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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 - #36935

October 27th 2010

Tim:

I don’t see any difference in principle between the mousetrap and the bicycle analogy, except that a bicycle is more complex, and therefore a better analogy for biological features such as the flagellum.

Can you tell me where Dembski says that no part of the flagellum could have any biological use outside of a flagellum?

“Unevolvable through naturalistic means” is not correct for ID theory; “unevolvable through chance means” would be the correct formulation.  “Chance” and “natural” are not co-extensive terms.  In *No Free Lunch* (p. 315) Dembski writes:  ” ... within a design-theoretic framework ...
it is possible for descent with modification to be driven by telic processes inherent in nature.”  “Inherent in nature” implies “non-supernatural.”  A process can be designed, yet natural.

I would ask you read, and comment upon, Behe’s rebuttal of Miller in *Debating Design: From Darwin to DNA* (ed. Dembski and Ruse), pp. 358-360, especially 359-360.  You say that Behe’s understanding of IC is different from mine, but I would suggest to you that what I have been saying is no different from what Behe says here.  Also, see Dembski, p. 268 of *No Free Lunch*, under “Redefining Irreducible Complexity.”


Tim - #36947

October 27th 2010

Rich (36935(,

“I don’t see any difference in principle between the mousetrap and the bicycle analogy, except that a bicycle is more complex, and therefore a better analogy for biological features such as the flagellum.”

The base components of the mousetrap are relatively useless on their own.  So as a biological analog they don’t “add to fitness.”  The bicycle wheel is not useless on its own.  So as a biological analog, it could “add to fitness.”  If something adds to fitness, it can be evolutionarily selected and locked in place for further adaptation at some later point.

“Can you tell me where Dembski says that no part of the flagellum could have any biological use outside of a flagellum?”

Page 301 in No Free Lunch.  He says it in his math.  If that wasn’t his framework, then he did a really lousy job of calculating his probabilities.  And while Dembski may be a lot of things, I don’t think anyone accuses him of being a terrible mathematician.  So I’m going to go with his laying out such assumptions in his math.  Also, his description of why he’s doing so substantiates that point as well.


Tim - #36948

October 27th 2010

Additional Reply to Rich (36935),

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

Define it however you like Rich.  Only unevolvable through natural means has any bearing on their being a designer.  And evolutionary theory doesn’t posit chance adaptation.  They posit chance genetic mutation and recombination as acted upon by non-chance natural selection.  If ID really means that a given structure couldn’t have evolved via chance, then they would be in perfect agreement with the evolutionary biologists.  So why are we arguing then?


Rich - #36956

October 27th 2010

Tim (36947):

Don’t forget that Behe says that the base of the mousetrap could be used for a doorstop.  And don’t forget Ken Miller’s famous Dover Trial theatrics of wearing one of the metal parts of the mousetrap as a tie clip.  The point is that we can imagine some use for some parts of almost any machine, if we think about it long enough, but that doesn’t change two facts:

(1)  The imagined function of the *part* isn’t the same as the function of the *system* containing that part;
(2)  The system being analyzed (mousetrap, bike, flagellum, whatever) will *cease to function* if that part is ripped out of it (because the system is irreducibly complex).

Am I being clear?  If so, do you object to either of these statements?

Also, you wrote:

“Page 301 in No Free Lunch.  He says it in his math.”

Well, please see p. 268 that I pointed out, from the same book.  He says the opposite in his *words*.  So does Behe, in the passage I indicated.  So I think you have made the wrong inference about Dembski’s assumptions, and Behe’s as well.

(continued)


Gregory - #36958

October 27th 2010

I’d like to try to negotiate a middle way btw Tim & Rich.

Tim, the problem in substituting ‘naturalistic’ for ‘Darwinistic’ is the ridiculous wap of ‘methodological naturalism.’

“A statement such as “such and such a process doesn’t arise via solely darwinistic processes, therefore designer” wouldn’t make much sense.” - Tim

I agree & this is where I part with the IDM; they put too much focus on Darwin, imho.

P. Johnson was speaking about ‘naturalism’ & cultural renewal. But he couldn’t say ‘socialism’ or ‘spiritualism’ as potential alternatives, could he?

“Only unevolvable through natural means has any bearing on their being a designer.” - Tim

Rich contrasts chance vs. design. God can use natural means.

