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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Rich - #37763

October 31st 2010

sy:

I agree very much with this principle that you state:

“the fundamental principle of science is to go with the data, even if it goes against your ideas.”

You then give the example of God’s creating life as a view that you would let go if it turns out to be wrong.

Does that work both ways?  For example, if it turns out that a much deeper knowledge of macromolecules acquired in the future leads to the conclusion that the probability of the formation of the DNA-protein system without guidance is extremely low, on the order of, say, 1 in 10^100, would it be incumbent upon biologists to acknowledge a role for design in the origin of that system as “the best explanation”?  Or would they be allowed to duck out with “the origin of the system cannot be explained by present science”?

What I observe is an artificial skewing of explanation when it comes to questions of origins.  Whenever the best explanation would appear to be intelligent design, the anti-design scientists say that the proper answer is agnosticism; but whenever the best explanation (though far from demonstrated) appears to be unguided, unplanned natural processes, that conclusion is quickly adopted.  Do you think this systemic bias is legitimate?


Tim - #37766

October 31st 2010

Rich,

Sorry for the hiatus again.  Been pretty busy.  OK, I’ve read through your posts and checked out the reference material you provided.  Here are my thoughts:

1)  I had the timeline wrong for when the TTSS was first introduced as a falsification of the “irreducibly complex” bacterial flagellum as laid out by Behe’s argument.  Behe’s first major publication proposing that the bacterial flagellum was “irreducibly complex” is Darwin’s Black Box, published in 1998.  Now, the ID theorists, Behe and Dembski, were introduced to the argument that the Type III Secretory System was a precursor candidate for the “motor” part of the bacterial flagellum by Kenneth Miller in 2000.  Dembski’s No Free Lunch, however, came out in 2002.  So at the time Dembski published this work, he was already aware of the TTSS.  So it wouldn’t make any sense to suggest he didn’t see it coming at the time of publication.

2)  Nevertheless, while Dembski acknowledges the TTSS’ candidacy as a precursor part to the bacterial flagellum, he then goes on to ignore this possibility completely when performing his probability calculations.  I find it incredible (and arguably disingenuous) that he would artificially inflate his numbers this way.

cont.


Tim - #37768

October 31st 2010

Rich (continued),

*typo on the date for Darwin’s Black Box, that was supposed to be 1996.

3)  Now, the concept of irreducible complexity appears to be poorly defined.  It was first defined by Behe in Darwin’s Black Box (1996) as ““By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.”  Behe then goes on to give the analogy of a mousetrap to illustrate what he means.  He colorfully mentions that if a particular part was gone, the mouse could “dance all night” on the trap without being caught.  Now, I think most people reading his definition, as fleshed out by his mousetrap analogy, would walk away with the impression that without all the parts of the irreducibly complex system assembled together, what you have is a non-functional paperweight.  That’s certainly the impression I had.  And the impression apparently Kenneth Miller had as well.

cont.


Tim - #37771

October 31st 2010

Rich (continued),

3) [continued]  In fact, I would note that Behe’s language of “any precursor to an irreducibly complex system is by definition nonfunctional” in his 1998 Molecular Machines: Experimental Support for the Design Inference supports that such a view of irreducible complexity was his original intent.  I would note that his 1998 article is still prior to the TTSS being presented to them as a fully functional candidate precursor to bacterial flagellum.  Again, what it looks like we have here is a re-defining of irreducible complexity when contradictory evidence rears its head.

4)  Behe and Dembski decided, after the TTSS was brought to their attention, to “clarify” their definition of “irreducible complexity.”  But to a lot of people (myself included) this starts to look merely like moving the goal post.  In response to the TTSS being introduced, Behe in 2000 “clarifies” his definition to state: “An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.”  Now irreducible complexity is a gradient, not a category?


Tim - #37772

October 31st 2010

Rich (continued),

4) [continued] So technically then if you could demonstrate that every precursor necessary to result in the formation of a particular structure could be accounted for with the exception of only one, then the result would be an “irreducibly complex” structure?  Since you’ve only, say, accounted for 90% of the evolutionary process, but since that last 1-% alludes you it is therefore “irreducibly complex?”  What is the value of such a definition then?  *I would note that I was unable to obtain Debating Design: From Darwin to DNA, but as it was published in 2004, it would represent a post-TTSS “clarification” of “irreducible complexity” and thus would still potentially fall under the umbrella of “moving the goal post.”  If you want to offer the definition provided in that book, that would be fine.

