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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Barry - #34966

October 16th 2010

Dave Ussery - #34965

” I guess right now I like best the approach described by Allister McGrath, in his “Open Secret” book, as well as his “A Fine Tuned Universe”.  Basically he argues that we need a new version of natural theology - not one based on a mechanical universe (which can easily give rise to deism), but one where a person, as a Christian, can see nature in a different level. “

I’m looking forward to the remaining review blogs and enjoyed reading the first installment. I’m puzzled why you favor the approach mentioned here. Why do you think you need it? And when you say, “...where a person…can see nature in a different level”, what exactly do you mean?


Gregory - #34967

October 16th 2010

Yes, David, what you say in #34965 makes good sense to me! And I agree with you about avoiding the word ‘Darwinism’. This is why the BioLogos Question page about Darwinism and Social Darwinism needs to be changed.

To BioLogos, the term ‘Darwinism’ actually *just* means ‘science’ and *not* ‘ideology.’

“BioLogos is the belief that Darwinism is a correct science”
“Darwinism is the scientific theory of evolution by natural selection, subsequently synthesized with Mendelian genetics and modern molecular biology.”
http://biologos.org/questions/biologos-darwinism-social-darwinism/

Coud you please help correct this perception, David?

BioLogos writes: “It is true that Darwinism may have religious implications…”

Yet this is *exactly* what Behe and others say about their ‘theory.’

Please allow that ‘anti-evolutionist’ is actually a *good* thing when it is anti-evolutionism as an ideology. It seems we are on the same page about this, David, which makes me glad! I am anti-evolutionism as an ideology and it seems, from what you wrote, that so are you.

But I am *not* anti-evolutionary biology or anti-science.

And as with you, I very much like McGrath as well.  Good night!


Roger A. Sawtelle - #34984

October 16th 2010

Dave Ussery #34965

I agree with you and Alstair McGrath that we need a new nonmechanistic cosmology which I am working on.  Is there any way to email you and him?

I do use the term Darwinism or better neoDarwinism, not because I am anti evolution, but because I disagree with the views of Dawkins and company who are neoDarwinians.

However evolution is a natural process.  Neither Darwin nor Dawkins owns it.  They espouse a view of evolution, which maybe true or not.  I think it has some major flaws and if I am going to identify them I need to call the system which has these flaws by its name, which is neoDarwinism or the orginal Darwinian theory.

Part of my criticism of Dawkins is his either mechanistic view of evolution or his relativistic view of evolution, depending on one’s point of view.  Ecology is not mechanistic or relativistic, which is the major reason that ecological evolution is much better explanation than neoDarwinism.


beaglelady - #34992

October 16th 2010

Gregory,

Starting in comment 34944, You haven’t been closing your bold tags and it’s messed up the formatting all the way down. 


Webmaster,

The blog’s editor should be checking for mismatched tags and should alert the user to any syntax errors.  (And, of course,  a preview function would be nice)


Gregory - #35026

October 17th 2010

Yeah, thanks beaglelady. i tried to fix the error by closing the boldface in the next comment, as had been done in the past. but it didn’t work this time. hope the moderator can sort it out.

sorry, folks, for the inconvenience. rest assured, my intention wasn’t to make it appear that everyone is SHOUTING at each other! = )) i much appreciate already Dr. David Ussery’s tone and willingness to engage (even if i’m related to the eastern Scandinavians) and i look forward to learning more from him and about Behe’s position too.


Johan - #35032

October 17th 2010

//- this seems to be a term mainly used by the anti-evolutionists!//

“First, Darwinism rejects all supernatural phenomena and causations. The theory of evolution by natural selection explains the adaptedness and diversity of the world solely materialistically. It no longer requires God as creator or designer .... Every aspect of the “wonderful design” so admired by natural theologians could be explained by natural selection.”—Ernst Mayr—

When evolutionists speak of evolution, they mean Darwinian evolution, and that is that the complexity and diversity of life is the result of blind material processes, this is the defining element of evolution. Nothing about the other components of evolution theory was new, and most ID proponents have no objection, however Darwin offered the mechanism: natural selection acting on random variation/ mutations. One can easily be an evolutionist while one rejects the Darwinian mechanism, Shariro and Michael Behe are good examples, Mike Behe might be an ID proponent and Shapiro is not. Richard Dawkins is a good example of a Darwinian evolutionist. Why is “anti-evolutionist” to clearly define terms?


Scanman - #35051

October 17th 2010

“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?”

This seems to boil down to whether or not God influences the natural order of things (common Theism) or whether he set the universe in motion and let the chips fall where they may (Deism).

I believe that Behe is arguing towards the idea of an (unknown to current sciences) external influence beyond random mutation.

As a Theistic Evolutionist, I believe that God controls the environmental pressures of the natural world that direct evolution….creating a path of least resistance.

Peace


Johan - #35067

October 17th 2010

//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.//

See what you did there? There is compelling evidence “for evolution by common descent”? Evidence for common descent is not automatically evidence for the Darwinian mechanism at the same time.

As the Darwin skeptic Jerry Fodor writes: “it’s important to see that the phylogeny could be true even if the adaptationism isn’t..the classical Darwinist account of evolution as primarily driven by natural selection is in trouble on both conceptual and empirical grounds.”


Bilbo - #35095

October 17th 2010

Hi Darrel,

This from James Shapiro in his comments at the Boston Review:

Localized random mutation, selection operating “one gene at a time” (John Maynard Smith’s formulation), and gradual modification of individual functions are unable to provide satisfactory explanations for the molecular data, no matter how much time for change is assumed. There are simply too many potential degrees of freedom for random variability and too many interconnections to account for.