Can one be a natural-physical scientist [NPS] *without* being a ‘naturalist’? This is a similar ideological question to what DaveW is struggling with. He doesn’t understand ideology, wants a primitive definition that simple dictionaries use & thinks I’m confused about it. This is funny & sad!

I’d answer ‘Yes, a NPS *can* reject naturalism, i.e. not be a naturalist.’

But the realm of NPS is *restricted* to natural-physical things. No meaning, no purpose allowed by definition.


Rich - #36959

October 27th 2010

Tim:

Regarding naturalism, I’ve asked you to consider a quotation from Dembski, again from the same book that you have read.  He indicates there that ID is not opposed to natural causes as such.  Behe has said that, too.  I agree with them both.

The problem is that a number of ID defenders (not usually the major theorists, but the non-scientist cheerleaders of ID) keep opposing ID to “naturalism” and “natural causes.”  The implication is that you can’t have design without “supernatural causes,” which in practice means miraculous interventions, with a “God of the gaps” filling in what evolution can’t do.  Such interventions are compatible with ID theory, but certainly not required by it.  I’m arguing here for ID in its strict, pure form, and in its strict, pure form, all it can do is detect design; it can’t speak about natural vs. supernatural causes.

Read Michael Denton, *Nature’s Destiny*.  Denton believes in macroevolution “from molecules to man.”  He refuses to posit any “interventions.”  But he’s resolutely anti-Darwinian.  For him Darwinian mechanisms can account for only the trivial bits of evolution; the bulk is pre-programmed.  That’s the sort of position Dembski alludes to in the quotation I gave.


Gregory - #36961

October 27th 2010

The problem with ‘non-chance natural selection’ (Tim) is that ‘human selection’ or ‘artificial selection’ (as Darwin called it wrt ‘directed’ breeding) use another definition of ‘agency’ or ‘choice.’ By giving agent-like power to ‘Nature,’ which is by all traditional definitions a ‘non-agent’ - i.e. Nature becomes a monolithic decision-maker modelled on human decision-making - Darwin hooped the pooch by analogy.

To say one could ‘ask’ Nature @ her choices is perhaps similar to the bibliolatry expressed eariler by Martin that ‘Scripture interprets Scripture.’ This is a loose analogy meant for rhetorical purposes & nothing more. Nature does not ‘select’ because there is no mind/Mind with which it can ‘select’. But this is a philosophical conversation & NPSs are generally content to say exactly what you’ve said about it. ‘Keep it simple, right?’

I like what Rich says: “I don’t care whether ID is called science or philosophy, if it has the potential to get at the truth about nature.”

He also asks: “Why are chance & design not treated as being on the same epistemological plane?”

I guess I’m just not convinced by the dichotomy. When I read ‘design’ I think designer/designing too. Implicationism?


Rich - #36962

October 27th 2010

Tim:

Regarding natural selection as a non-random element in evolution, bear in mind that “natural selection” is a metaphor (and was recognized by Darwin as such).  There is no such “entity” as “natural selection”, with an independent existence, “selecting” some species and rejecting others.  Natural selection is just a way of describing the fact that some creatures are ill-suited to survive in particular environments, and die out, whereas others are well-suited, and thrive.

Dawkins and others represent natural selection as having great creative powers, as acting in the place of an intelligent designer.  This is false.  Natural selection doesn’t create a single thing.  It doesn’t alter one nucleotide, let alone create new biological forms.  All it does is accept or reject what mutations have created.  And in neo-Darwinism mutations are chance events.  So ultimately, chance does the creating.  ID’s objection to neo-Darwinism is that chance does not have the power to assemble integrated complex structures in the time given.  Hence, ID appeals to the court of probability theory.

Denton’s evolution is not driven primarily by chance, and therefore is compatible with ID theory.  Denton is in fact a small-id theorist.


Gregory - #36963

October 27th 2010

Just curious, Rich, from your reading of Denton, both major texts, older and newer, and any articles you’ve read by him, does Denton address the topic of ‘intelligence/Intelligence’?

Leave aside the ‘interventions’ issue for now (as it sticks in the side of most TEs/ECs). Many people, it seems to me, could embrace a ‘design’ theory, *if only* it didn’t have the qualifying term ‘intelligent’ placed before it. That’s what leads to the implicationism - i.e. the designer must be ‘intelligent’ and therefore for all those people who don’t believe in aliens, the only option is God/Allah/YHWH.

Aside from Denton having been rumoured to say that the DI was ‘too Christian’ for him, could his arguments with ‘intelligent’ vs. ‘no intelligence’ be what drove Denton from the IDM?

