Is There an Edge to Evolution? Part 4

Bookmark and Share

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.

< Previous post in series Next post in series >


Share your thoughts

Have a comment or question for the author? We'd love to hear from you.

View the archived discussion of this post

This article is now closed for new comments. The archived comments are shown below.

Loading...
Page 8 of 13   « 5 6 7 8 9 10 11 »
Mike Gene - #38895

November 7th 2010

There was an article in Science magazine a week or two ago, about this - kind of interesting.

Yes, I noticed that and commented on it.


Dave Ussery - #38900

November 7th 2010

Mike Gene wants to know what type of evidence I’m looking for, with respect to supporting his claim that cytochrome oxidases were present in an ancestor bacterial genome, 4 billion years ago.

I am saying that there are well known, documented cases of genes being horizontally transferred between bacteria and archaea - so merely finding a gene in a couple (but not all) archaeal genomes is not very convincing proof that this gene has been around for 4 billion years!  Probably the sequence has changed so much that we would not recognize it today!  And in fact, when I examine all the genomes available, I find just this - not a single protein (including cytochrome oxidases) are conserved across all phyla.  And in particular anaerobes, which are more ancient, have an astounding diversity within them, with less than 1% of the proteins conserved between two bacterial ‘cousins’.

Now, you can say that these guys looking at the conservation of cytochrome oxidases used a data set (with half the genomes that I did), and they built a tree - but what I am saying is that I think it is dangerous to rely JUST on ‘the genetic clock’ type of data, with all the inherently bad presuppositions that go with this.

(continued in next post)


Dave Ussery - #38902

November 7th 2010

For example, as you probably know, Doolittle originally claimed Gram positives and Gram negatives had their last common ancestor around 1.5 billion years ago. 

But there are fossils of Gram positive and Gram negatives dating back much further - closer to almost 4 billion years ago.  The fossil evidence relies not only on morphology (two membranes vs. one, for example), but on lipid composition and geochemical analysis.  So my point is, relying JUST on the sequences of modern day organisms that one supposes is ‘ancient’ because they seem more like someone supposes early lineages to be is not so trustworthy….  And YES the cytochrome oxidases might actually form some sort of complex that could be detected by paleogeology.  dunno. But I just think this is an extraordinary claim, and as such relying on the presence of genes in modern-day organisms (I know people do this all the time!) is a bit dangerous, especially with all the horizontal gene transfer going on…

Did you know that the genes for photosynthesis can be transferred via a phage?

see http://www.ncbi.nlm.nih.gov/pubmed/19710652

so yes, gene transfer of systems like this is not only possible, it has been documented…


John - #38903

November 7th 2010

hmm wrote:
“Yes. Peer review is an amazing process…In fact, the author often cannot know, whether his/her paper is really read, understood and reviewed.”

You’re missing the point. Most of the reviews I’ve written have not been peer reviewed, even when they are published in journals that also contain primary literature (something the ID movement avoids, because those papers, by definition, contain previously unpublished data).

So the bottom line is that you have no idea whether the papers you cited were peer reviewed, because none of them belong to the primary literature.


John - #38904

November 7th 2010

Dave, I don’t think that your apologizing for pds’s ignoring your response to his request will result in engagement by pds.

It’s also worth pointing out that we know from comparative genomics that Behe’s claims about the eubacterial flagellum fitting any of his definitions of IC are simply false.


Dave Ussery - #38913

November 7th 2010

John, perhaps you are right - let’s see if PDS responds to the article “The evolution of the cilium and the eukaryotic cell”, which certainly appears to me (and most scientists) as being an article about cilium evolution, giving an explanation going from a simple microtubule complex to a cilium, via eight gene duplications.  But then again, there’s lots of big words in that article, and it IS rather complicated…  but on the other hand, this is what PDS asked for, so maybe he’ s happy now.  Let’s see.  Maybe some other ID people on the list can help PDS out here….

What I’m more curious about is whether Mike Gene will maybe step up and tell us about his new plans to move into synthetic biology.  I mean, with all his engineering and design theories, this would be a great way to bring in lots of money - as good publicity for ID.  Imagine - maybe he could get a huge 3 billion dollar grant from a company like Exon, who gave Craig Venter a ton of money to use synthetic biology to develop new energy sources…

so please tell us, Mike, what are your thoughts about ID and synthetic biology??


beaglelady - #38918

November 7th 2010

There was workplace bullying in Sternberg’s earlier job place and he resigned. Now he hasn’t so good research resources as earlier.

Has he actually tried to get funding for ID research?  Is anyone trying to get funding for ID research?  I’d be interested to know what proposals are on the table.


hmm - #38922

November 7th 2010

Resources are not the same thing than just money. For example relationships and access to databases are also very important resources. For example Guillermo Gonzales has been able to publish a lot of studies even without much funding.

I don’t even know, what could count as “ID reseach”, but when I read articles like this

http://bentham.org/open/toaaj/articles/V002/74TOAAJ.pdf

I sometimes wonder, why Gonzales doesn’t get funding. However, he has done research even without fundings.

( Gonzales published also these in 2009:
http://onlinelibrary.wiley.com/doi/10.1111/j.1468-4004.2009.50217.x/abstract
http://onlinelibrary.wiley.com/doi/10.1111/j.1745-3933.2009.00734.x/abstract )


Mike Gene - #38924

November 7th 2010

Hi Dave,

I am saying that there are well known, documented cases of genes being horizontally transferred between bacteria and archaea - so merely finding a gene in a couple (but not all) archaeal genomes is not very convincing proof that this gene has been around for 4 billion years!