Is that close enough to agreeing with Behe?


Bilbo - #35096

October 17th 2010

More from James Shapiro’s essay:

It has been a surprise to learn how thoroughly cells protect themselves against precisely the kinds of accidental genetic change that, according to conventional theory, are the sources of evolutionary variability. By virtue of their proofreading and repair systems, living cells are not passive victims of the random forces of chemistry and physics. They devote large resources to suppressing random genetic variation and have the capacity to set the level of background localized mutability by adjusting the activity of their repair systems.


Bilbo - #35097

October 17th 2010

And more from Shapiro’s essay:


The point of this discussion is that our current knowledge of genetic change is fundamentally at variance with neo-Darwinist postulates. We have progressed from the Constant Genome, subject only to random, localized changes at a more or less constant mutation rate, to the Fluid Genome, subject to episodic, massive and non-random reorganizations capable of producing new functional architectures. Inevitably, such a profound advance in awareness of genetic capabilities will dramatically alter our understanding of the evolutionary process. Nonetheless, neo-Darwinist writers like Dawkins continue to ignore or trivialize the new knowledge and insist on gradualism as the only path for evolutionary change.


Bilbo - #35098

October 17th 2010

And more from Shapiro:

However, the potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise. This is to be expected from the Creationists, who naturally refuse to recognize science’s remarkable record of making more and more seemingly miraculous aspects of our world comprehensible to our understanding and accessible to our technology. 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 - #35100

October 17th 2010

And finally from Shapiro:

A sounder perspective on the history of science would be very helpful to all concerned. For example, a parallel has been drawn by Allen Orr and others between criticisms of Darwinian orthodoxy and assaults on the Law of Gravity, presenting them as equally deplorable examples of anti-science obscurantism. Yet, if truth be told, gravity is far from a settled matter. The relativistic Law of Gravity at the end of the 20th century is not the same as the classical Law of Gravity at the end of the 19th century, and discovering how the continuous descriptions of general relativity can be integrated into a single theory with the discrete accounts of quantum physics is still an active field of research….

cont.


Bilbo - #35101

October 17th 2010

Shapiro cont.: 

... From a scientific point of view, then, the Law of Gravity has quite properly been under continuous challenge. Dogmas and taboos may be suitable for religion, but they have no place in science. No theory or viewpoint should ever become sacrosanct because experience tells us that even the most elegant Laws of Nature ultimately succumb to the inexorable progress of scientific thinking and technological innovation. The present debate over Darwinism will be more productive if it takes place in recognition of the fact that scientific advances are made not by canonizing our predecessors but by creating intellectual and technical opportunities for our successors.

Shapiro favors his hypothesis of “natural genetic engineering, ” and not ID.  But it seems obvious that he rejects neo-Darwinism on the same basis as Behe.  Behe also discusses Shapiro’s theory in his book, The Edge of Evolution.


Bilbo - #35104

October 17th 2010

And very briefly from Lynn Margulis (though I can quote longer sections, if requested):

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.

So Shapiro and Margulis, though they may never come out publicly and say that Behe’s arguments against neo-Darwinism are correct, believe that they are.  They just offer different alternatives than Behe does.


Bilbo - #35105

October 17th 2010

By the way, Margulis also said the following about Ayala:

Francisco Ayala is presenting at the “evolutionary mechanisms session” in Rome. He was trained in Catholicism, Spanish-style, as a Dominican. We were in California at a meeting with Whiteheadian philosopher John Cobb. At that meeting Ayala agreed with me when I stated that this doctrinaire neo-Darwinism is dead. He was a practitioner of neo-Darwinism but advances in molecular genetics, evolution, ecology, biochemistry, and other news had led him to agree that neo-Darwinism’s now dead.

I doubt Ayala would ever admit in public that he said that to Margulis.  Based on Ayala’s doubtful remarks about reading Stephen Meyer’s book, and his refusal to tell us what his religious beliefs are, even though he accuses ID of “blasphemy,”  and based on Margulis’s forthrightness, even on topics that are very controversial, I believe Margulis’s account of Ayala’s remarks.


Bilbo - #35106

October 17th 2010

So Darrel,

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


Unaplogeic catholic - #35127

October 18th 2010

no,neither agrees with Behe or Intelligent Design


Trevor K. - #35136

October 18th 2010

@Darrel Falk - #34892

So what you’re asking Darrel is for someone at a faculty to put his/her career at risk.
Why?
Because anyone daring to publicly disagree with the Darwinian evolutionary story will be fired. Plain and simple. That person will not be fired in the normal sense of the word, that person will be bullied and abused until s/he cannot stand it anymore and will have to leave. So for you to ask for anyone to make a public show of disagreeing with the evolutionary thought is decidedly underhanded.

So for the spam of the day : http://creation.com/enceladus-looks-young


Dave Ussery - #35139

October 18th 2010

Trevor K. - #35136

“Because anyone daring to publicly disagree with the Darwinian evolutionary story will be fired”

Umm, I disagree here.  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.

What I see is a lot of hype (and just plain lies - that is not telling the truth) about the ‘controversy’ here.  These guys in the ID movement want to work for 5 minutes, and get paid for a year.  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.  And they wanted to be treated on equal ground, as if they’ve done as much work as those 20 million other articles…  I simply don’t buy their false claims of persecution.

[written from the airport in Bejing, China]


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