Sunday, August 27, 2017

The Extended Evolutionary Synthesis - papers from the Royal Society meeting

I went to London last November to attend the Royal Society meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives [New Trends in Evolutionary Biology: The Program].

The meeting was a huge disappointment [Kevin Laland's new view of evolution]. It was dominated by talks that were so abstract and obtuse that it was difficult to mount any serious discussion. The one thing that was crystal clear is that almost all of the speakers had an old-fashioned view of the current status of evolutionary theory. Thus, they were for the most part arguing against a strawman version of evolutionary theory.

The Royal Society has now published the papers that were presented at the meeting [Theme issue ‘New trends in evolutionary biology: biological, philosophical and social science perspectives’ organized by Denis Noble, Nancy Cartwright, Patrick Bateson, John Dupré and Kevin Laland]. I'll list the Table of Contents below.

Most of these papers are locked behind a paywall and that's a good thing because you won't be tempted to read them. The overall quality is atrocious—the Royal Society should be embarrassed to publish them.1 The only good thing about the meeting was that I got to meet a few friends and acquaintances who were supporters of evolution. There was also a sizable contingent of Intelligent Design Creationists at the meeting and I enjoyed talking to them as well2 [see Intelligent Design Creationists reveal their top story of 2016].

  • Introduction: New trends in evolutionary biology: biological, philosophical and social science perspectives
    Patrick Bateson, Nancy Cartwright, John Dupré, Kevin Laland, Denis Noble
  • Review article: Why an extended evolutionary synthesis is necessary
    Gerd B. Müller
  • Research article: Evolutionary biology today and the call for an extended synthesis
    Douglas J. Futuyma
  • Review article: Developmental plasticity: re-conceiving the genotype
    Sonia E. Sultan
  • Discussion: Niche construction, sources of selection and trait coevolution
    Kevin Laland, John Odling-Smee, John Endler
  • Research article: Why developmental niche construction is not selective niche construction: and why it matters
    Karola Stotz
  • Review article: Biological action in Read–Write genome evolution
    James A. Shapiro
  • Review article: The evolutionary implications of epigenetic inheritance
    Eva Jablonka
  • Research article: Genetic, epigenetic and exogenetic information in development and evolution
    Paul E. Griffiths
  • Review article: Extended genomes: symbiosis and evolution
    Gregory D. D. Hurst
  • Review article: Domestication as a model system for the extended evolutionary synthesis
    Melinda A. Zeder
  • Review article: Evolution viewed from physics, physiology and medicine
    Denis Noble
  • Research article: The metaphysics of evolution
    John Dupré
  • Review article: The subject as cause and effect of evolution
    Peter Godfrey-Smith
  • Review article: Adaptability and evolution Patrick Bateson
  • Research article: The purpose of adaptation
    Andy Gardner
  • Research article: Human nature, human culture: the case of cultural evolution
    Tim Lewens
  • Review article: Human niche, human behaviour, human nature
    Agustin Fuentes
  • Review article: A second inheritance system: the extension of biology through culture
    Andrew Whiten
  • Review article: Early Homo, plasticity and the extended evolutionary synthesis
    Susan C. Antón, Christopher W. Kuzawa


1. Futuyma's paper is a notable exception.

2. That's me with Jonathan McLatchie in the photo.

35 comments :

  1. In the table of contents I don't see how ID was making a noise.
    i(t might be behind some ideas but not clear cut.
    At least there was questioning about evolutionism with a question about its accuracy as the meeting implied.
    If so many are not understanding modern evolutionism then that itself would be a notable matter . Why such error in paid specialists?

    The correction of evolutionism comes intellectually from YEC and ID.
    The others smell something is amiss but don't address the core of the problem of why this error endures.

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    1. "The correction of evolutionism comes intellectually from YEC and ID. The others smell something is amiss but don't address the core of the problem of why this error endures."

      You're on the money there, Robert.

