Is There an Edge to Evolution? Part 4

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November 3, 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.

In the first three parts of this series, molecular biologist, Dr. David Ussery examines, chapter by chapter, the arguments put forward in the book, The Edge of Evolution, by Michael Behe. This book, like Dr. Behe’s previous book, is written in an engagingly accessible style and has been highly acclaimed by many non-specialists who think that Behe has identified the limits of what science can explain without needing to insert an external Intelligence. David Ussery is a Christian molecular biologist who, like all of us at BioLogos, is deeply concerned that other Christians be aware that Dr. Behe has not identified biology’s edge. Furthermore, none of us are sure why anyone should expect to find an Edge—a place where nature ends and God begins. Nature after all—all of nature—is God’s. There is no aspect of creation which is not God’s. Here is David Ussery’s analysis of Chapters six and seven of Behe’s book.

Note: Title of Dawkins' book was corrected on 11/4/10.

Chapter 6 - Benchmarks

This chapter details how Behe decides whether some biological features are unlikely to have been produced by random mutation and natural selection. As an example, he chooses a quote from an article on how to evaluate proposed mechanisms for biological speciation, based on what seems “biologically reasonable.” Behe claims that the idea of whether evolution is “biologically reasonable” has not been fully tested for all of evolution, and proposes to do so in this chapter. To “judge whether random mutation hitched to natural selection is a biologically reasonable explanation for any given molecular phenomenon,” he uses two criteria: how many steps are necessary to create this?, and coherence - the ordering of steps towards a goal. Richard Dawkins goes through both of these steps in his book, Climbing Mount Improbable. I was surprised to find that, although Charles Darwin, Daniel Dennett, John Maynard Smith, Alan Orr, Jerry Coyne, and Francois Jacob are mentioned here, somehow Behe doesn't say anything about Dawkins classic book that deals specifically with the arguments in this chapter, written in 1996, around the same time as Behe’s Darwin’s Black Box. I think that Dawkins scores a valid point in his review of The Edge of Evolution, when he says that unlike Behe's first book, Darwin's Black Box, in the

…second is the book of a man who has given up. Trapped along a false path of his own rather unintelligent design, Behe has left himself no escape. Poster boy of creationists everywhere, he has cut himself adrift from the world of real science.

In this chapter, Behe concludes that evolution is a 'tinkerer', not an engineer. Fair enough. But then he concludes that “If Darwinism is just a tinkerer, then it cannot be expected to produce coherent features where a number of separate parts act together for a clear purpose, involving more than several components.” (Page 119). But what about Dawkin's Mount Improbable? What about the classic example of the eye? There are many books on this, as well as scientific articles. I encourage the interested reader to go to Amazon.com for example, and have a look at some of the books published on the evolution of eyes in animals. One can find exactly what Behe is claiming can never happen, laid out in clear detail, slow, gradual, evolution of complex systems such as the eye. And in my opinion (as a molecular biologist), there's not much difference in the evolution of the eye than the evolution of a complex biochemical system. Certainly there is a difference in scale, but the same principles apply. But please don't just take my word for it. Again, go to PubMed, type in “evolution complex systems,” and see what is there.

Chapter 7 - The Two-Binding-Sites Rule

In this chapter, Behe further explores his claims of incredulity. Now, instead of looking at single mutations within single genes, Behe examines the likelihood of evolutionary mechanisms producing two different proteins with shapes that will fit each other—that is with “binding sites” which are complementary. What are the chances, he asks, of having TWO binding sites evolve at the same time? The probability is so tiny, as to essentially be impossible, he claims. Yet once again, there are problems here with the initial assumptions. I really hate to sound like a broken record, but once again, the interested reader is invited to have a look at the vast literature in this field. I went to PubMed, typed in “evolution protein binding sites,” and got back more than 5000 articles. The title of one recent article was “Using peptide loop insertion mutagenesis for the evolution of proteins,” and another is “Beauty is in the eye of the beholder: proteins can recognize binding sites of homologous proteins in more than one way.” This brings me to one of the (many) flaws in this argument in chapter 7—there is a lot of room for change in the binding site; it does not have to be a 100% perfect match. It only has to be the right shape, and this can be achieved through many many different amino acid sequences. So the probability is not nearly as dire as one might expect from naive and bad first approximations.

