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 - #35264

October 18th 2010

What then do you make of her ‘post-Darwinist’ self-identifying label, Arthur? Do you think that the term ‘post-Darwinist’ (leaving aside completely the ID-journalist from Toronto who runs a Blog of the same name) is a possibly meaningful term for use by biologists or other scientists?

By following the link to your Blog, it says you are a Plant and Soil Scientist who contributes to Panada’s Thumb. Do you consider yourself a ‘Darwinian’ plant and soil scientist?

I am not a Darwinist, even though Darwin made speculations in my fields of scholarly research. His speculations have influenced the field, to be sure, and there are still some who insist on calling themselves ‘evolutionists’ too. But it is quite clear that the field, in general, has for a long time been post-Darwinian. Then again, I’m not a natural-physical scientist and feel no compulsion to call myself a ‘naturalist’.


Arthur Hunt - #35273

October 18th 2010

Rich:

“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.

That is Margulis’ criticism of “neo-Darwinism” in a nutshell.  Specifically, this is exactly, to a tee, the tenor of her “no mutations have been proven to cause evolution” assertion.

Gregory:

What then do you make of her ‘post-Darwinist’ self-identifying label, Arthur? Do you think that the term ‘post-Darwinist’ (leaving aside completely the ID-journalist from Toronto who runs a Blog of the same name) is a possibly meaningful term for use by biologists or other scientists?

Not especially.  It’s a meaningless phrase to me - it may mean that you were born after Darwin’s time, or it may mean you’re really full of yourself, or it may mean that you prefer the Modern Synthesis to earlier manifestations of evolutionary theory, or it may mean ...

You get my drift, I hope.


Gregory - #35276

October 18th 2010

Thanks for the link, Bilbo. Great interview with Margulis! Lots of gem quotations in that one.


Gregory - #35283

October 18th 2010

“it [post-Darwinist] may mean that you were born after Darwin’s time, or it may mean you’re really full of yourself, or it may mean that you prefer the Modern Synthesis to earlier manifestations of evolutionary theory, or it may mean ...”

... that Charles Robert Darwin was WRONG in a lot of ways and that new views are superceding his.

Do you accept that this could be one legitimate meaning of the term? I’d like a Yes or No on this please, Arthur, not evasiveness or rhetorical drift.

Thanks in advance,
Gregory


Trevor K. - #35311

October 19th 2010

@Dave Ussery - #35139

To those who doubt my claim that people get fired from their jobs for rejecting evolutionary thought, here’s the latest sample you might want to check out:

http://www.haaretz.com/print-edition/news/sa-ar-dismisses-chief-scientist-for-questioning-evolution-1.317201

http://www.ynetnews.com/articles/0,7340,L-3964117,00.html

Make up your own mind what you want to believe. Oh, I forgot, you’ve done that already.


Trevor K. - #35312

October 19th 2010

It won’t be long before those who are ardent theistic evolutionists join the camp of the atheistic evolutionists in bullying and abusing those of us who believe in the direct six-day creation of heaven and earth. It’s inevitable simply because you’ll be forced to put your money where your mouth is and show that you reject “the religious nuts”. The same as when new members of a gang are initiated - they have to prove that they are capable and willing to kill an innocent bystander picked at random by the thugs.


Trevor K. - #35318

October 19th 2010

Here’s the ultimate ironic situation :
An theistic evolutionist expelled because of his religious connection:http://www.guardian.co.uk/science/2008/sep/11/creationism.education

You either worship the Darwinian god of evolution or you worship the God of [six day] creation. You cannot serve both. That is quite clear from that article.


Trevor K. - #35319

October 19th 2010

Gregory - #35368

October 19th 2010

Trevor,

It is not clear what you’re trying to accomplish here. It seems like you’ve honed in on one particular natural scientific theory and liken it as a devil of some kind. Should I assume you hold the same distaste for other natural scientific theories too, or just re: evolutionary biology?

You write: “those of us who believe in the direct six-day creation of heaven and earth”

Then you’ve mistakenly chosen the wrong channel in coming to BioLogos. There is *not one* person on staff at BioLogos or who was responsible for founding it that believes in a “direct six-day creation.” Only perhaps one or two of several hundred posters at BioLogos thinks ‘six literal days.’

Are you a YEC? If so, BioLogos is working hard to convince you that this is a position that is unnecessary to hold, that it is possible and even healthy to believe in/accept an ‘old’ Earth and to be a believing Christian. That is, science is not an enemy and the ‘warfare model’ of science vs. religion is on the way out.

