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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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sy - #35727

October 21st 2010

Gregory wrote

“After all, BioLogos is mainly interested in cooperative dialogue and not in anti-theists promoting the ‘warfare model’ of science vs. religion.”

I think that is the crucial point to consider here. The web is full of opportunities for both sides of the warfare model to attack each other, and I believe all who post here should understand that such attacks serve no purpose. There is a tremendous amount to learn and we are clearly in the middle of a dynamic and exciting moment in the history of thought. Cooperative dialog is in fact the key to move new exciting ideas forward. Behe may be right about some things, and wrong about others, as well as everyone else involved in the debate. I have been both dismayed and thrilled at the writings of Dawkins. We need to remain open minded and cooperative to arrive at the commmone goal, truth.


John - #35735

October 21st 2010

Gregory wrote:
“(ego?)”

Ad hominem defense of RIch’s ad hominem attack. What’s yours, btw?

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

Dunno, so I qualified my answer. Do you?

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

Many, but there’s little opportunity after pds shrieks that the author is trying to deceive his audience because he confused two of Behe’s silly metaphors, which aren’t evidence.

Then there’s overwhelming evidence that pds was bearing false witness by claiming:
““The studies you cite seem assert general conclusions.  They don’t give specific examples.”
“I don’t think the studies you cite support your assertion.”

Do you agree wtih those statements?


John - #35736

October 21st 2010

Gregory continued:
“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?”

I’m neither. Why didn’t you go after pds for pretending to be familiar with the evidence relevant to the subject of the article, Gregory?

“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.?”

The former, but not with people like pds and Rich. What do you think?

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

Do you think that pds’s and Rich’s attacks will help?

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

But pds isn’t. He/she had to go on the attack with false claims.


John - #35738

October 21st 2010

Rich wrote:
“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. “

But other examples of anonymous critics AFTER publication are tenure referees and grant reviewers.

“Writing in both scientific and mainstream journals, *they signed their names*.”

But I’m not writing in a scientific or mainstream journal, Rich!

“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*. “

David Ussery criticizes Behe and does sign his name, but Rich doesn’t engage in dialogue.

pds dishonestly criticizes Ussery, claiming, “The studies you cite seem assert general conclusions.  They don’t give specific examples,” but Rich remains silent, despite the fact that pds does not sign his name.

I point out that pds hasn’t bothered to look at the evidence, which clearly refutes Behe’s claims, but you go for the ad hominem attack, *without signing your name*. What did Jesus Christ have to say about hypocrisy?


John - #35739

October 21st 2010

Rich wrote:
“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?”

The one spewing invective here is you. I’m attacking a specific point about EVIDENCE, from which you and pds run away.

Now, Ussery cited reviews that cite specific studies. Your buddy pds claimed, “The studies you cite seem assert general conclusions.  They don’t give specific examples…I don’t think the studies you cite support your assertion.”

Ussery is correct; Behe is misrepresenting the evidence so thoroughly that to claim that his arguments and conclusions are evidence-based is ludicrous.

I write that I think that pds didn’t bother to look at a single study and is bearing false witness, while pds was far more aggressive in his attack on Ussery.

Did you look at any of the studies cited in the those reviews before attacking me, *without signing your name,* Rich?


Rich - #35744

October 21st 2010

35739:

I’m not the one who is (1) claiming to be a scientist who has produced many articles in peer-reviewed journals; (2) claiming to have enough expertise in either biochemistry and/or evolutionary theory to refute Behe’s arguments; (3) making pejorative statements about other scientists’ alleged lack of productive research.  Were I in that position, I would definitely sign my name,  So there’s no hypocrisy.  I’ve made it clear here that I’m not a scientist (though I have some science training, and I’ve studied a great deal about evolution and intelligent design).  I’ve also explained somewhere (can’t remember the thread) that I keep my identity to myself because my ID sympathies are a real threat to my personal income security.  But a scientist with tenure or a secure job in some industry, and one hostile to ID (which is very unpopular with scientists) has nothing to fear, in terms of salary or career advancement, from bashing ID publically in his own name.  So the question arises why a scientist who repeatedly issues harsh and sniping judgments of other scientists who have had the courage to publish under their own names does not publish under his own name.


Dave Ussery - #35763

October 22nd 2010

I have been at a meeting on Synthetic Biology, in Shanghai, China, for this past week.  I did not even know that part II of the review was posted until today, when I was at the airport in Shanghai, waiting for my flight to Bejing.  I opened the page with all the comments, and had a look at them on my flight from Shanghai to Bejing.

