Friday, December 11, 2015

A "synthetic" view of the Modern Synthesis

I just re-read a 1997 paper by Francis Ayala and Walter Fitch (Ayala and Fitch, 1997). The opening two paragraphs describe the Modern Synthesis of Evolution in a very interesting way. The emphasis is on the history and the contributions of Theodosius Dobzhansky (1900-1975) but it makes another point that I'd like to mention.
Theodosius Dobzhansky (1900–1975) was a key author of the Synthetic Theory of Evolution, also known as the Modern Synthesis of Evolutionary Theory, which embodies a complex array of biological knowledge centered around Darwin’s theory of evolution by natural selection couched in genetic terms. The epithet ‘‘synthetic’’ primarily alludes to the artful combination of Darwin’s natural selection with Mendelian genetics, but also to the incorporation of relevant knowledge from biological disciplines. In the 1920s and 1930s several theorists had developed mathematical accounts of natural selection as a genetic process. Dobzhansky’s Genetics and the Origin of Species, published in 1937 (1), refashioned their formulations in language that biologists could understand, dressed the equations with natural history and experimental population genetics, and extended the synthesis to speciation and other cardinal problems omitted by the mathematicians.

The current Synthetic Theory has grown around that original synthesis. It is not just one single hypothesis (or theory) with its corroborating evidence, but a multidisciplinary body of knowledge bearing on biological evolution, an amalgam of well-established theories and working hypotheses, together with the observations and experiments that support accepted hypotheses (and falsify rejected ones), which jointly seek to explain the evolutionary process and its outcomes. These hypotheses, observations, and experiments often originate in disciplines such as genetics, embryology, zoology, botany, paleontology, and molecular biology. Currently, the ‘‘synthetic’’ epithet is often omitted and the compilation of relevant knowledge is simply known as the Theory of Evolution. This is still expanding, just like one of those ‘‘holding’’ business corporations that have grown around an original enterprise, but continue incorporating new profitable enterprises and discarding unprofitable ones.
The important point here is that evolutionary theory is a complex synthesis of sub-theories, hypotheses, and observations. While it may be convenient to refer to this synthetic version as the "Theory of Evolution," it's also very misleading.

I strongly recommend that we abandon that term and use "evolutionary theory" instead. Furthermore, we should be careful about using the term "Modern Synthesis" unless we are specifically referring to the version of evolutionary theory that was popular in the 1950s.

It's true that Ayala and Fitch would like to retain the term "Synthetic Theory" to refer to the expanded version of the Modern Synthesis. They want to emphasize that there have been important extensions to the original Modern Synthesis but these are merely add-ons. Darwin's basic idea of evolution by natural selection remains at the core of their version of the "Theory of Evolution."

That seems like a very pluralistic view but I'd like to note several things about this paper.
  1. The word "drift" appears only once and it's in the form "neutral drift." There's no mention of random genetic drift as a mechanism evolution that's been incorporated into the synthetic version of evolutionary theory.
  2. The word "neutral" appears five times but "Neutral Theory" is not mentioned. The authors do concede that "the neutral-selection controversy rages on."
  3. There are 50 references but not a single paper by Mootoo Kimura is mentioned. They do, however, discuss molecular clocks and discuss whether amino acid substitutions are really of "no adaptive consequence."
  4. There's a fairly well-known paper by Gould and Lewontin that might be relevant in a discussion about the synthetic version modern evolutionary theory. They neglected to mention it.

Ayala, F.J., and Fitch, W.M. (1997) Genetics and the origin of species: an introduction. Proc. Natl. Acad. Sci. (USA) 94:7691-7697. [PDF]

Gould, S.J., and Lewontin, R.C. (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. Roy. Soc. (London) Series B. Biological Sciences 205:581-598. [doi: 10.1098/rspb.1979.0086]

18 comments :

  1. Larry. no offence but ever since you banned Robert Bowers your blog seem to have died. what's wrong?

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  2. Died? I ban people on my blog, too, and it improves the discussion. Having one blowhard who won't shut up about nonsense fuels lots of contention, but doesn't enlighten the slightest bit.

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    1. Eric's comment (above) is the typical sort of passive-aggressive insult that is common from those frustrated that they are unable to challenge things they disagree with from a rational or science-based perspective.

