrel Falk asking tenured biologists who agree with Behe to come forward. Margulis quite obviously doesn’t agree with Behe, so I really don’t see why she is even remotely relevant, never mind why this whole comment section has been side-tracked into discussing her views..


R Hampton - #35689

October 21st 2010

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.

“Neo-Darwinism” includes LGT/HGT without equivocation and without downplaying it as ancillary. Why you are unable to accept this to truth suggests to me a basic misunderstanding of current Evolutionary theory. As proof, I quote from its detractors:

International Society for Complexity, Information, and Design (ISCID):
Neo-Darwinism is also called the Modern Synthesis (as such, it synthesizes or brings together together classical Darwinism with modern genetic theory).

Casey Luskin, IDEA Center:
Evolutionary biologists are increasingly appealing to epicycles like horizontal gene transfer, differing rates of evolution, abrupt molecular radiation, convergent evolution (even convergent molecular evolution), and other ad hoc rationalizations to reconcile discrepancies between different hypotheses about common descent.


Rich - #35690

October 21st 2010

Arthur Hunt:

You provide further evidence for my growing suspicion that Ph.D.s in the sciences, particularly biologists, are over-specialized to the point where general intellectual skills have suffered.

Throughout this thread you’ve been unable to grasp straightforward English statements, whether written by Margulis or any of us.  And when you have mangled our statements, and we have repeated and qualified them, you still don’t get them.

No one said that Margulis believes that random mutations are extremely rare.  I *quoted* Margulis to you, for Pete’s sake.  Can’t you read what she said?  And can’t you read what I said?  I said nothing about their *rarity* at all.  I spoke of their *creative capacity*.  Margulis said the same thing, in her own words, in the quotations which you won’t acknowledge.

Did you not read Behe’s *Edge* carefully?  About the inability of neo-Darwinian mechanisms to generate new body plans?  Can’t you see the connection with the Margulis quotations?

“Simply unbelievable” is right.  Unbelievable that philosophy Ph.D.s are driving cabs, and people who can’t follow an argument hold tenured positions in the sciences.


R Hampton - #35692

October 21st 2010

Relevant:
Gene transfer agents (GTAs) package random pieces of DNA up to 1,000 base pairs long (barely enough to fit one gene), approximately 1 in 20,000 carried an antibiotic resistance gene, McDaniel said. Nevertheless, the researchers found that approximately 50% of the natural bacteria acquired antibiotic resistance in some of the experiments.
http://www.the-scientist.com/news/display/57732/

High Frequency of Horizontal Gene Transfer in the Oceans, Science, October 1, 2010: Vol.330. no.6000, p.50
http://www.sciencemag.org/cgi/content/abstract/330/6000/50


pds - #35695

October 21st 2010

Arthur,

“So, according to Rich and pds, Margulis believes that random mutations are exceedingly rare.”

LOL.  Thanks for proving our point about not being about to follow arguments.

Simply unbelievable.


Rich - #35696

October 21st 2010

R Hampton:

Wrong again.

“Neo-Darwinism” or “The Modern Synthesis” was achieved roughly in the period from 1937-47.  It drew upon the work of Fisher, Haldane, Sewell, Gaylord Simpson, Mayr, and Dobzhansky, among others.  What it “synthesized” was classical Darwinian selectionism with Mendelian genetics and later developments in population genetics.  It did *not* include most of the things on the list in the second quotation above—which, by the way, if you read carefully, speaks of “evolutionary biologists,” and evolutionary biology is a much wider term than “neo-Darwinism.”

Anyone who uses “neo-Darwinism” to include HGT is using the term unhistorically and incorrectly.  Neo-Darwinism is a very specific model of evolution, the one predominant in the 20th century.  In the book quoted, Margulis explains what it is, and explains why she rejects it.  She is a specialist in evolutonary biology, as you are not.  I suggest you learn from her, rather than from amateurish attempts to cobble together blocks of discordant material from Crapipedia and elsewhere on the internet.  Try turning off your computer for a month and actually reading some *books*.  You will be amazed at the results.


R Hampton - #35698

October 21st 2010

(as such, it synthesizes or brings together together classical Darwinism with modern genetic theory)

Modern genetic theory did not exist in 1937 or 1947. You should know at least that much.


Rich - #35699

October 21st 2010

pds:

I want to reach you, but I don’t want my note or address to show up on your blog anywhere; I want you to be the only one who can receive it.  Is there an e-mail address I can use?


R Hampton - #35700

October 21st 2010

Debating design: from Darwin to DNA, Volume 10, Stephen C. Meyer, 2004

According to neo-Darwinists, mutation and selection—and perhaps other similar (those less significant) naturalistic mechanisms—are fully sufficient to explain the appearance of design in biological systems.