Well, that wraps up my response.  I’m off to take care of life responsibilities, so cheers Rich.


Tim - #37773

October 31st 2010

*typo:  Should be “10%” not “1-%”


Tim - #37774

October 31st 2010

*Another correction, Behe’s 2000 definition was in response to the Blood Clotting Cascade, not the TTSS.  Same difference though.


John - #37777

October 31st 2010

sy:
““As for your statement that most of the machinery of translation is RNA based, that is just silly.”

If Meyer agreed, he would have dealt with the evidence straight up.

“The ribosome is of course a wondrous structure, and absolutely required for the process. But remember that the peptidyl transferase ribozyme cannot transfer enough energy to allow the peptide bond to form.”

So what?

“The necessary energy is supplied by the activation of the amino acid in its binding to the protein amino acid tRNA synthetases.”

Which, unlike the ribosome, would have been relatively easy replacements for evolution to substitute for a ribozyme. Recall that even modern bacteria can tolerate large losses in translation specificity, such as amber, opal, and ochre suppressor mutants.

“And it is also these protein enzymes that provide all of the specificity necessary to allow the coding system to work.”

And they are the easiest components for evolution to replace, completely unlike the ribozyme ribosome in that respect.


Rich - #37778

October 31st 2010

Tim:

Thanks for your replies.  I understand better what you were getting at now.  Some observations:

1.  Note that in 1996 Behe spoke of irreducibly complex *systems*—meaning the final product—mousetrap, bicycle, flagellum.  In 2000 you quote him regarding an irreducibly complex evolutionary *pathway*.”  It appears to me that we have been talking at cross purposes because I have been talking about IC *systems* and you have been talking about IC *pathways*.

I confess that I have not done much thinking about the notion of an IC “pathway”—and maybe I should have.  I can’t at the moment say what Behe had in mind with this terminology, without looking more carefully at the context.  Possibly at that point he wandered into unnecessary confusion.  But I would point out that all I undertook to argue about was IC systems, not IC pathways. 

2.  In an IC system, if you take out any part, the system stops working.  This is true *even if the part you take out has a use by itself*.  So if you take the rear wheel off a bicycle, the bicycle stops working, even though the rear wheel has some use by itself.  And if the “TTSS” parts of the flagellum have a function by themselves, the flagellum is still an IC system.


Rich - #37782

October 31st 2010

Tim (continuing on IC):

2.  (continued) You will see from the earlier Dembski quotation I gave that Dembski makes the same point I just made, and so does Behe in the book you say you don’t have.

3.  I won’t vouch for all of Dembski’s math.  I studied probability theory years ago, but I never reached the level of Dembski.  If you say there are problems with the math, you’ll have to take it up with him.  But I think you are criticizing his assumptions rather than his calculations.  And if I understand you correctly, you think his error was to calculate the probability based on the non-existence of the TTSS or some other intermediate structure; you think he was wrong to calculate as if the flagellum arose “from scratch.”  You think he should have assumed the existence of a TTSS, and then calculated the probabilty on that basis?  Do I get you? 

If so, what question are we asking?  Is it:  “How does one get to flagellum from TTSS”?  Or is it:  “How does one get to flagellum from just plain bacterium with no TTSS”?  Unless you think that the very first bacteria had TTSSs, surely you have to calculate the probability of “TTSS from scratch” as well as that of “TTSS to flagellum.”  Aren’t you overlooking that?


John - #37783

October 31st 2010

Rich wrote:
“I confess that I have not done much thinking about the notion of an IC “pathway”—and maybe I should have.  I can’t at the moment say what Behe had in mind with this terminology, without looking more carefully at the context.”

Yes, you must confine yourself to words, Rich. Don’t even think about looking at the evidence.

“Possibly at that point he wandered into unnecessary confusion.  But I would point out that all I undertook to argue about was IC systems, not IC pathways.”

All you want to argue about is rhetoric.