Towards the end of this chapter, Behe brings up the work of Richard Lenski, at Michigan State University. Behe claims that, despite having grown E. coli in the test-tube for more than 40,000 generations, “nothing fundamentally new has been produced.” I've known Rich Lenski for many years, and recently he was here as an opponent for a Ph.D. thesis exam. Rich gave a wonderful talk, demonstrating that early on in his experiments, there was a clear, measurable increase in fitness from the [random] mutations generated in his evolution experiments. For example, a set of mutations which altered DNA topology (three dimensional structure) occurred in many of the strains, thereby increasing fitness. (DNA topology is the expertise of both Behe and myself—it is a real shame that Behe no longer works in the lab with DNA structures and evolution!) In some of Lenski’s later experiments, after the cells had been growing for more than fifteen years (!), a strain arose with an increased mutation rate. Following that, the frequency of newly generated mutations and diversity went through the roof. Early on, for the first 20,000 generations (ten years growing in the laboratory), the number of fixed genetic changes was, on average, just a small handful (usually less than ten). After this “mutator” strain arose, however, the number of fixed mutations (new genetic varieties which came to be present in all cells) rose to more than 250, and the number of single changes altogether rose to more than a thousand.

For me, this in a nutshell is what we see from the genome sequences. Lab stains don’t have much diversity compared to what we see in the natural world. On the one hand, we know that outside of the lab, there is an incredible amount of diversity within an organism (like E. coli). On the other hand, when we sequence a genome of a strain that's been grown in the laboratory for awhile, there are often just a small number of changes (a few hundred) associated with property differences. In nature, it is a whole different story. We have a paper that just came out a few weeks ago, comparing the genomes of sixty-one naturally occurring isolates of E. coli. Although some of the E. coli genomes are quite similar, others are VERY different - having more than a MILLION “extra” bases (DNA letters) in one genome, not found in another. The fraction of shared proteins between two strains ranges from nearly all (99.7%) to less than half (48%). Most E. coli genomes contain around 5000 genes, but if we look for all the different genes in all the genomes analyzed so far, we find more than 15,000 different gene families (or more than 3 times the size of any one E. coli genome!). Less than a thousand genes are conserved across all the E. coli genomes sequenced so far. What does this mean? As an example, pick an E. coli genome, and sequence it. Out of those 5000 genes, less than 20% will be found in nearly all other E. coli genomes, and for every one gene in this genome, there are perhaps another nine or ten E. coli genes that are found in other E. coli genomes, but not present in that particular E. coli genome. In addition to the 15,000 gene families discovered so far, we estimate there are probably around 30,000 more E. coli gene families in the intestinal tract of just a single person. This represents a tremendous diversity of genetic information. Since these many E.coli strains can readily exchange genes and parts of genes, there is an absolutely enormous potential to build new varieties of proteins. Behe’s naïve (to be frank) calculations don’t even scratch the surface in calculating this potential to generate new proteins and new protein interactions. He was not aware of any of this.

Take a look at the above figure. Note that the common lab strain of E.coli has 960 families of genes and from that it can build 4144 proteins. But there are other genes, found in some E. coli genomes, missing in others. How many other gene families are available, in nature to add to its protein repertoire? We estimate around 44,000 gene families are out there, in some E. coli genomes, but missing in others, in addition to the 960 present in the above strain.

So my point is, when Behe claims that in the E. coli evolution experiments 'Nothing fundamentally new has been produced.' (page 142), he is ignoring parts of the story which are extremely important. Since most people will not be familiar with the literature, we consider this to be misleading. There is a vast literature which shows just what can be done! Obviously evolution can happen in E. coli, on large scales, and it can be seen to happen under our very eyes, in the laboratory, under the right circumstances. With regard to the Lenski experiments, in my opinion, it is not being honest to only look at the first half of Rich Lenski’s experiments, where he saw little change, and to conclude that evolution does not happen in E. coli. The mutator (which arose halfway through) changed things dramatically.

The Figure above is a comparison of 61 E. coli genomes (each of the concentric circles is one strain of E. coli), showing the conservation of genes; for more details see Figure 5 in Oksana’s Microbial Ecology paper mentioned previously. The point I want to show here is that there are many large gaps (lighter-colored– regions of genes that are missing in many genomes, but present in others. Some of these regions encode novel ‘molecular machines’ – or what I think many (but not Behe) might call ‘fundamentally new’ complexes.


