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Is There an Edge to Evolution? Part 2

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October 18, 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.

Is There an Edge to Evolution? Part 2

An Analysis of Michael Behe’s book, The Edge of Evolution

In his previous post, Ussery discussed his personal reasons for being interested in “The Edge of Evolution.” He went on to discuss two aspects of the book he appreciates, and he showed that he and Behe are in agreement that all living organisms have arisen through common descent from a single ancestral species.

In this post, however, Ussery says that Behe has presented a vastly over-simplified view of what scientists know about the origin of genetic diversity in the history of life. Here is his analysis based on Chapters Two and Three.

The accompanying figure illustrates the amount of genetic diversity in the bacterial world and beyond. It shows that even a single species of bacteria (E. coli) contains a vast reservoir of different genes. The term “orthologous” refers to genes in different species that clearly resemble one another and are thereby believed to have a common ancestry. Genes which are not orthologous are found in the species on the right side but not on the comparator species on the left.

Chapter 2 - Arms Race or Trench Warfare?

This chapter is about one of the classic examples of evolution: malaria and sickle cell anemia in humans. Behe observes (correctly, in my opinion) that the mutations that are responsible for helping some humans fight malaria are bad mutations. 'The first point is that the two examples he cites, sickle and Hemoglobin C (HbC), (two mutations that help the body resist malaria), are quintessentially hurtful mutations because they diminish the functioning of the human body. A second point is that “the mutations are not in the process of joining to build a more complex, interactive biochemical system.” (page 34).

Fair enough—and it is well known that harmful mutations, in the sense of wrecking something or making a pathway not work, occur much more frequently than beneficial mutations. However, Behe goes on to claim that there are “absolutely no studies' to document a molecular basis for the “coherent development of a single trait in a Darwinian arms race.” But this is highly erroneous . True, the example he gives us is not a “good mutation” - but to just blatantly claim that nothing has been done is showing his ignorance of the literature.

For example, consider this from the abstract of a recent review article, with the title “Origins, evolution, and phenotypic impact of new genes,” published in Genome Research. “The array of mechanisms underlying the origin of new genes is compelling, extending way beyond the traditionally well-studied source of gene duplication. Thus, it was shown that novel genes also regularly arose from messenger RNAs of ancestral genes, protein-coding genes metamorphosed into new RNA genes, genomic parasites were co-opted as new genes, and that both protein and RNA genes were composed from scratch (i.e., from previously non- functional sequences).” This is a new article, but many of the references in this article date to long before The Edge of Evolution was written, and some even date to before Darwin's Black Box was published, more than a decade ago.

Then there's another article about recent evolution of beneficial mutations in humans. There are many, many articles published on this sort of idea, and to claim that not a single study has been done is essentially a play on the ignorance of the readers! It is as if the hope is that the readers are ignorant of the scientific literature, and either too lazy or not competent to have a look through PubMed and see what is really out there.

Chapter 3 - The Mathematical Limits of Darwinism

One of my Ph.D. students was a mathematician, and I can still remember trying to read through his paper—lots of formulas—and sometimes they were difficult for me to understand. I have since learned that many people in math departments have a strong disliking for statisticians - I used to naively think that the two are the same. In this chapter, it looks as though Behe has confused mathematics (in the title) with statistics (what is actually discussed in the chapter). What's worse, the numbers he uses are based on bad assumptions, and are way off from what is known in the field by experimentalists doing current research in this area. Thus, unfortunately, his conclusions are not as strong as they might seem at first glance.

First, in calculating the odds of a single mutation in a protein, one has to take into account the chances of a mutation in the DNA sequence, because this is where mutations happen in biology - this is part of the 'central dogma' of molecular biology - that the information flows from DNA to RNA to protein, but not from proteins back to DNA. Thus, if a protein has a particular amino acid changed, this can be traced back to a change in the DNA sequence. Behe says ”resistance to chloroquine has appeared fewer than ten times in the whole world in the past century” - but what is meant by this shorthand is that we have documented evidence of this happening only a few times - that's not the same as knowing definitively that this HAS happened only those few times. Lots of things [like mutations leading to drug resistance] happen all the time that don't get seen and documented.

