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Sunday, December 30, 2012

Post-Modern Evolution


From time to time TOF has touched upon the peculiarities of the various theories of evolution: Lamarck, Blythe, Darwin/Wallace, Mendel, Kimura, Shapiro, et al.   Prior posts include:
And some of the topics that have bubbled up include
  • the persistence of teleology in evolutionary thought (apparently tworked off Fodor, who dissed natural selection precisely because it was inescapably teleological)
  • the importance of the environment, including the organism's own behavior at shaping evolution
  • that genetics and molecular biology may be more important than natural selection
James Shapiro
Some of these thoughts were initially triggered years ago by an essay for the educated lay public by James Shapiro that deconstructed both Michael Behe (the ID-guy) and Richard Dawkins (the science popularizer).  Both, he said, were dealing with obsolete metaphors of genetics.  This resulted in a correspondent immediately denouncing Shapiro as a shill for the Discovery Institute.  He wasn't and isn't, but it is interesting to note that the first reaction of the Third Way-denialists was to make up something scurrilous about the guy. Similar thing happened to Eldrege and Gould when they introduced punctuated equilibrium.  Students of the history of heresies will recognize the behavior instantly. 



Just recently, I ran across a video of Dr. Shapiro at the International Workshop on Evolution in the Time of Genomics.  In the YouTube below, Prof. James Shapiro presents a "21st century" vision of evolution from the viewpoint of information theory and molecular biology.  It starts at around 0:38:00 (which is where I hope the clip will commence) and runs to about 1:15:00, which includes the Q&A after the presentation.  The initial demonstration is, of course, the usual ineptness of scientists in handling audio-visual equipment.
In listening to the talk, you can let most of the technical jargon wash over you.  You can still grok the sense of it from the plain English.  The technolalia is by way of illustrative example.  
Dr. Shapiro's point is that the usual model of slow, gradual mutations driven by natural selection is simply not the way evolution actually takes place in practice.  Researchers, he points out, have never managed to create a new species by selection; but they have created many new species by hybridization.  Selection, he says, is good for fine-tuning a species, but cannot account for the sudden appearance of new forms and structures.  It is not "natural selection," but "natural genetic engineering" that accounts for the biggies.  

Fans of Aristotle will recognize that natural selection was based on the post-Cartesian error that regards matter as "dead" and acted upon by outside forces.  It was the result of "physics-envy" on the part of "natural historians."  Shapiro's formulation, natural genetic engineering, whether he recognizes it or not, is more Aristotelian: it is not so much outside forces as it is interior powers that shape evolution.  As Thomas put it en passant:
Species, also, that are new, if any such appear, existed beforehand in various active powers; so that animals, and perhaps even new species of animals, are produced by putrefaction by the power which the stars and elements received at the beginning.
-- Summa theologica, Part I Q73 A1 reply3
The organism's response to the environment, especially to the environment in stress, calls upon the natural genetic engineering powers of the genome.  These are neither random nor deterministic.  In fact, the famous random mutations upon which so many have relied are quite often repaired by natural "proofreading" functions of the genome itself. 
If fortuitous mutations were the basis, the development of resistant bacteria would be hard to account for.  We would have to believe that a fortuitous mutation just happened to pop up following the invention of a medicine and then was naturally selected by surviving the treatment regimen.  But if we allow that (in Shapiro's words) the genome is not a read-only memory, but a read-write memory, it is the organism's encounter with the medicine that evokes an immunizing response.  That is, the mutation is not random. 


Starting about 0:53:00 Shapiro makes the interesting statement that specific mutations are "drawn to" specific loci in the genome by intercellular signals within the genome itself.  Physicists may perk up and think "attractor basins," though Shapiro himself does not commit during the Q&A when someone brings it up.  But it is certainly an example of natural teleology at work: there is an end toward which this mutational process works as an arrow toward a target.  Genetic change is therefor often specific and targeted
Those who do not understand what telos means tend to raise hackles at this point, since they assume the connection between natural telos and deity is simple and direct.  Discomfort with the conclusion leads them to deny the premise (as they oft deny the Big Bang, the freedom of the will, the consciousness of the self, and sundry other matters for similar reasons.)  But Thomas did not think the connection simple and direct.  He thought telos in nature was obvious, but that to get from there to deity required difficult reasoning. 

