Thursday, March 30, 2006

Where The REAL Action Is In Evolutionary Biology

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

Throughout the controversy over "intelligent design," it has occurred to me several times that the underlying problem in the ID vs evolution debate has centered around what could be called the "adaptationist program." As Lewontin and Gould pointed out in their "spandrels" paper, much of evolutionary biology from Darwin on has been shot through with a kind of "adaptationist ideology", in which the only things of interest are adaptations resulting from selection. Will Provine has pointed out that this focus, in a sense, simply replaces the God of the Bible with a "god" of natural selection.

What the last three decades of evolutionary biology at the molecular level have showed us is that the vast majority of evolutionary change is non-adaptational. Jukes, Kimura, Ohta, and others have conclusively shown that most of what happens at the genome level (and much of what happens at the proteome level) is non-adaptive. This new paradigm for evolution – the neutral theory – has been entirely ignored by "intelligent design theorists" and for good reason. Since it clearly isn't adaptive, then for a "designer" to have intervened to produce and/or guide it would argue that the "designer" is a kind of metaphysical dadaist who delights in pointlessness. Hence the insistence on the part of many IDers that there is no such thing as "junk DNA", nor even non-adaptive DNA (such as pseudogenes, transposon-derived regions, cDNA from retroviruses, etc.)

The relevence of this to the current discussion is this: by teaching students that evolution is all about adaptation, we miss some of the most interesting developments in recent theory and research. These developments decisively argue against the ID position and bring evolutionary biology much closer to the "modern" paradigm of quantum mechanical physics, in which "pointlessness" and randomicity underlies all of macroscopic reality. To paraphrase J.B.S. Haldane, the genome is not only queerer than we imagine, it is queerer than we can imagine.

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At 3/30/2006 11:49:00 AM, Blogger RPM said...

I like to point to the neutral theory as an example of real science being able to overcome the Darwinian paradigm while fake science (ID) fails to. When I teach students about evolutionary force, I like to point out that everything other than selection operates in a stochastic manner.

At 3/30/2006 12:14:00 PM, Blogger crevo said...

Actually, the neutral theory is quite in line with what ID'ers say, and especially Creationists. John Sanford (inventor of the "gene gun") has a whole book on it.

Likewise, I have a summary of a paper by Bergman from CRSQ.

From either an ID or Creationist standpoint, a lot of the changes that occur after design are going to be either neutral or deleterious. That's the natural result of long, ongoing processes.

The idea that such neutral processes could build up a genome is what ID'ers and Creationists disagree with, not that a lot of processes in effect today are neutral or maladaptive.

In addition, the neutral theory removes the only possible heuristic evolutionists had in developing novelty. Optimization theory seems to indicate that a neutral walk would be even less likely to produce functional change, new proteins, and new regulatory networks.

I find it odd that you say that neutral selection is "entirely ignored" by ID when Meyer's paper for the BSW spends several paragraphs on it.

At 3/30/2006 12:48:00 PM, Blogger Allen MacNeill said...

I guess what I should have said is that ID theory doesn't approach neutral evolution in the same way as mainstream evolutionary theory. According to John Stanford and most other IDers, the neutral and nearly neutral theories (of Kimura and Ohta, respectively) represent the degeneration of the genome, rather than its expansion.

This is a standard creationist line long predating ID theory, claiming (without the slightest shred of empirical evidence) that the genomes of all organisms were created in essentially perfect form and that all changes since their creation represent degeneration of that perfection. Indeed, young-Earth creationists lay the blame for this so-called degeneration to the Fall of Adam in Eden (also the source of the Second Law of Thermodynamics ... hilarious stuff ;-)

This line of reasoning is utterly without empirical support, and flies in the face of the day-to-day use of the neutral theory and its predictions by many mainstream evolutionary biologists. All you need to do is take a look at any college level text in evolutionary biology to find the real story about the neutral theory and its application to evolutionary theory as a whole.

At 4/11/2006 02:55:00 PM, Anonymous PvM said...

Neutrality in evolutionary theory is quite exciting and has little relevance to Intelligent Design, other than showing that natural selection is not the only player in evolution. For those interested in neutrality, I would like to point out that neutrality is an essential component for evolution to be evolvable, and even more shocking: neutrality is a selectable trait.

Neutrality has two 'side effects' which both are relevant to evolution, the first one is robustness to mutations, the second one is improved evolvability (neutrality basically flattens the landscape).

Various scientists have done some wonderful work in the area of neutrality and the relevance to evolution.

Marc Toussaint especially his paper M. Toussaint, C. Igel (2002): Neutrality: A Necessity for Self-Adaptation [ps.gz]. Congress on Evolutionary Computation (CEC 2002), 1354-1359.

Then there is the concept of cryptic genetic variation, yet another major source of variation for selection to eventually act upon.

Both cryptic variation as well as neutral variation can be seen as a form of 'diffusion' through the sequence landscape while remaining static in phenotype space. In other words, stasis and quick morphological evolution follow naturally from these concepts.

In fact recent work has shown how cryptic genetic variation significantly affects the calculates by Snoke and Behe, making evolution of binding sites far more likely than in their 'strawman-evolution' scenario.

In addition, Peter Stadler, Peter Schuster, Walter Fontana have done research on scale free networks, neutrality and RNA space showing how evolution on such networks is 'inevitable'.

People interested in these topics should check out keywords such as 'scale free network' 'RNA' 'evolvability' 'cryptic genetic variation' etc

None of this has much relevance to Intelligent Design. But then again, ID does not present much of any scientific theory.

At 4/14/2006 05:55:00 AM, Blogger Ed Darrell said...

How about a nice, fewer-syllable explanation of the neutral theory for us poor lawyers and teachers? What is neutral theory, in a nutshell, and what does "non-adaptationist" really mean? Examples would be nice.

Thank you.

At 4/14/2006 08:41:00 AM, Anonymous Peter said...

If you want to find a working definition or explanation of neutral theory, I recommend Wikipedia. It is a bit jargonish but the links to potential problem words (genetic drift perhaps) help to explain.

That said, I think that the larger layman creationist/IDer population's understanding is at least as important as the "specialist" (Gish, Morris, Behe, etc.) understanding. My experience with some rather vociferous street preachers, anti-evolutionist students and their friends suggests that they would find the neutral theory acceptable and indeed supportive.

For example, I made the collossal error of arguing with Penn, State's infamous Willard Preacher last week. He contends (and he is no straw man) that adaptation may happen up to a certain point but that the generation of new species is not occuring. The seemingly non-generative quality (I am a layman who has read woefully little technical literature) of the neutral theory plays, at least rhetorically, into his hand because it encourages an apparent or surface-level stasis of the genome.

It seems to me that the IDers et al needn't address neutral theory because it doesn't do much for them and has no obvious way of undermining their argument. It is neutral to their position.


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