“2.  In an IC system, if you take out any part, the system stops working.”

Then the eubacterial flagellum is not an IC system, because many parts can be removed, both experimentally and evolutionarily, without stopping it from working.

Those pesky data mess up all the ID fantasies, which is why you will never engage the author of the post on the subject of his post.


Rich - #37786

October 31st 2010

Tim (continuing on IC):

4.  Regarding the quotation from Behe:

“any precursor to an irreducibly complex system is by definition nonfunctional”

First, let me say that I’m not committed to the view that every statement, every fact, every argument presented by ID people is correct.  It would surprise me if *any* scientist went through an entire career without making many incorrect statements, getting inferences wrong, relying on inaccurate data, etc. 

Second, if this statement were taken in isolation, I’d say it was wrong.  I don’t have time at the moment to consider what it might have meant in context—I’d want to study several parts of Behe again.  But I don’t think he meant that no part of an IC system could have any function outside of the system.  And that was the point I was making with my references.

Third, I think the focus should be on the gist of Behe’s argument.  Let’s say you have a bacterium with a TTSS.  How does the bacterium evolve into one with a flagellum—*without losing TTSS functionality along the way before the flagellum is working*?  Unless every intermediate structure is selectable, there is no pathway.  So what is the pathway?  I don’t see either you or Miller providing one.


Rich - #37788

October 31st 2010

Tim (continuing on IC):

Some comments on Miller:

5.  First, when in the past I’ve discussed Miller, I’ve been “corrected” by people who say:  “Miller didn’t actually argue that the TTSS was a precursor to the flagellum.  He only gave it as an example of a subset of the flagellum that had functionality.”  Do you agree with that interpretation of Miller?  If so, you can’t really call TTSS-as-precursor “Miller’s argument” or “Miller’s challenge to Behe.”  If Miller *wasn’t* proposing the TTSS as a possible precursor, then even in Miller’s mind the evolutionary pathway remains unknown—which was part of Behe’s point (the other part being that it’s not only unknown but difficult to imagine).

6.  Second, I’ve heard (and claim no expertise) that prior to the TTSS-Miller-Behe debate, evolutionary biologists had already pegged the TTSS as a *later* evolutionary development than the flagellum, and possibly a sort of “decay product” or simplification of the flagellar apparatus.  (I don’t remember what the arguments were; maybe alleged evolutionary date of the proteins or something.)  Is this true?  And if it is, how could the TTSS, a descendant of the flagellum, be its ancestor?  Or was it both?  I’m confused.


Rich - #37789

October 31st 2010

Tim (finishing up on IC):

Tim, I know that I probably haven’t given nearly a satisfactory answer to a couple of points.  I’ve focused on the questions I can answer without having to do some intense re-reading which I don’t have time to do at the moment.  But I think that where I have answered you, I’ve tried to answer directly, sincerely, and without bluffing or faking about things I don’t know.  I hope you will take my answers as offered in good faith.  I have appreciated your attempt to stay on topic and your even tone, and apologize for my sharpness earlier on.  I was simply impatient because you sounded like some other people here who have routinely bluffed or lied about Behe, but I see now that, unlike those people, you have a textual basis for what you say.

I do strongly recommend that you read the Behe essay in the *Debating Design* book, especially the section I indicated.  Behe makes clear where the “disconnect” is between his argument and Miller’s critique; I think it’s useful.  You may not want to shell out money for the book, but you should be able to get it via interlibrary loan, unless you live in Tibet or Tierra del Fuego.  And it has essays by people from all camps, not just ID people.


Gregory - #37790

October 31st 2010

“Yes, you must confine yourself to words, Rich. Don’t even think about looking at the evidence.” - John

Which ‘evidence’ counts as evidence, John? Just the physical or biological evidence or other evidence too?

You seem to be demanding a non-biologist to step into the realm of your specialist biological terminology. Why insist? To somehow validate the ‘ownership’ that this one academic field has on the topic of ‘edge of evolution’ & ‘Darwinism’?