Starting around 0:56:20, Shapiro explains how macro-evolutionary change can be accounted for.  Apparently, the original ID claim (by Michael Behe, also a molecular biologist) that there are biomolecular structures that cannot be accounted for by incremental natural selection is not especially controversial.  Shapiro contends that these structures can be accounted for instead by natural genetic engineering and explains in this section of the talk how genetic change can be massive as well as targeted. 

Broad-scale change, all of a sudden...  IOW, "punctuated equilibrium is the default."  Creativity in evolution occurs through natural genetic engineering, after which fine-tuning takes place through natural selection.   Around 1:05:00, Shapiro mentions a biologist who disagrees with the new theory of natural genetic engineering and punctuated equilibrium and who claims per Darwinian orthodoxy that small, gradual changes can still account for everything, even crossing a chasm.  This is a fellow named Jerry Coyne, whom we have encountered before denying free will
(A similar distinction between micro- and macro- is made by Peter Schuster, "Evolution and Design: A Review of the State of the Art in the Theory of Evolution," in Creation and Evolution: A Conference with Pope Benedict XVI in Castel Gandolfo. )

Behe's mistake was to deduce deity from the incompleteness of one natural law.  This does not follow.  In the first place, it is bad theology.  Thomas reasoned to deity not from the apparent failure of natural laws but from the very existence of natural laws themselves.  As noted above, he expected the origin of new species to be accountable by the natural powers given to nature in the beginning. But then Behe even tried to instruct Cardinal Schoenborn on this matter! 

Summary for SF

Wall lizard among the wall flowers
The obvious benefit to SF writers is that in Hard SF we need no longer rely on long, indefinite time spans to evoke new species.  They can come about quite suddenly.  We are reminded of the Galapagos finches transplanted to a remote Hawaiian island that radiated within 20 years into all the different beak types seen in the Galapagos themselves.  Or the Mediterranean wall lizard that within a similar time span not only changed from carnivorous to herbivorous but developed a whole new organ in the effort. 

We may suppose that for complex organisms such as human beings this may take longer -- however many generations 20 years represents for finches and lizards.  But it is not beyond reasonable science to say that of an environment "that which does not kill me makes me stronger." 

9 comments:

  1. Thank you for this very interesting post. I only found my way here by chance, but this information is very helpful, as, after several years away from academia, I've recently found myself digging into modern critiques of Darwinian evolution. I'm rather disappointed that, while I knew of Dr. Shapiro, I didn't know any specifics about his research while I was doing graduate work at the UofC (in the biomedical side of genetics). Coyne I had the unpleasant experience of meeting during an "ethics" workshop, where he was teaching first year grad students to tell undergrads that they can't believe in both God and evolution. I'm happy to find that the UofC, which has a strong Darwinian Sciences cluster, is fair enough to also employ a scientist that's questioning long-standing Darwinian assumptions. I look forward to watching the video you included above. Happy New Year!

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  2. You hit upon a whole bunch of issues I've been pondering for years. First off, the Darwinism of Dawkins (and E.O.Wilson) was a response to the happy-happy talk of the proto-environmentalist, who wanted to see harmony in nature, even in natural selection. Wilson and Dawkins were defenders of orthodoxy (and reason) against what might be called a misguided teleology of environment - that the various competing parts of an environment *want* to be in harmony.

    So, we get the Selfish Gene. And then, the Extended Phenotype, which takes the concept of a the genes of within an individual member of a species - and extends it to the environment. Hmmm. To be sure, Dawkins is not trying to reestablish the hippy-dippy harmony he and Wilson just shot down on a more rational, mechanistic basis. Rather, he's trying to show how some of the odder behaviors and structures in nature can be explained within his theory.

    But, it seemed to me - and here's the tie-in with your thoughts above - he didn't go far enough. And here I must apologize, for I am not nearly as widely read as you on this topic, and have not yet had a chance to review the materials you've linked to above. Perhaps this all is discussed at great length in literature I've yet to read.