      As for Byers (not Bowers) I wouldn't have banned him. As a YEC his views are basically scientifically illiterate and he appears to have a problem with written communication, but at least his comments were derived from genuinely considered convictions. This differs from the trollish nonsense characterizing much of the creationist commentary here (see Eric's comment above). Robert Byers’ comments may not have added anything substantive to the conversations here, but they were usually not so frequent nor ill-mannered as to be disruptive.

      I have a soft-spot for people who, however misguided, at least make their case in an honest and sincere manner. I have little time for buffoons who seek only to disrupt or insult as a result of their limited skill set (Eric, above). Alas, the resident Beatnik poet might have been a casualty of a much-needed purge - things were getting out of control around here with the plethora of idiots gumming up the works. If Robert was banned, I would urge reconsideration, but only mildly since I have no justifiable say in such matters.

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    2. Died? I ban people on my blog, too, and it improves the discussion. Having one blowhard who won't shut up about nonsense fuels lots of contention, but doesn't enlighten the slightest bit.

      What discussion? You call 25 comments on your 10 posts since Nov 23 discussion? Your blog is certainly alive.

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    3. Eric, are you sure you are talking about traffic at PZ's Pharyngula? Only in one week (30 November -- 6 December), I have counted 27 posts with 1061 comments so far. That's quite a lot of dicussion by any standards.

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  3. Thank you for this. I've been confused by the use of the term 'The theory of evolution' for awhile now.
    'Evolutionary theory' seems a much better way of discussing the science.

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  4. I definitely agree. Neo-Darwinism is clearly a school of thought, not a theory. The Modern Synthesis stopped being a theory almost as soon as it was written. It's really just a brand now, like Darwinism. People still buy the brand but the message is negotiable.

    I would also say that it cheapens the concept of a scientific theory to refer collectively to mainstream thinking about evolution, or conventional wisdom about evolution, as "the theory of evolution". We should refer to it as "conventional thinking about evolution" instead. In no other field of science is it assumed that there must be a single theory that covers the entire field. This has never been true in evolution except for a brief period between the time the MS became official policy ca. 1959, and 10 years later when it was clear that this theory (allegedly covering all of biology) completely and utterly failed to anticipate the results of molecular sequence comparisons, which were then carved off into a separate field of "molecular evolution" with its own journals and conferences, in order to maintain the illusion that "evolution" was still covered.

    There is of course a second sense of "theory" as in "music theory" or "theoretical physics" where we mean "theory" to refer to a collection of abstractions rather than "theory" as a grand hypothesis. In that sense, "evolutionary theory" means the collection of all the abstractions. But that is clearly not what Ayala and Fitch are talking about.

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  5. Larry: The important point here is that evolutionary theory is a complex synthesis of sub-theories, hypotheses, and observations. While it may be convenient to refer to this synthetic version as the "Theory of Evolution," it's also very misleading.

    Yes, it is misleading to co-opt almost all of the theories in science into one that glorifies Charles Darwin and the great power of "evolution by natural selection".

    Larry: I strongly recommend that we abandon that term and use "evolutionary theory" instead.

    No, the phrase "evolutionary theory" will still be easily used as another name for "evolution by natural selection" that is supposed to fall apart without "natural selection" in its mechanism.

    I welcome the help explaining what "evolutionary theory" actually is, or at least was. But in this case if "evolutionary theory" can stand on its own without the "natural selection" variable then there is now a "Darwin's/Darwinian evolutionary theory" and "ID evolutionary theory". Otherwise "evolutionary theory" is an entirely Darwinian creation that would be as easily antiquated by a theoretical model that does away with generalization based variables that do not help computer model speciation.

    It's easy for me to adapt to whatever others decide. From my experience all "evo" words are assumed to be associated with Darwin's theory. The word "evolution" is another generalization (not a variable in the speciation mechanism) that terminology also had to be done away with completely. It can though be said that speciation is still evolution and I develop "evolutionary theory" too, even though the word is not needed or is used in its vocabulary. But in that case those who would need to mention it are defending terminology from another theoretical model that often has a picture of Charles Darwin shown along with it. A Google search for "evolutionary theory" defined it as:

    "The theory of evolution by natural selection, first formulated in Darwin's book "On the Origin of Species" in 1859, is the process by which organisms change over time as a result of changes in heritable physical or behavioral traits."
    http://www.livescience.com/474-controversy-evolution-works.html


    According to what the internet contains Charles Darwin is supposed to get the credit for all in "evolutionary theory" too. Other theories in it that he had nothing to do with barely factor in, anymore.

