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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sy - #35152

October 18th 2010

Dave is correct. Scientifically valid (by which I dont mean necessarily true, or proven) ideas may not always be suitable for publication in scientific journals. Behe and/or Shapiro could well be right, and their thoughts should be published in a philosophical context, but it is doubtful that they would get a hearing in a scientific journal, unless and until some pretty rigorous evidence were behind them. Shapiro’s ideas, which are an offshoot of punctuated equilibrium, as well as Margulis, offer a testable positive alterrnative to classical gradualism. I think the problem with Behe and ID in general is the lack of an althernative mechanism, even in a theoretical sense. While I happen to agree with Behe, that the answer is probably the creation of life by God the creator, that is not a view amenable to publication in a scientific journal.

By my last sentence I am not dismissing the ID idea. I do not believe that all truths are scientifically addressable. At least not by the methods and concepts of science we now use. I also think that we need to acknowledge the value of philosophy, which of course is the actual origin of science. If this sounds a lot like Gould’s NOMA, it is. I still think Gould was right on that.


Rich - #35155

October 18th 2010

“Unaplogeic catholic” (35127):

You don’t seem to have read Bilbo’s posts very carefully.

Bilbo asked:

“Will you admit that Margulis and Shapiro agree (implicitly, if not explicitly) ***with Behe’s criticisms of neo-Darwinism***?” (emphasis added)

And you replied:

“no,neither agrees with Behe or Intelligent Design”

Bilbo didn’t ask if they agreed with Intelligent Design; in fact, he explicitly acknowledged that they did not.  He asked if they agreed ***with Behe’s criticisms of neo-Darwinism***.

Behe’s criticism of neo-Darwinism is, put crudely, that random mutations, even cumulatively, don’t have the power to construct radically new body plans.  According to the quoted statements, Margulis and Shapiro agree with Behe on that much.

What, aside from your usual neo-Darwinian partisanship, prevents you from seeing this?  Why are you unwilling to grant that ID proponents might actually have some valid criticisms of neo-Darwinian theory, criticisms shared by many non-ID evolutionary biologists?  Are you determined to just reflexively say black when any ID proponent says white?

Bilbo:  Thanks for these excellent posts.


Arthur Hunt - #35163

October 18th 2010

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.  To be blunt, she’s being ridiculously pedantic, and her arguments, in the extreme, make her rather irrelevant to this particular debate.


Roger A. Sawtelle - #35164

October 18th 2010

Dave U.

I invite you to read my book, Darwin’s Myth: Malthus, Ecology, and the Meaning of Life. 

Maybe you will find a basis for writing that paper and having it published in Nature.


Dave Ussery - #35167

October 18th 2010

Roger, if you’ve written a book, why not go for it yourself?  I’ve already published a lot - (including 5 Nature papers - well, ONE Nature, and four in “Nature clones” - Nature Biotechnology, for example).  It’s not that I’m opposed at all to the idea - I think it’d be great - but just WANTING something to be true (or false) doesn’t make it so.  If your idea is scientifically valid and testable, why not try and get it published??


Gregory - #35178

October 18th 2010

Actually, Arthur, Margulis calls herself a ‘post-Darwinist’ because she thinks Darwinan ideas have actually been *bad* for biology over the long haul, they have stunted biology’s growth (thus republishing Kozo-Polyansky’s 1924 book to remind ‘western’ biologists of their ‘oversights’). She had no problem accepting the Darwin award due to Darwin’s historical role and contribution in the field. 

Symbiogensis is *not* the same idea as Darwin’s Victorian view of hyper-competition as the only possible source for defining a ‘mechanism’ of organic change..

I have one question for Dave: Do you consider yourself a ‘Darwinist’ or not? Hey, I’m a Weberian and a Sorokinian, no problem taking those labels in my field. I am not a Marxist. But what do you prefer to be called in yours?

I have no problem with a biologist accepting a *limited* form of evolutionary theory, that is, accepting that evolution is not an explanation for *everything* (e.g. like D.S. Wilson claims). But in the 21st century does a biologist *really* need to carry the label Darwinist anymore?

What I wrote above about the ideology of (neo-)Darwinism seems easy to push aside; nobody here but us ‘scientists.’


