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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John - #37052

October 27th 2010

Rich wrote:
“Scientist A says that a deerlike animal became a whale in 9 million years.”

Since you’re so big on what people say and write, can you point to an actual scientist saying something like that? Pretending that evolution happens to single organisms is one of the oldest deceptions used by creationists to make it look less feasible to laypeople.

Why are you using it, Rich?

“When asked how this happened, he says that natural selection filtered random mutations.”

Name a scientist who persistently tacks the adjective “random” onto the noun “mutations,” since real biologists know that mutations are only random WRT FITNESS.

“Chance built the new body plan.”

Name a single, working scientist who conflates evolution with chance.


Gregory - #37054

October 27th 2010

Comment removed by moderator.


unapologetic catholic - #37062

October 28th 2010

Thankfully, we can remove all doubt that Intelligent design necessarily calls for supernatural intervention.  The Discovery Institute’s website describes a discussion between Biologos scientists and ID theorists….and is disappointed that Biologos representatives can’t bring themsleves to concede miraculous interventiosn in the course of biological evolution.

Apparently Anika Smith didn’t get the Behe memo.

http://www.evolutionnews.org/2010/10/questions_and_answers_with_dar039791.html


unaplogetic catholic - #37065

October 28th 2010

“Scientist B says that a deerlike animal became a whale in 9 million years.  When asked how this happened, he says that the genome is preprogrammed for a number of possible evolutionary changes, which can be activated through environmental challenges.  Pre-programmed design built the new body plan.”

When did the preprogrammign happen?

What would a preprogrammed genome look like compared to a non-preprogrammed genome?

Does the size of the genome of a particualr species indicate pre-programming?

Would we expenct genomes of extinct speceis to have less-pre-programmign?

Woudl we be able to examien the genome of variosus pecies and determienthose that are pre-programmed to survive massive enviromentaal changes?

How did pre-programmignhel the dinosaurs?  Wouldn’t the pre-programmer(s) have pre-programed around ice ages, astroid strikes and famines?

Assuming pre-programming, why are some genomes (i.e. malarai, ebola) pre-programmed to successfully attack other genomes (homo sapiens) in the most destructive and painful manner?  Didn’t the pre-programmer of the human genome foresee the onslaught of pre-programmed pestilences?  Or did he even care or did he do it to enjoy the suffering or is it all a big game?


unapologetic catholic - #37066

October 28th 2010

Is it your position that the Discovery Institute is only claiming:

1.  that all of biology has evolved after an intial pre-programming without subsequent intentional interventions by the designer whose name shall not be mentioned, and

2.  after the initial preprogramming, all of life on this planet today shares a common group of ancestors and all humans on this planet have evolved through non-supernatural processes from other primates, and whose closest relatives are bonopos and chimpanzees?

As far as I can tell, maybe Denton and possibly Behe would accept this position.  All others would summarily reject this position including Meyer and Wells.  Dembski is self identified as a creationist and biblical inerrantist.  Most of the others at the DI are young earth creationists.  The remainder are old earth creationsits who reject common ancestry and common descent.

Even conceding the possibility of pre-programming, rejection of common ancestry and common descent, along with young earth creationism and geocentricism, are perfect examples of rejection of science in favor of religious dogma.


Gregory - #37070

October 28th 2010

“Most of the others at the DI are young earth creationists.” - unapologetic

Sling. Wrong.

And Dembki is *not* a creationist.


RBH - #37071

October 28th 2010

To add to unapologetic catholic’s observation, for Rich’s benefit I’ll repeat this from my comment from earlier in this thread:

Larry Arnhart reported this conversation with Behe:

At Hillsdale, after his public lecture, I challenged Behe in a small-group discussion to give us a positive statement of exactly how the “Intelligent Designer” creates bacterial flagella. As usual, he was evasive. But I didn’t let him get away. And finally, he answered: “In a puff of smoke!” A physicist in our group asked, “Do you mean that the Intelligent Designer suspends the laws of physics through working a miracle?” And Behe answered: “Yes.”.

If that’s not invoking a supernatural designer then invisible pink unicorns fly over the Eiffel Tower every Bastille Day.


Rich - #37072

October 28th 2010

UC:

As usual, you read into the words of Discovery people what you want to read into them.

The only Discovery person quoted in the article is Sternberg.  Sternberg did not use the words “supernatural,” “miracle,” or “intervention.”

He used phrases which were broad enough to be interpreted as consistent with a front-loaded naturalism.  He spoke of “whether or not there was divine activity somewhere in the past or in the present”.  (“Somewhere” can include at the beginning, setting up a wholly naturalistic process.)  He spoke of a ” role in the evolutionary process” for a sentient being.  (Again, that could be at the beginning of the process.)  He speaks of “evidence for divine action,” without specifying that the divine action would have to miraculously interrupt natural processes.  Throughout it’s clear that his concern is whether or not the genome shows evidence of design, not whether or not God had to intrusively break natural laws during the history of life.