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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Dave Ussery - #39193

November 9th 2010

Hi Arthur,

thanks for the link - I had a look.  I think there are several good, interesting talks here! 

thanks!


Ashe - #39194

November 9th 2010

durn, missed photosynthesis.


Arthur Hunt - #39195

November 9th 2010

Ashe, Blankenship’s talk was interesting.  The good news for you is that he is coauthor of an upcoming review in Annual Reviews of Plant Biology that captures his talk.


John - #39199

November 9th 2010

Dave Ussery wrote:
“have a look at the abstract for the article I mentioned above - read the last sentence in the summary / abstract.  I realise that I am assuming you guys know how to read…”

Dave, they won’t read it except to find quotes to pull out of context. Rich and pds are absolutely determined to avoid dealing with evidence. The only evidence they can handle is evidence that an authority who agrees with them filters and explains to them.

“... Thus the argument ‘no articles exist’ would not allow this, if that argument were true…”

You’re missing the point of Behe’s utterly dishonest argument. Behe is demanding that a single paper be written in a way that Behe knows scientists don’t use!

Behe is playing to Rich’s fantasy that science is like high-school debate, when in fact it is driven by data.


John - #39200

November 9th 2010

pds:
“Also, I am not asking for the actual pathway, but simply a plausible pathway.”

You are demanding that it fit in a single manuscript, too.

“I am not asking for a huge amount of detail, just enough to show that it is plausible, by showing the survival advantage of each step.”

And why would anyone in the field write a paper to cater to your parroting of Behe’s silly demands?

“If it really happened that way, surely someone can imagine a plausible pathway.”

So why would it be published in a single manuscript? Don’t real scientists tend to publish data?

“Once someone does, then we can weigh the probability.”

How can you do that?

“The fact that no one even tries is quite telling.”

What’s telling is your fear of evidence that has not been predigested for you by someone with whom you agree.

“My main point above is to correct Dave’s misreading of Behe and me.”

Now you’re pretending that your parroting of Behe is the result of independent thought on your part?


John - #39201

November 9th 2010

Rich wrote:

“No, pds is not being unreasonable.  He’s asking for the kind of detailed explanation in evolutionary theory that’s expected in every other successful science (physics, chemistry, engineering, etc.).”

He’s demanding that appear in a single manuscript, which is ludicrous. Behe knows it’s ludicrous, which is why he demands it.

“If evolutionary biologists can’t provide the details that are being asked for,…”

But they do. They just don’t put it in a single manuscript. If you can’t read multiple manuscripts…

“... then they should lower the level of certainty of their claims.”

Why? Because they choose not to put it in the form Behe demands, in a single manuscript?


Arthur Hunt - #39202

November 9th 2010

Rich’s approach to this debate is captured in his response to one of my comments in another thread:

Don’t misdirect with paragraphs full of technical jargon.

Not much chance of having an informed and constructive discussion with someone like this, I am afraid.


John - #39203

November 9th 2010

Rich wrote:
“They should say:  “We believe that the cilium could have evolved via a series of random mutations,…”

Real biologists understand that “random mutations” is a creationist canard. Why should they use it?

“... each conferring selective advantage upon the creature so that all intermediate stages were viable, but we cannot yet specify what those steps might have been, except in the most general terms.”

The reality is that they study parts of the system and count on a reader being intelligent, curious, and not afraid to read more than one manuscript from the primary literature.


John - #39204

November 9th 2010

Dave wrote:
“and MY main point is to actually read the articles!!!!”

They aren’t going to actually read the articles, Dave, they are afraid to. They have no faith in their position.

“Did either Rich or PDS actually bother to even read either of these two articles, which they so quickly dismissed as not giving any sort of plausible mechanism?”

Obviously, no. Nor will they discuss the actual evidence unless they acquire it through hearsay, which they will then falsely represent as something they really know, such as when Rich repeatedly makes the false claim that knocking out flagellar genes always stops flagellar function. Behe hasn’t made that claim for years, and Minnich elided it at the Dover trial.