You are aware that this is BioLogos’ mission, right?

Gregory

p.s. as it is, I don’t think you’re being fair to Dr. Ussery by projecting all of your angst about ‘creation’ and ‘evolution’ onto him.


Bilbo - #35379

October 19th 2010

Art:  “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.”


Margulis:  “I have not explicitly told you what I think is the major source of novelty in evolution, i.e., what heritable genetic variation does lead to speciation? If, as I claim, heritable variation mostly does NOT come from gradual accumulation of random mutation, what does generate Darwin’s variation upon which his Natural Selection can act?....

cont.


Bilbo - #35381

October 19th 2010

cont.

Margulis:  “... A fine scientific literature on this theme actually exists and grows every day but unfortunately it is scattered, poorly understood and neglected nearly entirely by the money-powerful, the publicity mongers of science and the media. Worse, much of it is not written in English or well-indexed. This literature shows that symbiogenesis, interspecific fusions (hybridogenesis, gene transfers of various types, karyotypic fissioning, and other forms of acquisition of “foreign genomes” or epigenesis) are more important than the slow gradual accumulation of mutation or sexual mergers.

It’s not clear that this is the same as your description of what Margulis says, Art.


Desotobul - #35404

October 19th 2010

I posit an “If”.—If the statement in Hebrews 11.3 is true then we are all puffing smoke.  Since there is no way to disprove this verse, in or out of context, then we’re discussing hypotheses only in an existence we know nothing about ,  none of which can lead anywhere. Search as we may, we cannot get around it.

“Through faith we understand that the worlds were framed by the word of God, so that things which are seen were not made of things which do appear.”—Hebrews 11.3

If we do not have the necessary and sufficient faith, which is more likely than not, we cannot understand God or His word.

“But the natural man receiveth not the things of the spirit of God: for they are foolishness unto him: neither can he know them, because they are spiritually discerned.”— I Corinthians 2.14

In order to understand God, the word says one must be born again from on high in order to regain the spirit that was lost in Adam.

“Let no man deceive himself. If any man among you seemeth to be wise in this world, let him become a fool, that he may be wise. For the wisdom of this world is foolishness with God. For it is written, He taketh the the wise in their own craftiness.”—I Corinthians 3.18,19


Arthur Hunt - #35429

October 20th 2010

I said:

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.”

Margulis (courtesy of Bilbo):

This literature shows that symbiogenesis, interspecific fusions (hybridogenesis, gene transfers of various types, karyotypic fissioning, and other forms of acquisition of “foreign genomes” or epigenesis) are more important than the slow gradual accumulation of mutation or sexual mergers.”

Bilbo:

It’s not clear that this is the same as your description of what Margulis says, Art.

Yeah, they’re pretty much the same thing.  Margulis is a bit more, um, graphic in talking about what is going on with all them microbial genomes, but otherwise ....

Of course, it may be that she would consider rats and mice to be the same species.  I don’t know.  But that just illustrates the pedantic nature of the argument, doesn’t it?


Arthur Hunt - #35430

October 20th 2010

Gregory @ #35283

“it [post-Darwinist] may mean that you were born after Darwin’s time, or it may mean you’re really full of yourself, or it may mean that you prefer the Modern Synthesis to earlier manifestations of evolutionary theory, or it may mean ...”

... that Charles Robert Darwin was WRONG in a lot of ways and that new views are superceding his.

Do you accept that this could be one legitimate meaning of the term? I’d like a Yes or No on this please, Arthur, not evasiveness or rhetorical drift.

Thanks in advance,
Gregory

So Darwin was wrong about mechanisms of inheritance, he didn’t know about DNA or RNA or lipid bilayers or mitosis or meiosis or .....  So I guess that makes us all post-Darwinists.

But as for the basics:

All life shares a common ancestry - Darwin was correct, and Margulis agrees with him.

Descent with modification - Darwin was correct, and Margulis agrees.

Natural selection acting on naturally-occurring variability - Darwin was correct (although not entirely so) and Margulis agrees with him.

So, Gregory, in what ways would you consider Margulis to be a “post-Darwinist”?  Can you make sense of what she is saying?


Gregory - #35435

October 20th 2010

These are quotes from Margulis’ speech at the Darwin 2009 event I attended & at which I also presented.

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

Nietzsche wrote: “Darwin forgot the spirit.”

If human beings are endowed with a ‘spirit’ as most people accept, though fewer than average for biologists, then something is missing in a purely naturalistic biology of people. To me, part of Margulis’ post-Darwinism is a kind of neo-vitalism, i.e. connected with her Gaia view of the universe.

