Is There an Edge to Evolution? Part 3

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October 23, 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 3

In his previous post, Dr. Ussery showed that Behe’s analysis of the probability of getting beneficial mutations is flawed at fundamental levels. Beneficial mutations do occur, new genes do evolve and he cited some research articles that demonstrate this and then showed the interested reader how to gain access to the vast scientific literature that exists. He expresses concern that Michael Behe has not chosen to make the general public aware of what is being done in this arena.

In today’s post he goes on to examine what Behe states is the limit of what Darwinian evolution can and cannot do.

Chapter 4 - What Darwinism Can Do

The title for this chapter is a bit deceptive, in that most of this chapter is not really about what evolution CAN do, but rather what the limits to evolution are (the topic for the next chapter). There is a short description of genome sequence analysis and the types of mutations observed in the laboratory, but in my opinion this chapter is really missing a thorough discussion of the astounding variety and diversity we find when we examine genomes.

Again, Behe emphasizes that he has no problem with evolution by common descent:

Over the next few sections I'll show some of the newest evidence from studies of DNA that convinces most scientists, including myself, that one leg of Darwin's theory - common descent - is correct. (page 65).

Once again, the problem is random mutations:

The bottom line is this. Common descent is true; yet the explanation of common descent – even the common descent of humans and chimps – although fascinating, is in a profound sense trivial. It says merely that commonalities were there from the start, present in a common ancestor. It does not even begin to explain where those commonalities come from, or how humans subsequently acquired remarkable differences. Something nonrandom must account for the common descent of life. (page 65, emphasis in the original).

I absolutely agree with Behe – there must be a ‘non-random’ account. But I’m a bit confused here, because natural selection is, by definition, definitely non-random. That’s the whole point! There is (random) variation, and then those variants that are better are selected. It is not at all random. But Behe’s claim here is that there are not enough random variants produced for evolution to occur. 150 years ago, at the time of Darwin’s writing, it was not known whether the variation was random or produced in some other manner – and in a sense this did not matter.

What was important for Darwin was that the variation was there, and that the method for non-random selection – also known as “natural selection” – could account for the non-random common descent of life. One of the analogies Darwin used was “artificial selection”, where, for example, dog breeders would breed certain traits, giving rise to a large variety of dogs within a short amount of time – merely by [non-randomly] selecting for desired traits. Darwin reasoned if this worked for breeders, why couldn’t it work in natural environments? And as far as “random variations” go, we have quite a bit of variance in dogs, from tiny toy poodles to St. Bernards.

More than half the chapter is devoted to species that have had duplications of their entire genome. Behe focuses especially on yeast, although he mentions in a footnote that other whole genome duplications have been documented. But again, the text written is more within the framework of the limits of evolution—what it can’t do, which should be the subject for the next chapter (I suspect a chapter strictly about what Behe thought evolution could do would be quite thin). The claim that “genome duplication…. has not given baker’s yeast any advantage it wouldn’t otherwise have had” (page 74) seems pretty harsh, especially now that more than two dozen different strains of yeast have been sequenced, and there are clear advantages in survival associated with duplication of many of these genes.

Perhaps, once again, Behe is not familiar with the literature and not willing to have a look at what has been published. I encourage the interested reader to go ahead and have a look at what is out there—go to PubMed, and type in the words “yeast genome duplication evolution” and have a look at the articles found. Today when I did this, I found 420 articles. The second one on the list has this statement in the concluding sentence of the abstract: “Our results provide a scenario for how evolution like a tinker exploits pre-existing materials of a conserved post-transcriptional regulon to regulate gene expression for novel functional roles.” Behe concludes the chapter by saying that “although Darwin hoped otherwise, random variation doesn't explain the most basic features of biology” (page 83).