Then, based on this vastly over-simplified estimate, he suggests that the odds of a parasite developing resistance to chloroquine is one in 1020, whilst the odds of developing resistance to another drug (atovaquone) is one in 1012. Since the former, he says, involves two amino acid changes, while the latter involves on one, from these two numbers, it is concluded that the chance of having mutations which change two amino acids in a protein is a hundred million times lower (10-20 vs 10-12) than that for just getting one.

But this just simply does not make sense. Even within E. coli, the well known work-horse of molecular biology, take the order of amino acids in any one of its 5000 or so proteins, and compare that arrangement to that in other E. coli strains and you will find LOTS of differences. For many proteins in E. coli, the level of identity between strains is around 80% - that is, about twenty out of every hundred amino acids are different - so to say that the odds for a double mutation (2 amino acid changes out of 100), is essentially impossible, when we observe 10 times that amount of diversity (20 differences for every 100 amino acids) in natural populations is speaking from ignorance. We see ten times the number of changes which Behe says is almost impossible all around us within a single species without even the need to generate new mutations.

I’ll discuss the vast differences found with various sequenced E. coli genomes later, but getting back to this chapter and the mutations in the two different spots within a single gene, Behe concludes:

On average, for humans to achieve a mutation like this by chance, we would need to wait a hundred million times ten million years. Since this is many times the age of the universe, it's reasonable to conclude the following: No mutation that is the same complexity of chloroquine resistance in malaria arose by Darwinian evolution in the line leading to humans in the past ten million years. (page 61, emphasis in the original).

But again, if one takes a deep breath, and looks at what is known, the mutational frequency that we can actually measure in humans is many times greater than that upon which Behe's assumptions are based. His argument is that the chances of getting useful mutations at two sites in the same gene are highly unlikely. But can we assess how likely mutations, which are likely to change the function of a gene, occur? One of the underlying assumptions of molecular biology is that sequence determines structure, and that this structure determines function. Hence, a major structural change is likely to have a different function. So how common are mutations that result in structural changes in proteins?

Surprisingly Common! One out of every 21 births in humans have some sort of STRUCTURAL change (and hence likely a functional change) in a protein, just from insertions from a single transposable element (alu), common in humans. It is already evident that Behe has a real problem with “random” mutations – but I think perhaps he is confusing ‘randomness’ with ‘purposelessness’.1 More about that in my next post.

Notes

1. I think many people don’t really understand randomness - for more on this see David Bartholomew’s excellent book “God, Chance and Purpose - Can God Have it Both Ways?” (Cambridge University Press, 2008), and also my “Purpose-Drive iPod” essay (Christian Century, 23 September, 2008, pages 11-12).


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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beaglelady - #35513

October 20th 2010

b allen,

I believe that pds perceives John as being consumed by anger, not Sy. 

Of course, when he goes on to say “I will pray for you and for all those who seem to hate the very possibility of design in nature.”  one could construe that to mean anyone who doesn’t agree with the IDM.


pds - #35518

October 20th 2010

b allen,

“John” said that he thinks I am being “deceptivve.”  You suggest I am “presumptuous,” while at the same time presuming I am writing to “Sy” when I clearly addressed it to “John.”

Your comment seemed a bit presumptuous to me on a number of points.  But I don’t mind.

Have delightful day.


b allen - #35537

October 20th 2010

my mistake. trying to get a bead on all the posts and comments back and forth to some up a simple point can get conveluted.  i was merely suggesting we may want to focus arguments against points and positions rather than people’s character, specifically.

i guess it’s unavoidable.

good day to all.


Bilbo - #35539

October 20th 2010

Hi Sy,

Along with everyone else, I hope you stick around.  Meanwhile, maybe you’re right about exaptation.  Maybe not.  I think you would enjoy Mike Gene’s book, The Design Matrix; a Consilience of Clues.  He begins with the hypothesis that the first cells were designed to make evolving (by neo-Darwinian processes) in a certain direction more likely.  Or check out his blog, even though he hasn’t been very active on it for the last few weeks.

designmatrix.wordpress.com


John - #35557

October 20th 2010

pds desperately ran away from his claim about the cited review:
“It saddens me that you seem to be consumed by so much anger.”

Anger? It saddens me to see you endorsing such fraud and being so evasive.

“I will pray for you and for all those who seem to hate the very possibility of design in nature.”