“All you want to argue about is rhetoric.” - John

The rhetoric is *WORTH* arguing about, John. What don’t you understand about this?! Can you really afford to live with your head buried in the sand, doing your lab work, but continuing to attack fellow Christians who simply have a different vision about ‘what counts as science’ than you do. Really, John, you are merciless in your condemnation of Behe & Meyer. Doesn’t it seem this way to you? I’ve not seen rare a good word from you about either of these two Christian scholars.

Contra Rich: You must confine yourself to physical evidence & have no thought to look at the ideologies & evaluations behind it. You duck Darwinism. The meta-science of this discussion has gone completely over your head.


gingoro - #37793

October 31st 2010

Rich and Tim, very good set of posts!

Tim@37772
‘“clarification” of “irreducible complexity” and thus would still potentially fall under the umbrella of “moving the goal post.”’

First I would suggest that refining ones definitions and terms is fairly normal occurrence in science.  One reason is that when one observes how others are understanding what one has written it may well be necessary to clarify one’s definitions.  Second as one’s thinking advances it is reasonable to make modifications that refine definitions etc. to account for possibilities that one overlooked. 

Excellent back and forth without the usual anti ID or anti evolution rhetoric. 
Dave W


John - #37799

October 31st 2010

Gregory wrote:
“Which ‘evidence’ counts as evidence, John? Just the physical or biological evidence or other evidence too?”

The claims about evidence that Behe and Rich make as foundations of their pseudoscientific arguments. Are you really trying to claim that Behe and Rich aren’t making explicit empirical claims? How do you describe the following claim from Rich?

“If you take the bacterial flagellum, and rip out the protein parts that are analogous to the protein parts of the TTSS, the bacterial flagellum will no longer work.  The flagellum needs all its parts in order to function.”

Is this not a claim about the biological evidence, Gregory?

“You seem to be demanding a non-biologist to step into the realm of your specialist biological terminology.”

You seem to be grossly misrepresenting my position. Behe and Rich CHOOSE to make claims about biological evidence the foundation of their “argument.”

That makes the rest of your rant a straw man.


John - #37800

October 31st 2010

And here’s another claim about the evidence:

“The removal of any one of the parts *of the flagellum* will cause the *flagellum* to effectively cease functioning.”

Do you believe it, Gregory? More importantly, does Rich believe it to be true, or just wish that to be the case?


Tim - #37803

October 31st 2010

Rich,

Thanks for your replies.  I guess where I’m at right now was that the original 1996 formulation of irreducible complexity did not seem to anticipate functional precursors. Behe’s 2000 definition seems to attest to this.  Please also note that earlier I actually gave you the reference to where that quote was pulled from, so it was certainly not taken in isolation.  In any event, I view the ID theorists “moving the goalpost” following functional precursor parts/systems (i.e., the TTSS and some new discoveries concerning the Blood Clotting Cascade) to “clarify” irreducible complexity in a way that I don’t find particularly useful scientifically. It essentially says that if you can’t explain every last evolutionary step of how something came to be, it’s “irreducibly complex” provided that Behe, Dembski, or other ID theorists think that the parts look as if they’re “purposely arranged.”  Concerning Dembski’s math, what I am arguing is that he did not allow for a TTSS-like precursor.  Whether or not evolutionary scientists feel that the TTSS specifically was a precursor to the flagellum, something very much like it could have been.  Inflating his probability calculation to not take this into account to me is shady.


Lurker - #37814

October 31st 2010

Sy-
Well, I’m not sure we disagree on all that much other than what view we default to. I see the evidence for an RNA ancestor and the general catalytic competency of ribozymes, and think that pathways to proteins and DNA are likely to exist. Which is not to say that elucidation of these pathways won’t be fascinating science (as you might have figured out, I work in this field).

First, about RNA genomes—I’m not sure we can say what precise form genomic organization will take. A mishmash of all ribozymes is possible, but some more ordered structure, from which ribozymes are transcribed, is also plausible. In a late RNA world, I would expect replication to be performed by a specialized RNA polymerase, on which other ribozymes, having no self-replication ability, would depend.

How far could such cells evolve? That’s something I think we’ll be able to test in the next few decades. Given what we know, probably they could evolve to something fairly sophisticated. For that matter a ribocyte that can replicate, divide, and metabolize is already pretty sophisticated. It’s important to distinguish between what is necessary and what is optimal.


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