    Molecular biology is the place to start any evolutionary discussion, because it is the molecules that make up the cells and creatures that have undergone whatever mechanisms are at play for the longest time and under the most varied circumstances. Even a single celled organism represents, under Darwin via Dawkins, an apex of evolution - it is the inconceivably complex result of *some* processes, having taken place over at least a billion years. Unlike modern animals and plants, a single-celled organism is dealing directly with an environment chock full of free-floating genetic stuff, stuff which can invade or be invited into a cell. Such invasions and invitations, along with mergers and acquisitions, as it were, were and are where the action is, and has been for a couple billion years, and at least potentially accounts for 'mutations', whatever that term means is this context. Evolution, under any mechanism, should first and primarily be concerned with how cells, or even smaller units such a viruses, deal with this.

    All the characteristics that Darwin observed, all the diversity and behaviors in animals and plaints, are like the paint on a house. The fundamental interesting part about a finch cracking seeds is really how it is that the finch can digest those seed and build 'finch' out of them. Read once about how mammals replaced birds as the apex predators in South America a few million years ago due, they supposed, to a slight advantage in metabolism. And how placental mammals have replaced marsupials almost everywhere, and for the same reason. How many other 'survival of the fittest' battles have been decided based on how well some fundamental molecular interaction, including the exclusion, inclusion or repair of genetic materials, takes place? All of them?

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  3. As I said before in one or another of your fora, as an undergraduate student of Dr. Salvador Luria, I would argue with him over the jokingly named Central Dogma of genetics; that is, genes render protein and not the then deposed Lamarckian notion of vice-versa, which I contended was myopic. Genes don't float in some theoretical-space, they're embedded in a protein machine and what exactly does all that fairly well-conserved supposed "junk" DNA do anyhow?

    Time proved me correct and Dr. Luria more cautious on those topics.

    It's, however, a mistake to refer to the well-stuffed lumber-room of "junk" DNA as mutation [as you've known me to rant about many times in the past, Michael]. I prefer Shapiro's choice of terminology of "natural genetic engineering". It provides a clearer picture of the process.

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  4. This discussion reminds me of a theme central to a very popular SF anime show. In the anime series Mobile Suit Gundam, the human population of Earth has largely migrated into space, with billions living in great constellations of O'Neill-type space colonies called "Sides". In one of these Sides, Side 3, a leader and philosopher named Zeon zum Daikun formulates a political ideology called Contolism, the basic precept of which is that living is space has triggered a sudden evolutionary jump within the human species. The results is the appearance of a "new type" of human being, with physical and mental abilities advantageous to beings living in the space environment ("spacenoids"). Based upon this philosophy, Zeon zum Daikun leads the Side 3 colonies to declare their independence from the Earth government and founds the Republic of Zeon in order to advance the interests of the New Type.

    Maybe Zeon zum Daikun was on to something...

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  5. Great post! Very interesting article and informative. Hope there'll be more articles like this to read. Keep it up.

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  6. At the far silly end, I've seen Darwinists who manage to acknowledge (some) of the NGE abilities of organisms, but who go on to employ pull-yourself-up-by-your-own-bootstraps logic by attributing it to the "evolution of evolution." That is, they acknowledge that natural selection can't reasonably account for certain structures on its own, so they argue that natural selection evolved, by natural selection, the ability to do things that natural selection can't otherwise do. I can't imagine a more clear-cut case of natural selection being used as a metaphysical fig-leaf for the reductionist worldview rather than an actual explanation.

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    1. Give Darwin his due. He never claimed reproductive pressue+resource crunch ever worked on an abstraction.

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  7. Btw, here's something of recent interest regarding Shapiro: http://www.huffingtonpost.com/james-a-shapiro/inconvenient-truths-why-a_b_2228277.html

    Particularly noteworthy is this reply of his to someone in the comments:
    But Richard's atheist beliefs are not irrelevant. They condition his every response. This was why I expressed frustration that he was unable to shake off the truths he had been taught. I thought this obstacle was more superficial and concerned academic "truisms," but it clearly involves more deeply held religious convictions. They explain a great deal of my inability to satisfy him with data and specific examples.

    Richard is free to hold whatever theological views he chooses. But when they set bounds to his scientific thinking, then he should make them apparent and not pretend they are irrelevant. As his own blog, cited by Seeking, attests, his atheist beliefs place limits on what abilities cells can have.

    Having observed bacteria for 40 years now, I am not ready to accept those limits. Every year we learn more and more about what bacteria and other cells are able to accomplish. Who could have imagined CRISPRs a decade ago?

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    1. Sweetly worded reply that touches on the heart of the matter.

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