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Thursday, January 17, 2008

The Plausibility of Life

The Plausibility of Life is an evo-devo book by Mark Kirschner and John Gerhart. I read it a long time ago and had pretty much put it out of my mind except for the occasional potshot [Evo-Devo: Innovation and Robustness in Evolution] [Animal Chauvinism].

A couple of days ago I was shocked into taking another look at the book. The shocker was Alex Palazzo of The Daily Transcript who wrote [Today's rant - the biggest story never covered].
The most insightful book on biology written in the past decade was Gerhart & Kirschner's book, The Plausibility of Life.
That's so far out of line with my opinion that I began to wonder if I had missed something important. Alex is a smart guy and he's not likely to be way off base.

Alas, in this case Alex got it wrong. This is certainly not one of the most insightful books on biology in this decade, or any other decade. It's pretty much adaptationist, animal chauvinistic, evo-devo-centric gobbledygook from a pair of scientists who don't understand evolution.

The central question of the book is, "... how can small, random genetic changes be converted into complex and useful innovations?" (p. ix). Apparently this is a puzzlement to evolutionary developmental biologists. One that has eluded them until the last decade of the twentieth century.

Kirschner and Gerhart's effort is a valuable update of some of these ideas, but it hardly constitutes "a new theory" to complement the Modern Synthesis.

Massimo Pigliucci
Have We Solved Darwin's Dilemma?
Kirschner and Gerhart have the solution.
In this book we propose a major new scientific theory: facilitated variation that deals with the means of producing useful variation.
Since the essence of their theory is "facilitated variation" you would think that this concept would be clearly explained in the book. It isn't. There's a lot of beating around the bush and hand waving about a fundamental new process of evolution but little in the way of concrete facts and evidence.

When I read the book for the very first time I was astonished to realize that by the end of the book I still didn't know what the authors meant by "facilitated variation." So, I looked it up in the glossary ....
Facilitated Variation: An explanation of the organism's generation of complex phenotypic change from a small number of random changes of the genotype. We posit that the conserved components greatly facilitate evolutionary change by reducing the amount of genetic change required to generate phenotypic novelty, principally through their reuse in new combinations and in different parts of their adaptive ranges of performance.
Is that clear? Of course it isn't. You have to go back and read very carefully to even begin to understand what they're talking about.

... Kirschner and Gerhart do not present any detailed examples of how the properties of developmental systems have actually contributed to the evolution of a major evolutionary novelty. Nor have they shown that alternative properties would have prevented such evolution. Although The Plausibility of Life contains many interesting facts and arguments, its major thesis is only weakly supported by the evidence.

Brian Charlesworth
On the Origins of Novelty and Variation
Here's how I see it. Animals have a number of conserved core processes like transcription, membrane trafficking, formation of eyes, compartments, etc. that contribute to the success of the organism. You can't mess with these core processes because that would be lethal. However, new phenotypes can arise when existing core processes are expressed in new combinations or at different times during development. The core processes have been selected for adaptability. In particular, they have evolved in a way that facilitates phenotypic variation by encouraging the evolution of new combinations and new timing while, at the same time discouraging evolution of the core processes themselves.

Over time, animal species have been selected for the ability to evolve by taking advantage of facilitated variation without threatening the core processes. This one of the definitions of evolvability.
In summary, we believe that evolvability—the capacity for organisms to evolve—is a real phenomenon. We believe that facilitated variation explains the variation side of evolvability, through the reuse of a limited set of conserved processes in new combinations and in different parts of their adaptive ranges due to genetic modifications of nonconserved regulatory components ....

Facilitated variation has arisen and increased by selection, we say. Since it facilitates the generation of innumerable complex, selectable heritable traits with only a small investment of random genetic variation, it is indeed the greatest adaptation of all, at least for animals since the Cambrian.
I'm not buying any of this. I'd like to see real evidence that the process of evolution in animals is different than evolution in prokaryotes. Whether you're dealing with the genetic switch in bacteriophage λ, sporulation in Bacillus subtilis, or the formation of heterocysts in cyanobacteria, it is always the case that the processes are controlled by a cascade of regulatory factors and drastic changes in the timing and extent of these regulatory genes can lead to significant phenotypic effects.

What's so special about animals that we have to develop a "major new scientific theory" to explain similar observations?


12 comments :

  1. If I am not mistaken, John Gerhart was the infamous ID guru Jonathan Wells' PhD advisor at Berkeley.

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  2. Not to be pendantic, but I think including a microbial eukaryote, such as Saccharomyces cerevisiae, in your ending examples of microbial processes. This would avoid the argument "Well them there's are bacteria and we're talkin' 'bout animals which is eukaryotes." which I expect some will consider upon reading your penultimate paragraph.

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  3. If I am not mistaken, John Gerhart was the infamous ID guru Jonathan Wells' PhD advisor at Berkeley.

    You're not mistaken. Gerhart is one of the leading developmental biologists of our era. Oh, to have been a fly on the wall in those committee meetings... especially given that Wells's productivity was very sub-par.

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  4. I hate to say it -- I'm one of those people who think the developmental perspective does contribute to our understanding of evolution -- but I hve to agree with you. I was very disappointed in that book. "Facilitated variation" struck me as nothing but an empty buzzword, poorly explained and offering no new insight.

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  5. I think my view matches PZ's mostly. Evo-devo contributes something, supplementing previous views into a more complete picture; and I agree that the book wasn't the best book of the past decade for the field. It was a good book however, and worth my time to read even if it was unclear at important points.

    But, Larry, what do you think the best book of the decade was? (just curious)

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  6. PZ opines (not surprisingly),

    I hate to say it -- I'm one of those people who think the developmental perspective does contribute to our understanding of evolution ...

    I agree with you. All biology perspectives contribute to our understanding of evolution.

    My beef is with those who think that developmental biology is going to radically change our view of evolution. That's just silly hyperbole.

    The important contribution of developmental biology is merely an extension of what Jacques Monod said 35 years ago, "What's true of E. coli is also true of an elephant." We now know that his prediction is correct.

    We know that small changes in regulation can produce large changes in phenotype. These ideas were incorporated into thinking about evolution about 25 years ago.

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  7. dan asks,

    But, Larry, what do you think the best book of the decade was? (just curious)

    You mean other than The God Delusion? :-)

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  8. We seem to live in an age where people feel they have to hype everything as the latest revolutionary advance. Maybe it's lingering damage wrought by Kuhn. Maybe it's the extreme tightness of both research funding and the academic job market. I don't know, but from the perspective of one who has been out of academic science for a long time now, it does seem odd compared to the atmosphere and mores that I remember.

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  9. The important contribution of developmental biology is merely an extension of what Jacques Monod said 35 years ago, "What's true of E. coli is also true of an elephant."

    Actually, Monod predicted the extension. The untruncated, truer, and much funnier quote is: "What is true for E. coli is alo true for the elephant - only more so."

    In any case I'd argue that the huge advance in thinking about evolution over the last 15 years has again come from bacteria. It is the recognition that large amounts of horizontal gene flow have dominated the evolution of microbial populations. The ongoing revolution is in understanding the vast complexity of mixed microbial and phage populations.

    Evo devo is deeply interesting and important, but it has not fundamentally changed our large-scale view of evolutionary pattern and process. The microbial genomic and ecology efforts have.

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  10. God Delusion? Not a bad pick. ;-)

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  11. Say what you will about the contents of the book (I've never read it) but it does have a nice looking cover. :-)

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  12. Dawkins is deluded about "God". The result is his God Delusion.

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