I met Denton and wasn’t inspired by him or his words. A rather dry scientist-without-spirit, a nullity (Weber 1919) this was my impression. But as for identifying what Darwinian mechanisms cannot account for in natural history and organic change/development, he seems to compare well with Margulis and other biologists who are trying to rid themselves of ‘Darwinism’ and its dogmatic ideologies. I see no problem with that.


Rich - #36965

October 27th 2010

Gregory (36961):

Let me try to make things clearer:

Scientist A says that a deerlike animal became a whale in 9 million years.  When asked how this happened, he says that natural selection filtered random mutations.  Chance built the new body plan.

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.

Scientist B wants to put A’s theory to the test using probablistic analysis:  how likely is it that chance mutations would have produced a whale?  That’s scientific testing, not religious interference with science.

My question to you is:  why should explanation A be the only one that is a “scientific” explanation, and explanation B be automatically discounted as “religious” or “metaphysical”?  Both accept mutations; both accept that mutations interact with environment to help some creatures survive and not others.  Both are naturalistic; neither requires miracles, God of the gaps, etc.  So why are chance explanations permitted, and design explanations not?


Gregory - #36967

October 27th 2010

The numbers question sounds like one for Tim instead of me.

I imagine that he will have a problem with your phrase: “natural selection filtered random mutations” and linking that with ‘chance’ as type of agency.

‘Pre-programmed’ - does this mean there is/was a programmer/Programmer?

If so, the question ‘how was it pre-programmed’ seems to fit securely in the realm of ‘doing science.’ But no IDist has an answer for this, which weakens their theory. I don’t say it destroys their theory, but surely it weakens it.

I liked your response in #36696 & was waiting for more. One problem I find with BioLogos is sometimes, but not always, it appears to hold science ABOVE religion & philosophy. In this sense, it also commits ‘scientism’. But I agree with you that BOTH the IDM AND BioLogos would prefer *not* to commit ‘scientism.’ There seems to be some cultural or political reason in the USA why many people are drawn into scientism in ‘the most scienfitic country in the world.’

Fuller says this: “Darwin’s theory of evolution…explains organic change by nothing more intelligent than random variation and natural selection.” (“Science”, 2010: 89)

I’d ask Tim if he thinks ‘NS’ is ‘intelligent’?


Tim - #36968

October 27th 2010

Rich,

I was simply asserting that natural selection is not random chance.  Whenever you drill down a word you arrive at some disconnect between the linguistic device and reality.  What I was getting at is the idea that natural selection does not operate along the lines of random chance.  If you want to rephrase that to say that the environmental fitness landscape, incl. access to resources, competitive pressures, etc., does not exert random chance pressures on adaptation of the organism, then fine.  Also, I never implied natural selection alters any genome directly.  The influence is indirect through what lives and procreates, and what dies.

By the way, I reject your logic in:

1)  Neo-Darwinistic mechanisms for genetic mutations are random chance events
2)  Neo-Darwinistic natural selection operates on these random chance events
3)  Therefore neo-Darwinism is a random chance process

That would be like me saying:

1)  Texas Hold-em relies on a random chance dealing out of 52 cards
2)  Players’ choices to select bid/fold options relies on these random chance events
3)  Therefore Texas Hold-em is a random chance card game

*And yes, I know the player is an “intelligent agent.”  Don’t read into the analogy too far.


Tim - #36969

October 27th 2010

Continued Response to Rich,

I just noticed all your earlier replies prior to the last one.  I have other obligations to attend to, but will go back, read, and respond as I have time.


Rich - #36971

October 27th 2010

Gregory:

Denton freely uses the word “design” in his second book, especially in the conclusion.  I didn’t count how many times he used the word “intelligence,” but he uses it, and “intelligence” is implied throughout.  He describes the whole process of evolution as the output of a cosmic computer program!  Computer programs are created only by intelligence.

If asked if he was an ID proponent, I’d guess he’d say no.  I think he doesn’t want to be identified by a label that many associate with conservative American Christianity, because he’s neither American nor conventionally Christian.  He’s more of a Deist, I’d say.  But he’s definitely an intelligent design theorist, with a small “id.”  So no, I don’t think you could say that he objects to the “intelligent” in intelligent design.  I think he just wants to separate design as a theoretical perspective from conservative religious piety.