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  6. I know that the emphasis of Ayala and Fitch's piece is on Theodosius Dobzhansky. But I find it strange that in the history of the Modern Synthesis, they said that

    In the 1920s and 1930s several theorists had developed mathematical accounts of natural selection as a genetic process.

    Which theorists? Why R.A.Fisher, J.B.S. Haldane, and Sewall Wright, that's who. Their names were left on the cutting-room floor.

    So, Larry, that's also why Kimura's name wasn't mentioned -- he was in very good company there.

    Actually Sewall Wright in particular was a big influence on Dobhzhansky, so it's hard to see why he wasn't at least mentioned.

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  7. Stimulated by these comments I decided to have another look at the original paper of Fitch and Margoliash (Science 155, 297 (1967)), wondering how many of the people mentioned they referred to, and what sort of evolutionary theory underlay their method of analysis. Rather to my surprise, the answers were "none of them", and "none". No doubt I would need to make a more thorough investigation of Walter Fitch's scientific development, but the suggestion seems to be that he wasn't too interested in the points you rais.

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    1. I think that the passage reflects Friancisco Ayala's perspective more than Walter Fitch's. Francisco was Donzhansky's student, and had a long association with Dobzhansky. Walter Fitch trained in comparative biochemistry, but his work on the Fitch-Margoliash algorithm made use of a simple process of random substitution of amino acids, without any need to inquire exactly which evolutionary forces caused that. So I am not surprised at what you found in the Fitch-Margoliash paper.

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    2. What theory were you expecting early molecular evolutionists to use? They had to develop their own theory of evolution, because what little the MS had to offer them was wrong. Anfinsen, Dayhoff, Vogel, Zuckerkandl, and others compared molecules, and inferred differences that they interpreted as individual evolutionary changes. For them, an accepted mutation was the unit step in evolution. They referred to these discrete changes as "mutations" that were said to be (individually) accepted or rejected by "selection" (which was the editor, not the composer of the genetic message, in the famous words of King & Jukes). They reasoned that if part of a protein remains constant between two species, while another part changes, the latter part is less important for the function of the protein. Over time, this mode of reasoning became central to molecular studies, and today it is a cornerstone of genomics.

      The architects of the Modern Synthesis, to the extent that they considered any of these ideas, rejected them. The idea that evolution happens by the acceptance or rejection of individual mutations was the mutationist heresy. Evolution was depicted as a complex process of shifting gene frequencies from one multi-locus optimum to another. Evolution happened in the interior of an allele-frequency space.

      Until origin-fixation models were proposed in 1969, there was no theory in population genetics that related the rate of evolution to the rate of mutation. Indeed, Dobzhansky, Simpson, et al were quite clear that there was no close relationship between the two, because the "gene pool" served as a kind of magic buffer. A number of quotations showing this view are collected here:

      http://www.molevol.org/the-shift-to-mutationism-is-documented-in-our-language/

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  8. Trivia: Dobzhansky died from a heart attack in the backseat of Ayala's car as he was rushing him to emergency room.

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    1. I believe that Francisco played a major role in encouraging Dobzhansky to move to UC Davis after he left Rockefeller University in New York, and in making sure his needs were looked after.

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    2. Yes, and I think that Dobzhansky helped him a lot when he moved to United States from Spain. But that's not unusual of Dobzhansky as people say he was very close to his graduate students. Francisco was described to me by some people who knew him as a very courteous person. Although I believe he doesn't like when people pester him about Templeton and his position on science and religion.

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  9. Robert Byers is more like a dash of absinth in your drink. He does no harm, solicit no acolytes to his fantasy world and most of the time is just another source of lulz.

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  10. Is there a good popular introduction to the mathematics of the modern synthesis? I've read various Dawkins, Gould, etc., and haven't seen any of the mathematics. Or maybe an undergraduate textbook focusing on the math?

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    1. IIRC - the math is in Joe Felsenstein's free pop-gen textbook. But not labeled as such, directly.

      http://evolution.gs.washington.edu/pgbook/pgbook.pdf

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