It was “an earnest young man” in “the audience” who spoke of “supernatural miracles.”  And as this conference includes OEC, YEC, TE and ID representatives, Anika Smith’s “several of us [unspecified] were disappointed” cannot be pinned on ID.


beaglelady - #37073

October 28th 2010

You know what, John, just being a ‘scientist’ will not earn you the respect of anyone here. One must be a compassiate human being too.

Is that why you claimed that gingoro was a “zoocentric misanthropist” over on this thread?


Rich - #37076

October 28th 2010

UC:

Continuing from above, I’ll repeat my observation that one of the things that characterized both atheist and TE interpretations of ID material is *careless reading*, externally motivated by the desire to prove that ID is nothing more than “creationism”.  You in particular, UC, are among the most notoriously careless of readers.  And when your errors are pointed out, *you never retract*.  Direct quotations mean nothing to you.  For you, rumor and hearsay and your own suspicions trump everything else.  This attitude does not reflect science.  This attitude does not reflect scholarship.  This attitude is just prejudice.


Gregory - #37077

October 28th 2010

That’s a technical term, beaglelady. And it carries a legitimate meaning in this discussion that many people miss. Not a sling at all. Would you like to discuss it? There’s no lack of compassion therein. DaveW knows he’s in a tough spot. How will he respond?


Rich - #37084

October 28th 2010

UC (37065-37066):

You keep speaking of “The Discovery Institute.”  I am not speaking of The Discovery institute.  I am speaking of ID as a theory of design detection.  ID is bigger than the Discovery Institute.  It is an approach taken by many who are not fellows or members of Discovery. 

The position I outlined about pre-programming was not representative of “the Discovery Institute.”  But it is a position (a) that is theoretically possible under the broad rubric of ID; (b) that is actually advocated by some intelligent design theorists, e.g., Denton, and possibly also Sternberg.

As for your other remarks:  what Dembski and Meyer believe *personally* is different from what they would allow as within the bounds of ID.  They do allow for the kind of position I outlined, even if they don’t subscribe to it personally.  For Dembski, see the quotation I gave to Tim.

“Mostly young earth creationists?”  Where do you get “mostly”?  Did you count them up?  Or did you just guess?  Name the young earth creationists, then count the total number of fellows, and tell me whether “mostly” follows.  And if you are wrong, retract (for a change).

I’m still waiting for your retraction regarding Behe as a “creationist.”


Gregory - #37085

October 28th 2010

“Mostly young earth creationists?”  Where do you get “mostly”?  Did you count them up?  Or did you just guess?  Name the young earth creationists, then count the total number of fellows, and tell me whether “mostly” follows.  And if you are wrong, retract (for a change).” - Rich

We had a conversation about this at BioLogos a month or two back. If memory serves me correctly, I think the number was well under 10%, more like 2%. Paul Nelson is the only one that comes to my mind out of >36 Fellows.

Unapologetic (I refuse to call him or her ‘Catholic’ anymore) is just as much a ‘creationist’ as Behe is. Of course, Behe is not a ‘creationist’ and neither is Dembski. Both believe in ‘creation’, i.e. they believe that “God created the heavens and the earth.”

I suppose unapologetic believes the same thing. One can never be sure what he believes because all he is focussed on is attacking ID.

There must be some serious ‘pressures’ in the United States on this topic that we non-Americans simply can’t possibly understand. E.g. a supposedly Catholic Christian attacking an actual Catholic Christian who remains consistent with Church doctrine that “God created the heavens and the earth.”


Rich - #37086

October 28th 2010

RBH:

We have very different ideas of what constitutes scholarship.

I say that, if one wants to determine the position of an author, one gathers together all the author’s publically accessible statements (books, articles, interviews, podcasts, etc.) and works it out from those.

You say that one should overrule conclusions derived from all those sources on the basis of an unconfirmed conversation reported by Larry Arnhart.

I disagree.

I also note that, even if Arnhart reports Behe’s words correctly, he may not have caught the sense of them.  Those of us who know Mike Behe a bit know that he has a playful side, and I can just see him saying “in a puff of smoke” with a twinkle in his eye, to tease Arnhart (whose atheism is self-acknowledged). 

In any case, even if Behe *personally* believes that the designer may have had to intervene now and then, he is on record, repeatedly, as saying that ID does not require supernatural intervention.  ID is about design detection, not supernatural versus natural causation.  Once you’ve detected design, you can then argue about whether “intervention” was needed to actualize the design.  But that’s not part of ID as a scientific enterprise.