I doubt it.

“Ussery misrepresented what Behe wrote.”

You misrepresented what Ussery wrote, very blatantly. I was taking issue with YOUR misrepresentations, beginning with “The studies you cite seem assert general conclusions,” when Ussery very clearly cited a REVIEW. You’re afraid to read it, correct?

“I have seen Behe wrongly attacked with “literature dump bluffs” where the literature did not say what people said it did.”

Really? If YOU haven’t read the literature cited, YOU can’t possibly make such a statement if YOU are honest. Now, please list the primary literature that YOU, personally, read from one of these alleged bluffs to justify such a claim.

What does your Bible say about using hearsay, pds?

Note that you made a claim about “studies,” when Ussery cited a single review. Did you read it, or were you bearing false witness?


John - #35558

October 20th 2010

pds:
“Neither Ussery nor you have given any specific examples that would contradict what Behe really said.”

But you made a claim about what was in “studies,” when Ussery pointed you to a specific review that cited studies. Do you have the slightest idea how many studies were cited in the review?

“In this context, I will not spend much time going on Ussery’s treasure hunt.”

Exactly! You characterized “studies” without even bothering to read the cited review, much less any of the studies cited in the review.

What’s the Ninth Commandment again?

I said, “Behe has made no effort to test anything, pds. He hasn’t done empirical work in 15 years, so it is disingenuous to describe his book as any sort of scientific effort.”

pds replied, “I am not at all confident that that is even true. “

Hilarious! You’re the one that made the assertion that he made an effort to test something. Writing a book, aimed at laypeople, can’t possibly represent such an effort. The term “test,” in science, means to test a hypothesis.


John - #35559

October 20th 2010

pds:
“Regardless, do you really believe that only “empirical work” constitutes “scientific effort”?”

Straw man. You’re implicitly admitting that YOUR claim, that Behe made some sort of “effort to test the power of random variation and natural selection to generate original biological forms,” isn’t supportable.

The key term that you are running away from is “test.” How does quote-mining reviews constitute testing a hypothesis?

“I find it hard to believe that any true scientist would make such a foolish assertion.”

That’s probably why you moved the goalposts and falsely attributed such an assertion to me.

“Scientists think outside the box and ask new questions using existing data all the time.”

Behe isn’t asking any new questions. Even those scientists whose contributions are theoretical generate testable hypotheses and induce others to test them empirically. NO ID proponent has EVER performed an empirical test of an ID hypothesis.

“Were Watson and Crick making any “scientific effort”?”

Yes, they generated testable hypotheses with new data that some say they stole. Behe doesn’t even bother to read the primary literature!


John - #35564

October 20th 2010

Rich, who claimed that he wasn’t going to respond to me, responded anyway:
“And what empirical work has John done in Behe’s field in the last 15 years, that he is in a position to judge Behe?”

Much more! Infinitely more, in fact, because that would require producing only a single datum!

But how is that germane to my comment, pointing out that pds was characterizing studies that he clearly is afraid to read? He can’t even be bothered to read a review!

“Let’s see John’s data, and let’s have the explanation how it shows Behe is wrong.”

Why? How would it be relevant to my pointing out that Behe has done no empirical work in 15 years?

“John has made no argument here from primary scientific literature showing why Behe is wrong.”

David Ussery did exactly that, pointing his readers to a review that cites the primary scientific literature. I am challenging pds’s characterizations of it, because pds clearly is afraid to read the review or any of the studies cited in it.


John - #35565

October 20th 2010

Rich wrote:
“Some scientists have the courage and the integrity, when criticizing another scientist, to stand up and let the world know who they are…Others take nasty swipes from the shadows, never having to face the scientist they are criticizing, never rendering themselves vulnerable to the same sort of scientific criticism they level at others.”

Rich, you are utterly ignorant of the nuts and bolts of science.

Anonymous criticism is a STAPLE of the scientific endeavor in the Western world. Why, I just got back a manuscript review today! Do you really think I should demand that the editor reveal the names of the reviewers, or can you see that I’d look like an idiot if I did so?

“It appears that we have some people of the latter type posting comments here.  I wonder what would motivate a bona fide scientist to behave in this way.”