For more on what evolution CAN do, I mention “The Edge of Evolution” in a footnote in the last chapter (Evolution of Microbial Communities) of my textbook on Comparative Genomics. It is in a section on “Where Does Diversity Come From?”, and I make the statement that some anti-evolutionists “claim that there is not enough diversity in bacterial populations for evolution to occur.” I encourage the interested reader to have a look at this section, as I think it is a nice culmination of a story I’ve slowly built up through the previous chapters on bacterial genomics.

I readily admit that this is something that takes time to understand and cannot easily be explained in a 10-second sound bite – this textbook came from a course I’ve taught at the Technical University of Denmark since 2000. Currently the course meets in the autumn semester, for 8 hours a week, for 13 weeks; this year I have 54 students. So this takes time to explain, but my point here is that the claim that nothing has changed over the past 10 years, in terms of evidence for evolution and documented diversity, is simply wrong.

Chapter 5 - What Darwinism Can't Do

The title of this chapter reminds me of a book by Lenny Moss, called What Gene’s Can’t Do. I think this is a wonderful book, kind of countering the “gene-centric” popular culture. It’s a well-written book, and in my opinion he makes some valid scientific points. Unfortunately, although Behe could have had a similar good discussion here, instead we are treated to poor quality left-overs. This chapter is kind of an update on “irreducible complexity” as outlined in Behe's previous book, Darwin's Black Box. In spite of strong protestations from many (including myself) in their reviews of that work, Behe still clings to the idea that no one has ever published anything about the evolution of these complex molecular machines. “Despite the amazing advance of molecular biology as a whole, despite the sequencing of hundreds of entire genomes and other leaps in knowledge, despite the provocation of Darwin's Black Box itself, in the more than ten years since I pointed out that a situation concerning missing Darwinian explanations for the evolution of the cilium is utterly unchanged” (page 95).

Again, the interested reader is invited to visit PubMed, type in “cilium evolution” and see for oneself: are we to believe that articles with titles like “The evolution of the cilium and the eukaryotic cell” and 'Origin of the cilium: novel approaches to examine a centriolar evolution hypothesis” simply don't exist? Perhaps if one closes their eyes, and clicks their heels three times, thinking, “They don't exist, they don't exist”, maybe these articles can simply vanish!

Last week I gave a lecture in my course about the 10th anniversary of sequencing the human genome. In the field of genomics, much has happened in the past 10 years. There has been an explosion in the amount of genomic data available, and also in the strong, clear evidence for evolution in exactly the manner Behe claims is impossible and will never happen. To put this in perspective – when I first came to the Center for Biological Sequence Analysis in 1997, there were four bacterial genomes sequenced. Last week, in my course I showed an update of the currently sequenced genomes: there are now more than four thousand genomes sequenced, and the number is growing on a daily basis. And the more genomes we sequence, the more we learn about how evolution works. When I was growing up, the preacher in our church used to say, “Did you hear about the guy who said ‘It can’t be done?’ Well he got run over by the guy doing it!” I think there is some truth in this – Behe says it can’t be done, and a decade later, despite this vast amount of data, he claims things remain “utterly unchanged”.

In my next post, I will examine Behe’s discussion of whether random mutation hitched to natural selection is a biological explanation for various molecular phenomena.


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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pds - #37162

October 28th 2010

Dave,

You said:

>>>2) Would you be willing to define “fitness landscapes,” and to provide a concrete example or two in which darwinian evolution cannot make the leap you describe?

For example, consider the human eye - I would say that it is impossible for evolution to now ‘get it right’ and to evolve a human eye without the blind spot - without the blood vessels on the wrong side - NOW.  But of course evolution CAN (and has) ‘got it right’ in the past - for example, in the eyes of an Octopus, where the blood vessels come in from the back, and there is no blind spot.  . . . .<<<<

Are there any examples from the actual biological world that are beyond what you think evolution can do?


John - #37166

October 28th 2010

Gregory wrote:
“If memory serves me correctly, I think the number [of YECs] was well under 10%, more like 2%. Paul Nelson is the only one that comes to my mind out of >36 Fellows.”