I never claimed to have “very convincing proof that this gene has been around for 4 billion years.”  In fact, I agree we do not have such ““very convincing proof.”  What we have is some circumstantial evidence that speaks to the plausibility of the oxidases pre-dating oxygenic photosynthesis.  And yes, I am well aware of just how common horizontal transfer is.  It makes much design sense when it comes to terraforming the planet.


Mike Gene - #38925

November 7th 2010

Probably the sequence has changed so much that we would not recognize it today!

Yes, the ftsZ/tubulin story indicates there is a significant element of robustness to protein function.  The ID people go off track in treating proteins as some delicate material than oh so easily breaks.  That doesn’t sound like something a clever designer would employ.  Proteins are more amazing than that.

And in fact, when I examine all the genomes available, I find just this - not a single protein (including cytochrome oxidases) are conserved across all phyla.

I’m still not getting this.  Are you saying we can only infer an ancestral gene/protein if it is universally retained and strongly conserved across all known lineages?

what I am saying is that I think it is dangerous to rely JUST on ‘the genetic clock’ type of data, with all the inherently bad presuppositions that go with this.

Perhaps you can expand on this.


Mike Gene - #38926

November 7th 2010

But there are fossils of Gram positive and Gram negatives dating back much further - closer to almost 4 billion years ago.  The fossil evidence relies not only on morphology (two membranes vs. one, for example), but on lipid composition and geochemical analysis.

I’d love the references for this. 

Did you know that the genes for photosynthesis can be transferred via a phage?

Yes.  I view bacteria as a huge, global, super-organism where individual cells are in constant biochemical communication with each other.  It is this bacterial network that terraformed the planet to serve as the foundation to facilitate the subsequent evolution of more complex cell types. 

What I’m more curious about is whether Mike Gene will maybe step up and tell us about his new plans to move into synthetic biology.

I have never expressed such plans, as I lack the level of expertise and experience for such a move.  If I could go back in time, I would definitely put myself on a track to get into the very belly of such research.


Dave Ussery - #38927

November 7th 2010

Hi Mike,

great!  so are you going to try and get some money to use ID based design for some ‘terraforming”??


Mike Gene - #38928

November 7th 2010

I mean, with all his engineering and design theories, this would be a great way to bring in lots of money - as good publicity for ID.

I have no interest in bringing about any “good publicity for ID.”  Neither do I have “engineering and design theories.”  What I offer is an alternative perspective that explores the possibility that evolution and design have interfaced with each other. 

so please tell us, Mike, what are your thoughts about ID and synthetic biology??

For starters, Synthetic evolution.


Mike Gene - #38929

November 7th 2010

Dave,

great!  so are you going to try and get some money to use ID based design for some ‘terraforming”??

What are you talking about?


beaglelady - #38933

November 7th 2010

Resources are not the same thing than just money. For example relationships and access to databases are also very important resources. For example Guillermo Gonzales has been able to publish a lot of studies even without much funding.

Funding is a big part of it and I’ve heard ID people complain that they don’t get sufficient funding.  So I’m just wonder what ID-related research projects are on the table and awaiting funding.


John - #38960

November 8th 2010

beaglelady wrote:
“So I’m just wonder what ID-related research projects are on the table and awaiting funding.”

None, unless you want to pretend that quote-mining the secondary literature to deceive laypeople is research in the same way that grad students and postdocs labor long hours in the lab or field to learn things that no human has ever learned before.

And it will remain that way.


johan - #38961

November 8th 2010

//So I’m just wonder what ID-related research projects are on the table and awaiting funding.//

Evolutionists are actually doing the research for ID theorists when do these long term evolution experiments. ID theorists couldn’t ask for more.


johan - #38962

November 8th 2010

@Mike Gene

//What I offer is an alternative perspective that explores the possibility that evolution and design have interfaced with each other.//

I think Thomas Nagel said something relevant here when he wrote:

“It[evolution] is not just the theory that life evolved over billions of years, and that all species are descended from a common ancestor. Its defining element is the claim that all this happened as the result of the appearance of random and purposeless mutations in the genetic material followed by natural selection due to the resulting heritable variations in reproductive fitness.”

What you are trying to do Mike is argue against the very core of evolution theory by trying to argue for a guided form of evolution as unguided evolution is precisely the point of evolution theory. Evolution can dispense itself of all components (be this natural selection or even universal common descent) but it cannot dispense with the notion that evolution is purposeless and unguided, as this is evolution.


John - #38965

November 8th 2010

Johan wrote:
“Evolutionists are actually doing the research for ID theorists when do these long term evolution experiments. ID theorists couldn’t ask for more.”

So how is it that the lazy ID theorists can only point to experiments that allegedly test their hypotheses after they’ve been done and the lazy ID theorists can think of a way to spin the results so that they claim they expected them?

If your claim is true, when will we see someone from the ID camp point to an experiment BEFORE it is done and say, “My ID hypothesis predicts X, if we don’t see X my hypothesis is wrong?”

Maybe you could be the first with that kind of courage, Johan?


johan - #38966

November 8th 2010

@John

“My ID hypothesis predicts X, if we don’t see X my hypothesis is wrong?”

ID theorists do not expect random mutations to produce IC biochemical systems. Therefore a long term ID experiment wouldn’t look much different from a long term evolution experiment, the only difference is the evolutionist would have to conclude that his research “sheds light on evolution” or confirms something about evolution since he received a grant for doing evolution research. It’s just not gonna look good if your research doesn’t prove evolution.

The Lenski experiment with E.coli or the long-term evolution experiment with Drosophila turned out to be very supportive of ID expectations, despite the fact that these were done within an evolutionary framework. In fact, it makes for a stronger case for ID when the evidence for ID comes from evolutionary experiments done by evolutionists themselves.


Page 8 of 13   « 5 6 7 8 9 10 11 »