R Hampton - #35703

October 21st 2010

The Design Revolution: Answering the Toughest Questions about Intelligent Design, William A. Dembski, 2004

“Much of biology these days is committed to genetic heritability, though there is now increasing evidence that epigenetic factors play a role in hereditary transmission ... It can accommodate all forms of what is typically meant by Darwinian evolution, including new-Darwinism, whose incidental changes are accidental errors in the genome ... Other forms of incidental change include genetic drift, lateral gene transfer, and the action of regulatory genes in development.

Evolutionary biologists debate the precise role and extent of hereditary transmission and incidental change ... for instance, the introduction to Margulis’s book Acquiring Genomes

>

, in which she slams neo-Darwinism for having the wrong picture of incidental change. (According to her, symbiogenetic change, and not random genetic mutation, is the primary form of incidental change that drives evolution.)”


pds - #35704

October 21st 2010

Public service announcement:

Discovery Institute v. Biologos: The Debate

Should be interesting.


pds - #35706

October 21st 2010

Rich,

If you leave a simple comment on my blog (say anything), I will get your email but no one else will see it.  I will then send you an email, and you can email me back.


Arthur Hunt - #35707

October 21st 2010

Did you not read Behe’s *Edge* carefully?  About the inability of neo-Darwinian mechanisms to generate new body plans?  Can’t you see the connection with the Margulis quotations?

I not only have read Behe’s books, I understand them.

Behe has no problems with the creative capacity of mutations in protein coding genes.  He just doesn’t think that random mutations can occur often enough to permit the organism to take advantage of this creative cpacity.  This is why he hypothesizes that intelligently-designed mutational changes do the task.

Margulis doesn’t think that mutations in protein coding genes can account for any significant evolutionary change.  Regardless of their rates of appearance.

Rich and pds think these two (quite different) perspectives are the same.

Go figure.


R Hampton - #35710

October 21st 2010

Margulis comments on the place of LGT/HGT within “neo-Darwinian” evolution (chat transcript, March 12, 2007)

TimMc: So, your claim is that a buildup of simple mutations is not only not sufficient for speciation but also plays no significant role?

Margulis: Of course random mutations occur and are important for evolution in honing, modifying and generally influencing the big steps.

TimMc: So, you see mutations as having a *shaping* role rather than a *production* role.

Diogenes: and by “big steps” you mean a macroevolutionary mechanism other than random mutation + natural selection?

Margulis: There is a huge difference between virus, plasmid, small replicon horizontal gene transfer which OF course can be documented and “GENOME ACQUISITION”. It is the same kind of difference that one sees between a family and a town. The difference is in the size of the unit and the suddenenss of the change through time. Genome acquisition involves at least a single autopoetic entity (CELL or organism composed of cells). Small (plasmids, [answer is cut off]

Margulis: I think I meant: small replicons include plasmids, phage, viruses (whether RNA, DNA ir reverse transcipt), etc.


Rich - #35750

October 21st 2010

Arthur:

“Rich and pds think these two (quite different) perspectives are the same.”

No, we don’t.  And we didn’t say so.  We said only that they both agree in what they reject, i.e., they reject the claim that random mutations are sufficient to explain all of macroevolutionary change.  Both agree that one cannot get from marine worm to lobster or reptile to mammal if the only source of novelty is random mutations.

You are right that Behe grants some creative powers to random mutation, whereas Margulis (based on the quoted statements) appears to grant none.  That would be one important difference in their critique of neo-Darwinism.  But you are ignoring the emphasis Behe puts on the inability of neo-Darwinian processes (note how they use the same term in the same way) to produce new body plans.  For Behe the creative powers of random mutation are limited.

Finally, the focus of my comments was never Darrel’s challenge or comparing Behe to Margulis.  The focus of my comments was your attempt to deny by obsfuscation that Margulis (a) defines neo-Darwinism as she does and (b) rejects neo-Darwinism as she defines it.  She is an evolutionary biologist who is self-consciously *not neo-Darwinian*.


pds - #35829

October 22nd 2010

Rich,

If you leave a public comment on my blog, you just have to say “Hi, pds.”  I can delete your comment after that. 

Should I look for it?


R Hampton - #35852

October 22nd 2010

pds, Rich

One of you should create a “disposable” email account, then it wouldn’t matter if you were to make it public. Once you get the message from the other, you would never have to look at the account again. You could even deactivate it.

I maintain two accounts, one strictly for immediate friends and family, and one for the public. I get all sorts of junk in the public account, but I could care less as its main purpose is to protect the private (trusted) account.


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