First, I want to say that I am impressed by all of the comments and critical discussion on this.  I think that criticism in science is extremely important!  On the plane I read another chapter in my book about Robert Boyle.  In 1665 Boyle had published a book about some of his early experiments with a vacuum pump.  This book got lots of criticism, from two different groups of people.  First, there were the traditionalists, who were really angry that Boyle had challenged Aristotle.  To this, Boyle wrote a rebuttal, which included the first statement of what is now known as “Boyle’s Law” - that the volume of air is proportional to its pressure.  There is a plaque on the wall in Oxford, denoting where Boyle did these experiments.  Boyle was refining the method of doing experiments to test ideas, and he was also developing a new area, known today as chemistry.

more in my next comment…


Dave Ussery - #35764

October 22nd 2010

The OTHER criticism of Boyle came from another camp of people - this time from the materialists, (like Thomas Hobbes) who thought that Boyle’s mechanistic philosophy justified their atheism.  At the time they were very critical of the idea of doing EXPERIMENTS to test an idea.  Although Boyle today is certainly viewed as having one the argument, the author of the book (Michael Hunter) notes that in a sense Hobbes has a point, that when one is doing an experiment, the model is important.  At the time of Boyle (and certainly for Newton who followed), it was thought that there was an objective reality, where one could step outside of nature, so-to-speak, and just observe what is true. Today, after Einstein, we know this is no longer true - everyone has a ‘world-view’, and this is necessary to interpret what we see.  For example, when we THINK we see something clearly, actually this is a complex approximation, and sometimes the brain can be tricked into seeing things that aren’t there - or sometimes NOT seeing things that really are. 

Critical discussion is important - but let’s try and not get too personal here - yes, I am a Christian.  No, I am NOT a materialist.  Yes, I believe in God.  Yes, I think life has purpose.


sy - #35778

October 22nd 2010

Dave

Your remark about using models by necessity when doing experiments is fascinating, and I think is something that we need to consider when we construct our view of reality. And the example of Boyle is perfect, since his law was eventually incorporated into the famous equation of state called the ideal gas law. This is of course a model which is very good at describing the state of a gas, but since no gas is truly ideal (there are always small deviations from ideality, like intermolecular forces) it is not absolutely accurate. No model ever is.

We have done, and can do a lot of great things with models, and that is all we have to work with.  The goal of scientific theory and experimentation is find and refine the best, most accurate and, if possible, most elegant, model we can.  But we need to always be aware that we rarely if ever have an absolutely true picture. We have seen this process in physics, throughout the last century, and I believe we are starting to follow a similar pattern with biology, but that is worth an entire post, in itself.


Bilbo - #35875

October 22nd 2010

Comment removed by moderator.


Rich - #35897

October 22nd 2010

Bilbo:

I enjoy your posts and appreciate your arguments for what is a minority position around here.  However, I do think you’re being rough on Dr. Ussery.

I don’t think you should infer dishonest manipulation of quotations on his part.  That’s exactly what “John” does when accuses several ID people here of “bearing false witness” because they disagree with his interpretation of the facts.  Aside from the fact that it’s offensive for someone whose speech to other human beings is as belittling and un-Christian as “John’s” to pretend to be speaking out of a Biblical concern against bearing false witness, it’s not a fair argumentative tactic.  It imputes motives.

I think it’s better simply to show, if you can, that Dr. Ussery is misquoting or quote-mining or neglecting certain of Behe’s words, and then *ask* him why he proceeds in an intellectually faulty way, rather than implying an answer, i.e., that he must be doing this out of lack of Christian ethics.

I take Dr. Ussery at his word for his faith.  I’m as vexed as you are by the obsession with attacking Behe on this site, but I think we should infer lack of understanding of Behe’s position before inferring lack of faith.


John - #35918

October 22nd 2010

Rich wrote to Bilbo:
“I don’t think you should infer dishonest manipulation of quotations on his part.”

I agree.

“That’s exactly what “John” does when accuses several ID people here of “bearing false witness” because they disagree with his interpretation of the facts. “

That’s utterly false. I’m accusing pds of bearing false witness when he wrote to Ussery, “The studies you cite seem assert general conclusions.  They don’t give specific examples…I don’t think the studies you cite support your assertion.”

There’s plenty of evidence to support that, since pds has run away from any discussion of any specific study.


John - #35919

October 22nd 2010

Rich’s ad hominem con’d:
“Aside from the fact that it’s offensive…it’s not a fair argumentative tactic.  It imputes motives.”