Rich - #35184

October 18th 2010

Arthur Hunt:

Whether Margulis’s opinions are relevant to Dr. Ussery’s statements and therefore to Darrel Falk’s challenge I do not know, so I will not comment on your charge that Bilbo’s quotations are irrelevant.  However, you have made one false statement in your post:

“her criticisms have little to do with “neo-Darwinism””

I don’t know as much biology as you do, but I do know the English language as well as you do, and I do know what Margulis says in the lengthy interview recorded in *The Altenberg 16*.  Bilbo’s quotations are from that interview.  One doesn’t need a Ph.D. in biology to know that her attack on the central doctrine of neo-Darwinism (not “evolution,” just neo-Darwinism) is crystal clear.  I suggest you read that interview before offering any more corrections.

I’m not endorsing Margulis’s critique of neo-Darwinism, but you shouldn’t deny that she is making it.  If you want to say her arguments are bad, then do so; but don’t mischaracterize her position.


unapologetic catholic - #35210

October 18th 2010

“One doesn’t need a Ph.D. in biology to know that her attack on the central doctrine of neo-Darwinism (not “evolution,” just neo-Darwinism) is crystal clear.”

Actiually, it would be helpful.  Margulis is not using “neo-darwinism” as you and Bilbo define that term.  That’s to be expected.  She is using it as a term of art (a sub disciplienof biology) between biologists and it means somethin different than you think it does. 

She has made it quite plain that she is not attacking “mainstream” nor is she a supporter of intelligent design or sypatehtic to Behe’s views.


Roger A. Sawtelle - #35216

October 18th 2010

Dave U,

Thank you for the suggestion.  My ideas are scientifically valid and verifiable, however I question if I am able to put them into the form necessary for that medium.  That is why I wrote the book. 

Lynn Margulis is credited for pointing out the symbiotic origin of complex organisms, which is contrary to the neoDarwinist view that evolution is based on cell mutation.  She has an ecological view of evolution, similar to mine, although I do not claim to be of the same stature as she.


Rich - #35218

October 18th 2010

unapologetic catholic (35210):

I’m sorry, but you don’t know what you are talking about.  You haven’t even read the source we are all discussing, so how would you have a clue what Margulis means in the passages in question?

Margulis gives a detailed discussion of what she does and doesn’t accept in modern evolutionary theory, and is very specific in what she rejects from neo-Darwinism.  And it’s *exactly* what Bilbo and I understand by neo-Darwinism.  You’re dead wrong—as usual.

Do your homework before you speak.  I am getting weary of your constant arbitrary statements, supported by no texts, evidence or reasoning.  You make statements about Behe when you know next to nothing about Behe, you make statements on the Roman position on evolution without having done proper research, and now you are doing the same about Margulis.  Your methods of debate are completely irresponsible.

Bilbo and I both said very clearly that Margulis did not support ID.  So why do you say the same thing as if you are correcting us?  Are you paying attention to the discussion at all?  Or do you just fire out negative posts at anyone you associate with ID, on general principle?


Bilbo - #35223

October 18th 2010

Ussery:  “What I see is a lot of hype (and just plain lies - that is not telling the truth) about the ‘controversy’ here. 

Were you referring to me?


Unaplogetic catholic - #35226

October 18th 2010

For those interested, Margulis has had some very interesting ideas in biology.  She is the perfect example of science at work.  She first proposed the endosymbiotic theory that eukaryotic cells were formed absorbing early forms of prokaryotes.  The discovery of mitochondrial DNA in eukaryotic cells supports her argument.  She also backed up her arguments experimentally.  Her idea appears to have substantial evidence.  In her opinion symbiosis and parasitic infestation are responsible for much more genetic change than inter-species competition—what she refers to as “neo-Darwinism.”  “Neo-Darwinism” is shorthand for “interspecies competition.  She is of the opinion that neo-darwinism as an evolution driver is overemphasized at the expense of symbiotic and parasitic sources.  There is much disagreement with her position on this and not all of the scientific work supports her position.


Unapologetic Catholic - #35228

October 18th 2010

Margulis is not a supporter of ID.  She does recognize that evolution is essentially correct. So she will be highly crtical of Behe.  She firmly accepts common ancestry and common descent.  She does nto dispute tha tnatural selction ocrrius and is a driver for evolution. There are no unexplained gaps from the Cambrian.  Her main disagreement is the relatvie importance of symbiosis compared to interspecies competition and natural selection.
 
She does have some non-mainstream ideas, which she supports by publishing peer reviewed papers and engaging her critics.  Her papers are very challenging and are still being debated.  That’s how science works.

ID proponents, instead of doing the work and engaging scientists, often offer inconsistent “dueling cliches.”  Here’s an example: “There is a monolithic orthodoxy that won’t tolerate dissent and the entire edifice is about to collapse because of all the dissenters.”  Margulis’s work demonstrates there is no orthodoxy and differing opinions backed up by actual science will get a hearing.