Gregory - #37090

October 28th 2010

RBH is perhaps just a bit bitter that his ‘multiple designers theory’ (MDT) hasn’t attracted much attention.

One might wonder if in MDT any distinction was made between ‘natural’ and ‘supernatural’ designers. But I don’t think RBH believes in anything ‘supernatural’ (or perhaps even non-natural), so that might be a stretch.

His MDT is ‘anthropocentric’ or even karmic, i.e. neo-Darwinistic, wherein no God or Creator is allowed into the picture.


unapologetic catholic - #37093

October 28th 2010

And you missed Behe’s earlier points where he is on the record saying ID *does require* supernatural intervention:

Michael Behe in a Godspy interview saying that irreducibly complex systems “cannot have evolved”—

Godspy Interviewer:  “You claim such a system could not have evolved incrementally, and would need to have been designed somehow.  If Neo-Darwinists can show how these structures could have evolved, then it would prove your point false, right?

Behe:  That’s correct.”

and Behe in the Edge:

““Here’s something to ponder long and hard: Malaria was intentionally designed. The molecular machinery with which the parasite invades red blood cells is an exquisitely purposeful arrangement of parts.”

So, who designed malaria?


I know you excused Behe’s multiple candid admissions in the past as speaking in a “pop context, but really isn’t that all Behe does is speak in the “pop” context?  He"s certainly not publishing any scholarly works on irreducible complexity.


Rich - #37096

October 28th 2010

UC:

You’re bluffing again.  I already showed your misinterpretation of the Godspy article on another thread.  Behe does not confirm belief in “intervention” or “miracles” in the quotation above.  He confirms belief in “design.”  A design might well be implemented wholly through natural means.  Every time a child is born a design has been implemented through wholly natural means.  But the design for the child is there, implicit in the zygote.  It is not unscientific miracle-mongering to infer a design in the zygote from the result.  There is nothing in Behe’s argument that rules out front-loaded design expressed within a naturalistic evolutionary process.  He says so repeatedly.  You turn a blind eye to the quotations when they are shown you.  That’s intellectual dishonesty.  You’d fail in my classes for that.  (Not for disagreeing with me, but for refusing to admit textual evidence.)

You have made two false claims:  (1) That Behe is a “creationist,” as that word is normally understood; (2) That Behe makes “intervention” or “supernatural interference” essential to ID theory.  I have demonstrated many times that these statements are false.  You should retract.


Rich - #37113

October 28th 2010

Tim (36968):

I’ll meet you half-way.  Natural selection contributes to the evolutionary process by fixing successful mutations in the population, and driving out unsuccesful ones.  So future evolution takes off from a point at which certain mutations are already fixed; had a different set of mutations prevailed (due to different competitive conditions), the platform for future evolution would be different.

Nonetheless, natural selection is passive; it has to wait to see what changes are thrown up before it can “do” anything.  And the changes, according to neo-Darwinism, are random.

Thus, if, as Dawkins claims, the camera eye has been developed 20 or 30 times, one has to ask:  how likely is it that random mutation would produce a camera eye even once?  Let’s say we could calculate it and we came up with a probability of .25.  Not bad.  But now, let’s say that happened 20 times independently.  How probable is that?  Not very.  So in such a case we’d have to consider two possibilities:  (a) macroevolution didn’t happen at all; there were 20 separate creations of the eye; (b) macroevolution did happen, but the mutations weren’t random.  ID people divide into two camps over this.  I’m in camp (b).


pds - #37159

October 28th 2010

Dave,

You said:

>>>you say you want to see a paper for “a Darwinian explanation for the step-by-step origin of cilium” - so I go to the literature databases, and see if I can find something - does this approach make sense?<<<

I replied and said yes.  Any progress?


John - #37161

October 28th 2010

Rich keeps claiming that some sort of ID theory exists:
“Now if only a number of anti-ID commenters on this site would follow that wise advice, and actually carefully read a substantial amount of ID theory before rejecting it!”

“As for your remark about a “supernatural” designer, as if that is some sort of objection, the question whether the designer is supernatural or not is neither here nor there as far as ID theory is concerned.”

“Unevolvable through naturalistic means” is not correct for ID theory; “unevolvable through chance means” would be the correct formulation.”

“Such interventions are compatible with ID theory, but certainly not required by it.”

“Denton’s evolution is not driven primarily by chance, and therefore is compatible with ID theory.”

Yet a DI Fellow with a last name says,
“Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a real problem.”

Interview: The Measure of Design, A Conversation About the Past, Present & Future of Darwinism & Design, Touchstone 17 (6): 60–65.

Whom should we believe—Rich or DI Fellow Paul Nelson?


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