Gregory, it looks like Dembski has gone YEC:
“In writing The End of Christianity today, I would also underscore three points: (1) As a biblical inerrantist, I accept the full verbal inspiration of the Bible and the conventional authorship of the books of the Bible. Thus, in particular, I accept Mosaic authorship of Genesis (and of the Pentateuch) and reject the Documentary Hypothesis. (2) Even though I introduce in the book a distinction between kairos (God’s time) and chronos (the world’s time), the two are not mutually exclusive. In particular, I accept that the events described in Genesis 1-11 happened in ordinary space-time, and thus that these chapters are as historical as the rest of the Pentateuch. (3) I believe that Adam and Eve were real people, that as the initial pair of humans they were the progenitors of the whole human race, that they were specially created by God, and thus that they were not the result of an evolutionary process from primate or hominid ancestors.”


John - #37167

October 28th 2010

More Dembski on the flood:
“Yet, in a brief section on Genesis 4-11, I weigh in on the Flood, raising questions about its universality, without adequate study or reflection on my part. Before I write on this topic again, I have much exegetical, historical, and theological work to do. In any case, not only Genesis 6-9 but also Jesus in Matthew 24 and Peter in Second Peter seem clearly to teach that the Flood was universal. As a biblical inerrantist, I believe that what the Bible teaches is true and bow to the text, including its teaching about the Flood and its universality.”


John - #37168

October 28th 2010

pds asked:
“Are there any examples from the actual biological world that are beyond what you think evolution can do?”

Yes, replacement of several essential ribozymes with protein catalysts. For the ribosome, this evidence is so powerful that Meyer mightily fudged it and outright lied about it in Signature in the Cell.

Of course, he knows that he can get away with it because he knows that his audience will never check up on him.


John - #37170

October 28th 2010

Gregory wrote:
“Have you made a single fruitful contribution to cooperative dialogue between science & religion since coming to BioLogos, John?”

Yes. In Part I, you asked about the edges to evolution. I offered the ribosome. You, predictably, ran away.

Look just above, in which I correct your misconception about YECciness in the DI.

“Yes, I did call DaveW’s perspective ‘sophomoric.’ He has not studied ideology anywhere close to as deeply & widely as I have. & maybe he’ll learn his lesson here.”

The point was that it was not fruitful by Karl’s standard, not whether you felt it was justified.

“But you know what, John, I still respect DaveW & I even like him! Which is more than can be said for you.”

“Sophomoric” and “learn his lesson” are not terms that convey any respect or affection.

“You know what, John, just being a ‘scientist’ will not earn you the respect of anyone here.”

Huh? When have I demanded or requested respect from anyone here, Gregory?

“One must be a compassiate human being too. You have a lot to learn in this area. I’d rather you went away.”

So in your mind, biomedical research is not a compassionate activity?


Gregory - #37179

October 28th 2010

John, here ya go, guy: http://www.uncommondescent.com/intelligent-design/coming-clean-about-yec/

That’s from SIX DAYS AGO. Is that new enough for you? What part of “It’s not true” doesn’t make sense to you? Will you persist in calling Dembski a YEC after today or not?

I asked: “Have you made a single fruitful contribution to cooperative dialogue between science & religion since coming to BioLogos, John?”

You answered: “Yes. In Part I, you asked about the edges to evolution. I offered the ribosome.”

Please tell, how is this a “fruitful contribution to cooperative dialogue between science & religion”? I see no fruit here; just the science, with no religion.

With regard to ‘running away,’ I had thought someone in a field of science who could assess ribosomes, which you claim as an ‘edge of evolution,’ would speak. This is not my speciality, though I sometimes enjoy reading about it.

I assume, though I haven’t explicitly read you saying it, that you are not religious. I also assume, based on your words here at BioLogos, that you are rather *against* than *for* the potentially fruitful dialogue between science and religion, which is the mission of this site. Am I wrong with these assumptions?