“I see the gene duplications listed, first this one, then the next then this then that… etc.  in details, just like PDS is asking for.  So this is what I mean when I say not LIKING the article is not the same thing as denying its existence…”

Denial is all they’ve got.


John - #39205

November 9th 2010

Dave wrote:
“once again, they are relying on the ignorance of the readers - they can just say “oh, these articles never really said this…”, and someone who hasn’t read them themselves might agree.”

Exactly, but you’re missing a bigger, more sinister point: Rich and pds KNOW that they must avoid reading and discussing these articles. They are complicit in Behe’s deception.

“But please don’t take my word for it!  Have a look yourselves…”

Not gonna happen.

Rich wrote:
“Does the article in question provide a *narrated* hypothetical evolutionary pathway of this sort:”

See, Dave? Rich is so afraid of engaging you on the evidence that he goes beyond Behe. Heck, if you showed him a *narrated* pathway (whatever that means), he’d demand that it be put on YouTube with Morgan Freeman narrating it, or he wouldn’t even look.

Rich and pds are AFRAID to look at the evidence.


Rich - #39212

November 9th 2010

Dr. Ussery:

It sounds as if this article (for which I did read the abstract, by the way) provides more than the usual number of detailed steps. I praise the authors for attempting to do this.  However, do we have any time constraints within which all these mutations are supposed to have happened?  For example, do we know whether the cilium evolved over 10 million years, 100 million years, or 500 million years?  One of the reasons that I prefer examples from multicellular creatures, particularly vertebrates, is that the fossil record gives us some time constraints for the evolutionary process.  For example, we know that if an artiodactyl became a whale, it had to do so in roughly 9 million years.  So, if whale evolution theorists can provide some detailed hypothetical pathways of the type you are describing, and if they will give their estimates of the number of mutations required, the Darwinian mechanism can be tested, by calculation, to see how probable it is.  But what time constraints do we have when we are talking about microbes whose features allegedly evolved over an unspecified length of time, hundreds of millions or even billions of years ago?


troy - #39215

November 9th 2010

John:

“Rich and pds are AFRAID to look at the evidence.”

Maybe, but you don’t really know. This kind of amateur psychology doesn’t contribute anything useful to the discussion.

They will always find holes in our knowledge, but no matter how many holes they find, they don’t have an alternative theory with fewer holes. Let them criticize evolutionary theory, but keep demanding that they offer an alternative with fewer holes. They can’t and they won’t.


John - #39219

November 9th 2010

troy wrote:
“Maybe, but you don’t really know.”

It’s an eminently testable hypothesis, and I’ve tested it many times. The only science opponents that engage on the evidence are those for whom it is not a major interest. But when they see that the empirical predictions of their testable hypotheses are false, they quickly develop an aversion to evidence if their commitment to ID is strong enough.

“This kind of amateur psychology doesn’t contribute anything useful to the discussion.”

I disagree. I think that my commenting on the far more likely reason Rich and pds make such silly demands may make them take the dangerous step of engaging Dave Ussery. It’s clearly much more likely to contribute than Dave writing, “it is obvious reading isn’t your strength…”

“They will always find holes in our knowledge, but no matter how many holes they find, they don’t have an alternative theory with fewer holes. Let them criticize evolutionary theory, but keep demanding that they offer an alternative with fewer holes. They can’t and they won’t.”

I’m well aware of that. However, Dave doesn’t seem to understand that Rich and pds will go to amazing lengths to avoid engaging him on the subject of his 5 posts.


DBB - #39230

November 9th 2010

I read the article “The Evolution of the Cilium and the Eukaryotic Cell.” Not once in the entire article was any mathematical or probability analysis attempted.  In the Discussion I find such sentences as “It has been conjectured that the cilium began in a cell polarized from its division center[Mitchell, 2004].  Mithchell went on to speculate that the earliest ciliary motility was a gliding rather than the complex bending motility.”  “Given that the 9+2 cilium with its full set of HC-Dyneins was in place before the last common ancestor of the extant eukaryotic cell,  one must also assume that the ciliary basal body was in place, suggesting also the existence of a complex division center prior to the last common eukaryotic ancestor.” “The proteins of the IFTD systme are related to the transport of vesicles from the Golgi.  This fact inspired Jekely and Arendt [Jekley and Arendt, 2006] to conjecture that the cilium began from a system that transported coated vesicles to the membrane”  No statistical analysis. Use of such words as:  “conjectured,  went on to speculate, one must also assume, inspired Jekely and Arendt to conjecture” ... leads me to conclude that evolutionary theory of the cilium is only speculation.