An interesting question is why most TEs are cool to Denton’s ideas.  He accepts an old earth, common descent, naturalism—all the things they insist upon.  But few of them have much nice to say about him.  Of course, he violates the TE rule that one must defer to consensus science, i.e., neo-Darwinism.  That’s probably it.


gingoro - #36985

October 27th 2010

Tim@36947
“The bicycle wheel is not useless on its own.  So as a biological analog, it could “add to fitness.”  If something adds to fitness, it can be evolutionarily selected and locked in place for further adaptation at some later point.”

One problem in either example is that although intermediate biological mechanisms could be created,  do they in fact add any reproduction advantage?

With the bike one can figure out uses for all the intermediates whereas with the mouse trap it is hard to see any real none contrived use for the case when the whole trap is together except for the bit of bent metal that holds the cheese.  And of course different paths could result in other configurations with out much apparent use. 

It all boils down to the question, “Is the backside of Mt Improbable a nice easy climb or are there insurmountable cliffs”?  I don’t see any realistic way to provide an answer one way or another.
Dave W


R Hampton - #36998

October 27th 2010

My question to you is:  why should explanation A be the only one that is a “scientific” explanation, and explanation B be automatically discounted as “religious” or “metaphysical”?

Because question B is a lot like the Drake equation with all of its associated problems. For ID to be accepted, it first has to prove that the Dembski/Meyer proposed CSI is logically and accurately calculated (at present, it has been rejected on grounds related to Information Theory). So when ID proponents base their theory on flawed statistics and then refuse to amend their errors, Science must reject ID.

I’ve posted other authors/papers critical of ID’s misapplication of Information theory before, but this one is worth reading as well:

Dissecting Dembski’s “Complex Specified Information”
Thomas D. Schneider (last updated December 1, 2008 )
http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/dembski/specified.complexity.html


Gregory - #37006

October 27th 2010

“you think *everyone* who is an ´evolutionary biologist´ is by definition also an ´evolutionist´?”  - Gregory

“Yes” - DaveW

You’ll forgive me if I think this is as sophomoric as BioLogos’ definition of ‘Darwinism’ - just *the science*, as if ideology didn’t exist!?

“In general I do not think words ending in IST imply an ideology.  Certainly not scientist, chemist, physicist, biologist, sociologist.” - DaveW

A scientist is a person who does science, a chemist is a person who does chemistry a sociologist is a person who does sociology; an ‘evolutionist’ is an ideologue who may or may not do evolutionary biology. This fallacy is easily shown by reversing the above statement, which you accepted.

Do you think *everyone* who is an ‘evolutionist’ is an evolutionary biologist? If not, then what does ‘evolutionist’ imply that ‘evolutionary biologist’ does not? I contend it is ideology.

I have little problem with eVo biology but many problems with evolutionism & evolutionists.

“An evolutionist may have an ideology or may not.” - DaveW

Have you ever studied *ideology* in any depth, DaveW? I’m just curious because it appears that this is an entirely new thing for you.


Gregory - #37015

October 27th 2010

At least you admit above, DaveW, that ‘evolution-ISM’ is an ideology.

You wrote: “When it comes to the ISM suffix, it seems to always imply an ideology”

So, then final nail in the coffin of your former perspective is this:

What do you, Dave W, call people (i.e. how do you name those) who adhere to the ideology of evolution-ISM?


John - #37049

October 27th 2010

Karl A wrote:
“John, Rich has been around long enough to persuade many of us of his sincerity and well thought-through positions,…”

Can you provide me with a single example of Rich’s sincerity?

“... although we may not all be particularly sympathetic to ID arguments.”

What do you think of his distaste for evidence and his attempt to present science as debate instead of lab or field work to test hypotheses?

“He has his biases, so do the rest of us.  Impugning his motivations (“deceptions”)…”

Are you claiming that describing evolution as mere “chance” represents bias and not deception?

“... and painting all ID espousers as “hucksters””

Not espousers, promoters. Do any of them have sufficient faith to empirically test an ID hypothesis? That fact makes them hucksters who reject science itself.


John - #37050

October 27th 2010

Karl A:
“As a point of contrast, just look to the discussion happening between Rich, Gregory and Tim.  There’s real, informed, fruitful dialog happening.”

I don’t see anything fruitful there. I see Tim politely challenges Rich for using the classic creationist deception I described above, and Rich neither supports nor retracts it. How is that fruitful?

When Gregory, playing boring labeling games, calls DaveW’s answer “sophomoric,” is that your idea of fruitful dialog, Karl?


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