R Hampton - #37180

October 28th 2010

What does ID predicts as to the number of mutations per individual? It has important implications re: the calculation of “neo-Darwinism” being improbable, so I question if this empirical data matches their theoretical assumptions:

A Comprehensive Map of Human Genetic Diversity
http://www.technologyreview.com/blog/editors/25943/

The initial findings show that everyone carries 250 to 300 mutations that alter the function of the protein that the gene produces. Approximately 50 to 100 of these mutations occur in genes that have previously been linked to inherited diseases. (But because everyone has ...two copies of each gene—one from their mother and one from their father—as long as an individual carries one normal copy, they are likely to be healthy.)


beaglelady - #37196

October 28th 2010

Gregory,

It’s not for you to say whether or not John’s contributions have been fruitful.  All viewpoints are welcome here.  Since he is a professional in the natural sciences his input is quite valuable.


beaglelady - #37197

October 28th 2010

Dembski might not be exactly a YEC, but he is certainly becoming more of a creationist. At a debate some years ago I heard him say that he takes Genesis figuratively.  It appears that he has recently changed his tune.  It’s possible that he fears being expelled from his teaching position.


Gregory - #37202

October 28th 2010

My goodness, beaglelady, you sure have a thing for me!!! ‘Anything but what Gregory says,’ seems to be now one of your mottos.

Be kind to your neighbours! Have charity!

Since you feel so much like defending John (might be the only one at BioLogos!), please do tell of one ‘fruitful contribution’ John has made *to cooperative dialogue between science & religion*.

The “all viewpoints made are welcome here” is just plain relativism personified. Why have a select few people been banned from BioLogos if “all viewpoints made are welcome here”?

Oh, he’s a scientist? Oh, then *everything* he says must be valuable!? Please spare me this scientistic worship, beaglelady. I’m sure your local Episcopal deacon would scold you for it.

beaglelady wrote: “Dembski might not be exactly a YEC…”

So John is ‘wrong’ in your opinion, on this topic. He says Dembski is YEC. I say he’s not. Who do you believe?

But hey, I just said it, so it must be wrong.


Alan Fox - #37205

October 28th 2010

Is there an ID theory? What is it?


John - #37207

October 28th 2010

Gregory wrote:
“That’s from SIX DAYS AGO. Is that new enough for you? What part of “It’s not true” doesn’t make sense to you?”

The lack of a statement of belief as to the age of the earth. The failure to offer dates for Adam & Eve and the worldwide flood.

He’s been squeezed hard and is walking back his walkback.

“Will you persist in calling Dembski a YEC after today or not?”

Will he tell us how old he believes the earth is, and when the historical events of Genesis took place? I predict that he will not. Will you explain how belief in a literal, worldwide flood doesn’t place the believer in the YEC camp?

“Please tell, how is this a “fruitful contribution to cooperative dialogue between science & religion”? I see no fruit here; just the science, with no religion.”

In the same way this very post on which you are commenting does. Evidence matters.


John - #37208

October 28th 2010

Gregory:
“With regard to ‘running away,’ I had thought someone in a field of science who could assess ribosomes, which you claim as an ‘edge of evolution,’ would speak. This is not my speciality, though I sometimes enjoy reading about it.”

I did speak. You ran away. Do you want to resume? Why is the most central enzyme in translation made out of RNA?

“I assume, though I haven’t explicitly read you saying it, that you are not religious. I also assume, based on your words here at BioLogos, that you are rather *against* than *for* the potentially fruitful dialogue between science and religion, which is the mission of this site. Am I wrong with these assumptions?”

Yup.


Alan Fox - #37210

October 28th 2010

He says Dembski is YEC. I say he’s not.

Presumably, Bill Demski can speak for himself. Why should anyone else be concerned about Dembski’s beliefs?