I don’t impute motives without evidence. Here’s my direct challenge to pds’s claim:
—————
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.
——————
Then, following my pointing to a specific study, pds wrote:

“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’m waiting for pds to respond. The lack of response is damning. You could step in to help pds, you know…


John - #35920

October 22nd 2010

In fact, has a single one of the ID-friendly commenters here had anything to say about the evidence other than pds’s sweeping dismissal of it?


Rich - #35923

October 22nd 2010

John:

If were familiar with the teachings and practice of Christianity, you would know that “bearing false witness” does not mean “making an error” or “stating something without adequate proof.”  It means willfully telling an untruth about another person which could lead to that person’s legal or moral condemnation by the community.  You have accused several people here of doing that.  And aside from the fact that “bearing false witness” isn’t about intellectual arguments, but about people, it’s a very serious moral and spiritual charge.  You don’t throw around a charge of “bearing false witness” lightly, as a polemical debating tactic.  Not if you are a practising Christian or Jew.

I made no “ad hominem” comment when I reported that you have several times charged people here with “bearing false witness.”  I was reporting what you have done.

I also made no “ad hominem” comment when I reported that you have made many ad hominem comments against Behe and other ID proponents.  I simply reported the facts. 

I am not interested in your technical debate with pds.  That’s between the two of you.  I’m only interested in getting you to see how brutal your manners appear to others.  But probably you don’t care.


pds - #35988

October 23rd 2010

John,

I have already responded to your criticisms, and you seem to ignore it.  You repeatedly misrepresent my comments.  I find your tone and style unpleasant.  I don’t plan to respond to you further.

Have a nice weekend.


Bilbo - #35999

October 23rd 2010

Comment removed by moderator.


Dave Ussery - #36000

October 23rd 2010

An apology

I apologise if some of my posts above seemed a bit clumsy or terse - I was writing quickly at an airport, without much sleep!

I want to thank again everyone for lots of comments - many of them constructive.

I have read through all the comments up to now, and have a THREE minor points.  Each will have its own comment

#1 - from ahumanoid - #35169 October 18th 2010

E. coli does NOT have a “low fidelity DNA Polymerase” - the error rate overall (after proof-reading) in E. coli is around one in a hundred million.  I originally thought Behe had overestimated this, but did some checking and found him to be right.  I stand by my inclusion of E. coli polymerase. I do not know of anything with a BETTER fidelity than the E. coli polymerase.  Does anyone on the list know?  It’s pretty much the same number for human polymerase as well.  AND this is the same number Behe quotes, and is in the general literature as well. 

In practical terms, this means that an E.coli can divide a hundred times without a single error (assuming it’s well-fed and ‘happy’), whilst a single human cell will have 60 errors with EVERY duplication, since they are so much larger.


Dave Ussery - #36001

October 23rd 2010

#2 - John - #35565 - October 20th 2010

There was a bit of discussion about h-index, what it means.  Basically this number reflects how well-cited an author is.  It is actually kind of easy to write and publish papers that no one ever reads (or cites as a reference in other papers).  The h-index is the threshold representing the largest number of times a person’s paper has been cited n times.  Uhhh, kind of hard to explain - if someone had an h-index of 10, that means that they have published 10 papers, each of which has been cited at least ten times.  The scale is pretty brutal - so I am impressed with John for having an h-index of 23 - this is quite good.  It gets progressively harder.  I know of people who have h-indeces around 50, but this is quite rare.  When we hire people, we take their h-index, divide by how many years since their Ph.D. - if it is greater than 1, this is considered good enough.  That means every year, on average, they’ve published at least one paper that is cited once a year.


Dave Ussery - #36002

October 23rd 2010

# 3 Bilbo - #35875- October 22nd 2010

Dave,

Sorry to hear that you are a Christian.  I was hoping your frequent misquoting and quoting out of context of Behe was the work of an atheist.  Perhaps the leaders of Biologos should proofread your next blog entry before publishing it.

—————————————————————————————————————
Dave - 23 Okt.

Bilbo, this is pretty strong [and personal] here. 

Are you REALLY disappointed to learn that I say the Nicene Crede, that I believe in Jesus Christ as the son of God?  wow! 

My “misquotes” of Behe are straight from the text - I try and include the page number.  I apologise if this doesn’t agree with your reading, but this is an OPINION (my opinion) not a scientific exact proof, with no mistakes. Good grief, it is only a book review meant to stimulate discussion. I’m a person - yes, I make mistakes - the question is whether it is possible for you to admit others might not think the same as you, without invoking their motives as being evil?

Um, so what exactly WOULD it take to convince you that perhaps everything Behe says is not true? Or is this possible?


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