Rich, you’ve challenged the notion that I am a bona fide scientist and I’ve challenged you to bet real money on your challenge. You ran away.

Now, how much are you willing to bet that I’m not a working scientist (my h-index is 23)?

More importantly, what are you doing to eliminate the grand tradition of anonymous review of manuscripts in science?


John - #35566

October 20th 2010

Bilbo wrote:
“He [the pseudonymous Mike Gene, Rich!] begins with the hypothesis that the first cells were designed to make evolving (by neo-Darwinian processes) in a certain direction more likely.”

What does he think happened before life was cellular, then?


John - #35578

October 20th 2010

Ussery:
“But this is highly erroneous…but to just blatantly claim that nothing has been done is showing his ignorance of the literature.

“For example, consider this from the abstract of a recent review article…many of the references in this article date to long before The Edge of Evolution was written, and some even date to before Darwin’s Black Box was published, more than a decade ago.”

pds:
“The studies you cite seem assert general conclusions.  They don’t give specific examples.”

Really?

“Why don’t you give a specific example of a study that contradicts Behe’s assertion?  It seems that you need to if you are going to assert that he is “highly erroneous.””

He did, but you refuse to examine the data. Here’s a specific one cited:

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

How did you determine that the data from this study:
1) are not a specific example, and
2) do not directly contradict Behe’s assertion?

pds:
“I don’t think the studies you cite support your assertion.”

I don’t think you looked at any studies before writing that and are bearing false witness.


pds - #35579

October 21st 2010

John,

Instead of your rambling personal attacks, why don’t you just summarize a study that you think contradicts what Behe actually said.  That will show me whether you understand what Behe is saying.  That should be easy for you.


sy - #35581

October 21st 2010

Thank you Gingoro, Rich, Beagle Lady, Bilbo, and others who responded to my comment about withdrawing. I am quite moved by your welcoming spirit of fellowship and found your comments to me heartwarming. I thank God (as I have done many times) for the good fortune He has bestowed on me, by allowing me to interact with so many people of good will, and with love in their hearts.

I had not intended to return to this blog, but I think the Lord guided me back here, to see your comments. I would be honored to continue to post comments on this site, which I have long felt is one of the most important sites for discussions of faith and science. I will however strive to keep my remarks as humble as possible (not an easy task for any academic) always bearing in mind that the shadow of my anonymity cannot become a protective cloak allowing me the freedom to say anything I wouldnt say with my identity clear.

Once again, God bless all here.


sy - #35583

October 21st 2010

Bilbo

Thanks for the reference to Gene’s book and blog. I have actually come to the same conclusion, but using a somewhat different mechanistic approach. I do think that detailed analysis of genetic code evolution is a very fruitful way to find some signatures of design. And I think the general idea that cells were designed to evolve is highly controversial, subject to attack from all sides, and an elegant and wonderful truth.


Rich - #35595

October 21st 2010

sy:

Glad you are back.  I knew you were a good fellow when I contradicted something you said about Steve Meyer and you were willing to have a discussion about it, instead of just firing back with all kinds of venom against Meyer and ID—which is par for the course around here.  I don’t mind being contradicted by someone like yourself, who is intelligent, polite, makes an effort to listen before rendering judgment, and will give and take points. 

And yes, you are right about academic egos.  Like most academics, I fight to contain my own ego.  And not just my ego, but my sense of indignation against unjust statements which seem to me to be made out of malice aforethought.  I find self-control much easier when those around me are behaving in a gentlemanly way.  When the tone descends, I’m always tempted to descend with it.  So I hope you stick around, and continue to model polite disagreement.


Rich - #35598

October 21st 2010

pds:

You wrote to an aggressive poster here:

“Instead of your rambling personal attacks, why don’t you just summarize a study that you think contradicts what Behe actually said.  That will show me whether you understand what Behe is saying.  That should be easy for you.”

I agree entirely.  This poster is prone to ad hominem remarks.  And “ad hominem” doesn’t just refer to personal insults; it refers to any attempt to draw the discussion away from the argument and toward the person.  Behe’s empirical research record over the past X years is irrelevant to the correctness or incorrectness of his arguments.  Plenty of people experiment all the time and still draw false conclusions, and plenty of others rarely or never experiment (e.g., Einstein) and yet advance their field with new ideas.  The only thing that matters is whether or not an argument is cogent.  If Behe’s argument is fatally flawed, and this poster has the scientific knowledge to show it, let him do so—without nasty jabs, such as accusing people who disagree with him of “bearing false witness.”  Let’s see two or three paragraphs of expository prose that stick entirely to the argument of Behe’s book.