Rich - #35232

October 18th 2010

Unapologetic Catholic:

In your first post, you told me absolutely nothing about Margulis that I did not already know.  Further, you did not address *the interview with Margulis we were discussing*.  Not surprising, since, apparently, you haven’t read it.  Had you read it, you would realize that she defines neo-Darwinism exactly as Bilbo and I have been doing.

In your second post, you repeat that Margulis does not support ID, which we already granted twice.  (Wax in the ears?)  You say that she recognizes (slanted word) that evolution is essentially correct (true, she does think it correct).  You then go on to say that because she accepts evolution “she will be highly critical of Behe”.  But this just further confirms your ignorance of Behe which I have demonstrated many times on these threads, since Behe also accepts evolution.  You are apparently incapable of learning from your errors, because you stubbornly stick to them.  Finally, you downplay Margulis’s criticism of neo-Darwinism; it’s sterner than you are presenting.  Read the interview. 

By the way, what is your *source* for Margulis’s views?  Another quick look at Wikipedia?  Or have you actually *read* anything by her?


Bilbo - #35238

October 18th 2010

UA:  “Margulis’s work demonstrates there is no orthodoxy and differing opinions backed up by actual science will get a hearing.


James Shapiro:  “But the neo-Darwinian advocates claim to be scientists, and we can legitimately expect of them a more open spirit of inquiry. Instead, they assume a defensive posture of outraged orthodoxy and assert an unassailable claim to truth, which only serves to validate the Creationists’ criticism that Darwinism has become more of a faith than a science.


Bilbo - #35239

October 18th 2010

Margulis interview can be found here;

http://www.suzanmazur.com/?p=195


Bilbo - #35248

October 18th 2010

Art:  “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.


Margulis:  “The point of contention in science is here: (3) Where does novelty that’s heritable come from? What is the source of evolutionary innovation? Especially positive inherited innovation, where does it come from?

It is here that the neo-Darwinist knee-jerk reaction kicks in. “By random mutations that accumulate so much that you have a new lineage.” This final contention, their mistake in my view, is really the basis of nearly all our disagreement.”

So yes, for Margulis, she seems to equate novelty with “new species”, which is not what most biologists mean by “species.”  But the important point is that she denies that neo-Darwinism can account for novelty.


Johan - #35252

October 18th 2010

Dave,

You write:

“But don’t just take my word for it - have a look yourself - go to PubMed, have a look - there are 20 MILLION articles published there - and how many do the ID crowd have?  They are very proud they have maybe half a dozen mediocre articles.”

a)And how many of these articles have nothing to do with evolution? How much knowlede would we lose if we had to remove the word “evolution” from these papers? A biology/genetics paper doesn’t just count as a paper for evolution because people happen to toss the word “evolution” around.

b)You can have a million speculation papers for evolution, it’s irrelevant, we don’t determine science based on how many papers you have, but rather on what your papers demonstrate. And if Dembski is onto something, you will have to show why he is not, on his own terms, not by saying “you only have a dozen papers”


Arthur Hunt - #35253

October 18th 2010

Margulis:

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. 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.

In other words, species are not defined by just the genome of the obvious “host”, but rather by the entire conglomerate of all commensal organisms, mutualists, pathogens, and other microbial passers-by that happen to associate with a population of organisms.

Put another way, in Margulis’ eyes, the difference between a rat and a mouse lies not in the rodents’ genomes, but in the collection of microbes that co-inhabit the rodent’s bodies.

Leave aside the matter of whether or not she is correct.  For the sake of this thread, I would argue that it is a petty pedantic exercise to criticize “neo-Darwinism” from this perspective.  And that, for this reason, she would be a pretty poor contributor along the lines suggested by Darrel.


Rich - #35263

October 18th 2010

Arthur Hunt:

As I said, I have no comment on the relevance of Margulis to the above article.  However: 

It’s not “pedantic” to write:

“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.”

That’s a frontal assault on neo-Darwinian theory as conceived by Gaylord Simpson, Dobzhansky, Mayr, etc. 

“Pedantic” refers to the habit of some people of trying to catch people out on little slips or errors which are not germane to the main point.  If I said that neo-Darwinism was false because in some photos some people glued some moths on trees, that would be pedantic criticism; it would show merely that some neo-Darwinists were overzealous in their argumentative tactics, but would not be serious evidence that the neo-Darwinian mechanism was false. 

Margulis here is saying that the main narrative of the Modern Synthesis has been substantially false.  She may utterly wrong; I’m not qualified to say.  But her criticism isn’t pedantic; it’s root and branch.


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