John - #39232

November 9th 2010

Art wrote:
“Rich’s approach to this debate is captured in his response to one of my comments in another thread: “Don’t misdirect with paragraphs full of technical jargon.” Not much chance of having an informed and constructive discussion with someone like this, I am afraid.”

Exactly. Then there’s this from comment 19519:
“However, I have been studying TE/ID/Darwinism for several years now, and have read probably ten thousand pages of books (almost all read whole, never skimmed), blogs, e-mails, arguments, rebuttals, rejoinders, etc.,…”

All arguments. No primary scientific literature, the stuff with the evidence.

Then Dave points pds to a paper from the secondary literature, but the most Rich can do is read the abstract. One can easily predict Rich’s reactions if one form or another of prodding embarrasses him into reading the paper:

1) It doesn’t have enough narrative detail. Therefore, what would fit his desperate modification of Behe’s silly demands would never fit into a single paper.

2) It doesn’t have the evidence in the paper. Of course, being a review, it cites the evidence, but it’s an excuse to avoid the evidence.


John - #39234

November 9th 2010

DBB comes back with a variant on my #2 above, pretending that the evidence cited in the paper doesn’t even exist:

“I read the article “The Evolution of the Cilium and the Eukaryotic Cell.””

But DBB won’t look at the evidence cited in the article.

“Not once in the entire article was any mathematical or probability analysis attempted.”

That’s because it’s a review. Do you know what that means, DBB?

“In the Discussion I find…”

Then you couldn’t have read it very well. This is not the primary literature, so there is no Discussion section for you to find anything in. The whole manuscript is review and discussion.

You have some incredible filters in place there. Again, Behe’s whole purpose in specifying so many aspects of the single manuscript that he demands are clearly designed to ensure that no such manuscript exists or could ever exist.

The gambit that Behe or anyone else gets to specify what one’s opponents have to cram into a single manuscript is insane.


Dave Ussery - #39244

November 10th 2010

DBB - #39230 - I read the article “The Evolution of the Cilium and the Eukaryotic Cell.”  Not once in the entire article was any mathematical or probability analysis attempted.

Hi DBB,

Maybe I should have added, not only does one need to READ the article, but also to UNDERSTAND what is being said.  Have a look at Figure 2.  See those numbers on the branches? These are called ‘bootstrap values’, and they represent how many times the same branch occurs - that is, in a sense how reproducible is the tree.  They DO discuss this quite a bit in the paper.  Obviously you don’t know who Temple Smith is, nor have you heard him give a talk.  Believe me, there’s lots of math here!


John - #39255

November 10th 2010

DBB, apologies. I was wrong about the Discussion. I was confusing one of the two papers Dave cited with the other.

Dave is right about the presence of probability analysis in Figure 2, though. How could you miss that?


pds - #39267

November 10th 2010

Dave,

I largely agree with what Rich has said here.  It does seem that the article has some discussion of Darwinian pathways.  Thank you.  So at least you are now on the same dialogue page with what Behe is talking about. 

I don’t have access to the entire article.  Even if I did, I am not the best person to evaluate how many steps are discussed and whether the survival advantages are plausible at each stage.  But this is where the ID-TE dialogue needs to take place, IMO.  One of the contributors at Telic Thoughts would be better able to discuss this.

Have you followed this thread (despite the title)? 

http://telicthoughts.com/ussery-dishonest-again/

The current discussion is not about you personally.  I would like to see Pez and Sal or others respond to your article.  Looks like DBB is already addressing the content.

BTW, I did read everything you posted here about your article.  You are really in no position to condescend about reading abilities.


pds - #39268

November 10th 2010

John,

As I said before, I don’t read your comments.  Too many personal insults and bad logic.

Biologos,

How many personal insults from John will you allow?  Your “double standard” on comments is (once again) glaring.

For example:  http://thedesignspectrum.wordpress.com/2010/11/08/biologos-deletes-call-for-civil-discourse-by-all-sides/


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