Gregory - #37221

October 28th 2010

“I assume, though I haven’t explicitly read you saying it, that you are not religious. I also assume, based on your words here at BioLogos, that you are rather *against* than *for* the potentially fruitful dialogue between science and religion, which is the mission of this site. Am I wrong with these assumptions?” - Gregory

“Yup.” - John

Oh, o.k. then. How am I wrong, John? I’d like to learn.

Are you religious? Are you a Christian? Are you *for* rather than *against* fruitful dialogue between science and religion?


John - #37229

October 28th 2010

Gregory wrote:
“So John is ‘wrong’ in your opinion, on this topic. He says Dembski is YEC. I say he’s not. Who do you believe?”

I wrote, “it looks like Dembski has gone YEC.” Would you not agree that it looks that way?

Clearly, he’s hedging.

“Are you religious? Are you a Christian?”

Yes squared.

“Are you *for* rather than *against* fruitful dialogue between science and religion?”

I’m for it.

Fruitful dialogue can’t happen with people who reject the amazing evidence that God has provided for all to see, people who insist that hearsay is more important than evidence, a viewpoint that is rejected in the Bible itself.

Fruitful dialogue can’t happen with people who desperately try to misrepresent science as a debate club instead of people working at the bench and in the field to generate data by testing their hypotheses.

Go back and read Ussery’s post. Do you want to discuss it, or do you want to label people?


beaglelady - #37231

October 28th 2010

The “all viewpoints made are welcome here” is just plain relativism personified. Why have a select few people been banned from BioLogos if “all viewpoints made are welcome here”?

You misquoted me. I said, “all viewpoints are welcome here.”  That is how I understand the BioLogos Ground Rules for Commenting.  They said that they “welcome both critical and supportive voices.”  They also expect participants to be polite and to make comments relevant to the topic being discussed.


sy - #37254

October 28th 2010

John

I am curious about your comment that the most important enzyme in translation is made of RNA. Are you referring to the ribosome itself? I always thought that the aatRNA synthases were the most important enzymes in the process. Are you implying that the ribosome is a direct descendant from the RNA world? Sorry if I missed some earlier discussion on this, but I havent been able to find it.


John - #37257

October 28th 2010

sy asked:
“Are you referring to the ribosome itself?”

No, the specific part of the ribosome known as the active site, or peptidyl transferase.

“I always thought that the aatRNA synthases were the most important enzymes in the process.”

Why would they be more important than the ribozyme that catalyzes the formation of peptide bonds?

“Are you implying that the ribosome is a direct descendant from the RNA world?”“

Why would an intelligent designer use RNA for this purpose? It’s clear why evolutionary mechanisms would have a hard time replacing it with protein.

Do you know of two other similar examples, sy?

Why does Stephen Meyer fudge this and lie about it in his book, when the data are 10 years old and prompted the awarding of the Nobel Prize for Chemistry?


Rich - #37262

October 29th 2010

Gregory:

Your question (37221) stimulated the following thoughts:

Whether or not someone should be called a Christian depends on what you think “Christian” means.  Belonging to a church of some denomination? Holding to correct theological doctrine, however that is defined?  Holding to the inerrancy of the Bible?  Having had a personal religious experience of Jesus Christ?  Living a Christlike life out of a Christlike spirit?

I think the last is the best definition.  I measure a Christian not by what he says he believes about Jesus, but by how well he exemplifies the spirit which dwelt within Jesus.  I’m reminded of some phrases from Calvin:

“Christ never is where His Spirit is not ... where zeal for integrity and holiness is not in vigor, there neither is the Spirit of Christ nor Christ Himself; and wherever Christ is not, there is no righteousness, nay there is no faith; for faith cannot apprehend Christ for righteousness without the Spirit of sanctification.”

I often fall far short of sanctification myself, and whenever I do, I fully expect that some will doubt the existence of real conviction in me.  I do not fault them for this.  One should be a Christian not only in theory but in practice.


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