“You neo-Darwinists - Use your heads! Of course it’s a group! What is individual here? It’s a community!” – Margulis

Obviously, she wants to ‘go beyond’ the edge of the neo-Darwinian paradigm.

“Nature *does* make jumps because parts become more symbiotic.”

In Darwin’s gradualism, no jumps!

“They [Darwinists] still won’t let me publish on spirochites!”

Post-Darwinism means coming up with new biological theories OR ideas that either *reject* or go beyond Darwin’s ideas, like Margulis’.

You seem to hear post-evolutionary, when post-Darwinism is said, Arthur. They are not the same. ‘Basics of evolution’ does not equal ‘Darwinism.’


Gregory - #35437

October 20th 2010

Another question for you, Arthur (though you still didn’t answer if you consider yourself a Darwinian plant & soil scientist):
Is there possibly any ideological or worldview reason a person might choose to ‘hold onto’ the label of ‘Darwinist’ &/or ‘Darwinism’ when the ideology is quite clearly so dispiriting? If so, do you think this might go to explain the correlation between being an evolutionary biologist & being an atheist or agnostic? Could atheists & agnostics be less inclined to ‘let go’ of ‘Darwinism’?

I defined ‘Darwinism’ above: “an ideology that crosses the boundaries from natural-physical to human-social sciences.”

Some people simply will *not* let go of the label ‘Marxist.’ Even when shown problems & they grudgingly agree to flaws & inconsistencies in Marx’s ideas, they argue that ‘improvements’ upon Marx, even 100yrs later, should *still* be called ‘Marxist’ b/c they agree with the same ‘general principles’. This appears to be what you are also doing with Darwin’s ‘basics’.

BioLogos is caught on this too, by defining ‘Darwinism’ as ‘evolution by natural selection’. On this, it is plainly wrong. It under-estimates the power of ideology. New ideas are here: time to drop Darwinism!


Gregory - #35439

October 20th 2010

“A science which hesitates to forget its founders is lost.” - A.N. Whitehead

BioLogos’ definition of Darwinism (Questions page):
“Darwinism is the scientific theory of evolution by natural selection, subsequently synthesized with Mendelian genetics and modern molecular biology. BioLogos accepts the correctness of this evolutionary model based on a massive database of supporting evidence, but views God as the author of this process.”

How could God author the process of ‘Darwinism’ when Darwin himself didn’t subscribe to this?!

A Christian who accepts biological evolution (within limits, which *all* scientific theories have) - no problem. A Christian Darwinist - contradiction in terms. A Christian evolutionist - unnecessary forced integration (and usually poorly argued on philosophical ground) of science & religion.

David Ussery hasn’t answered yet @ whether he takes the label ‘Darwinist’ or not & he probably won’t.

It’s a shame that so many Christians who are biologists & who also accept biological evolution can’t ‘come out of the closet’ (they don’t seem to know they’re in!) by rejecting the dispiriting notion of ‘Darwinism’ & publically absolving themselves of that outdated label.


Gregory - #35443

October 20th 2010

Even some atheists these days are saying, “I’m an atheist, but I’m *not* a follower of Richard Dawkins.”

Why can’t BioLogos catch on to the signs of the times by publically distancing itself from the dispiriting ideology known as ‘Darwinism’?

In this thread, for example, David Ussery could say: “I am *not* a Darwinist, but I accept biological evolution in so far as…etc.”

Or is it now kosher to disagree with the IDM at *all* points, perhaps out of force of habit and not reasoning, and thus to deny Michael Behe any *right* to identify LIMITS to Darwinism?


Rich - #35451

October 20th 2010

Arthur asked:

“in what ways would you consider Margulis to be a “post-Darwinist”?

Margulis tells us precisely the major way in which she is “post-” (and anti-) Darwinist:

“(3) Where does novelty that’s heritable come from?  What is the source of evolutionary innovation? ......  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…...

“... 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.  [But] 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**.”

Lynn Margulis, in Suzan Mazur, *The Altenberg 16* (Berkeley: North Atlantic Books, 2010), pp. 278-9 (emphasis added).

Arthur, the meaning is plain.  She rejects the heart and soul of neo-Darwinian theory.  Not “evolution” (descent with modification), but the neo-Darwinian explanation of it.


pds - #35496

October 20th 2010

Arthur Hunt 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” . . .  <<<

On this point of fact it seems quite obvious to me that Rich and Bilbo are correct, and Arthur Hunt is wrong.


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