Gregory - #35603

October 21st 2010

“my h-index is 23” (ego?)

“Anonymous criticism is a STAPLE of the scientific endeavor in the Western world.”

And what about the Eastern world (or better yet, the Northern and Southern worlds)?

Oh yeah, and by the way, what positive or fruitful contribution(s) do you think science AND religion can have in a positive conversation?

After all, BioLogos is mainly interested in cooperative dialogue and not in anti-theists promoting the ‘warfare model’ of science vs. religion. If you are a ‘warfare model’ promoter who is non-religious, then why come here?

Do you think science and religion can work collaborativey together or do you prefer to think of them as totally independent, as competing with each other, or as NOMA, etc.?

I don’t think your h-index will help much in answering this as an everyday human person.

At least David Ussery (not sure of your h-index, David, sorry, didn’t check) is welcoming to religion transcendening science.


Rich - #35610

October 21st 2010

Gregory (35603):

When John writes:  ““Anonymous criticism is a STAPLE of the scientific endeavor in the Western world,” he is deliberately misleading.

As he indicated elsewhere, he is referring to the process of peer review, by which anonymous peers review articles and books for publication.  Neither I nor you nor anyone else objects to this process, so his attempt to drag it in is a red herring.

What he deliberately suppresses is the fact that *after* the scientific work has been published, *then* normal scientific practice is for critics to *identify themselves*. 

Here we are talking about *published* works of Behe.  If one is going to criticize published works of Behe, *and wants one’s criticism to be taken seriously by the scientific community*, one does not publish those criticisms anonymously on a blog site. 

Of course, if one does not care if one’s criticisms are taken seriously by the scientific community, and just wants to vent anger against Behe, one can write anonymous comments and intimate without proof that one has expertise in the area.  That’s what John does here, and it’s his right; but no one in the scientific community cares in the slightest about anything he writes in this forum.


John - #35627

October 21st 2010

Rich goes off the rails completely:
“...he is deliberately misleading.”

“As he indicated elsewhere, he is referring to the process of peer review, by which anonymous peers review articles and books for publication.  Neither I nor you nor anyone else objects to this process, so his attempt to drag it in is a red herring.”

It’s anonymous criticism, exactly what you were talking about: “Some scientists have the courage and the integrity, when criticizing another scientist, to stand up and let the world know who they are…Others take nasty swipes from the shadows, never having to face the scientist they are criticizing, never rendering themselves vulnerable to the same sort of scientific criticism they level at others.”

“What he deliberately suppresses is the fact that *after* the scientific work has been published, *then* normal scientific practice is for critics to *identify themselves*. “

No, Rich, you are utterly wrong. No journal in biology engages in such a practice. When papers say, “Edited by…” they are referring to the editor, not the anonymous reviewers.

But since you’re claiming that normal scientific practice is for the anonymous critics to identify themselves, point out ten journals that do so.


Rich - #35640

October 21st 2010

Re 35627:

I never said that “anonymous critics” (i.e., peer reviewers) had to identify themselves.

I said that “critics” had to identify themselves, i.e., *critics of the published work, writing their criticism after it has been published*.  For example, book reviewers.  The context of my post, and previous posts on this thread, ought to have made that clear.  All of the scientists I named in 35412 wrote about Behe *after his books were published*, and *they signed their names*.  Ditto for Richard Dawkins, Sean Carroll, Paul Gross, Michael Ruse, Jerry Coyne, etc.  Writing in both scientific and mainstream journals, *they signed their names*.

But the author of 35627 writes sweeping condemnations of Behe’s published work, condemnations which contain very little science and much ad hominem invective, *and does not sign his name*.  This would not be permitted of a reviewer in Science, Nature or any other scientific journal.  Nor would most of the ad hominem remarks.  The question is:  would a really competent scientist, capable of refuting Behe point by point on the scientific claims made in his books, write anonymous invective on a blog site not frequented by 99% of the life sciences community?


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