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  2. Pity that the correctors of evolutionism are spectacularly ignorant of their very own 'beliefs' that they cannot even try to mount a defense of it, and instead feel the need to attack evolution.

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  3. Larry, there is a major problem with saying that "all of the speakers had an old-fashioned view of the current status of evolutionary theory."

    Our understanding of evolution just keeps changing. The current literature reflects the latest changes. However, that is not the same thing as a scientific theory. "Whatever people think" is not a theory. If whatever we think today is not consistent with what Mayr, et al. believed, then this is a change that ought to be noted.

    Everyone knows that evolutionary thinking has changed in the past 60 years. The issue is whether conformists like Futuyma get to invoke a watered-down version of those changes and claim that they are already part of something called "the Modern Synthesis".

    Müller addresses this issue. It happens again and again. Someone argues that X is not consistent with the standard theory and requires a modification, and they get shouted down by people who object that plenty of good neo-Darwinians already know about X, therefore it is nothing new.

    The problem is that this is not a scientific argument about theories. It is an argument about people.


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    1. What Larry meant by that was nobody mentioned the random genetic drift. We ALL know that but Robert Byers...

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    2. Arlin, I'm puzzled by your response. We agree that the Modern Synthesis of the mid-1960s is not correct or complete. We agree that the addition of Nearly-Neutral Theory and updated population genetics was an important addition to evolutionary theory.

      I agree with Gould and others that what this meant is that the Modern Synthesis is dead and should be replaced. Futuyma and others think that the term "Modern Synthesis" should be retained as the name of current evolutionary theory. They think that the changes from 50 years ago can be easily incorporated into the original view of Mayr et al.

      I think they are wrong and I think you agree.

      However, that's not the point. The point I'm making about many of the EES proponents is not that they are "conformists." It's that many of them are still thinking of evolutionary theory as it was in the 1950s. They have not incorporated mutation and random genetic drift into their view of evolution. They are old-fashioned adaptationists.

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    3. I think this is mostly misunderstanding. Yes, I agree that the changes of the past 50 years cannot be shoe-horned into the MS of the 1960s.

      But there is a difference here. Let me try again to frame the issue. In the Nature debate of 2014, the conformist side (Wray, et al.) argue that Darwin studied earthworms, therefore niche construction is mainstream and no EES is needed. The problem is that this kind of argument mixes up a theory of evolution with an intellectual tradition. Darwin stated his theory of evolution repeatedly, and it didn't include niche construction. Darwin's followers repeatedly stated their understanding of the mechanism of evolution, and it didn't include niche construction. I don't think it occurs anywhere in the keystone works of Dobzhansky, Simpson, Mayr and Stebbins.

      Perhaps they were all secretly having an affair with niche construction, but they were married to neo-Darwinism.

      Müller makes this distinction when he argues that the "fact that innovative evolutionary mechanisms have been mentioned in certain earlier or more recent writings does not mean that the formal structure of evolutionary theory has been adjusted to them".

      So, I don't quite understand (or don't agree) with what you are suggesting when you seem to refer to an automatic process of "addition to evolutionary theory".

      Into the 21st century, Mayr claimed that random fixation of neutral alleles might happen, but it isn't evolution, therefore "neutral evolution" is a misnomer. Neutral evolution was never incorporated into his view. What do you mean when you say that neutral evolution is an "addition to evolutionary theory"?

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    4. When I say that Neutral Theory was incorporated in modern evolutionary theory, I mean that the modern version contains Neutral Theory plus the older view of natural selection. As I've explained many times, we agree that Mayr's views are wrong and that the "Modern Synthesis" is dead.

      With respect to things like "niche construction" I agree that it's a part of explaining the history of life and in that sense it's part of an evolutionary explanation. Where we disagree, I think, is whether this has to be part of modern evolutionary theory.

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    5. It is not clear to me how you can separate the history of life from evolutionary theory. It sounds very much like saying you separate the history of the continents from plate tectonics, or the evolution of the Milky Way galaxy from cosmology. A suppose a Popper would draw a distinction between history, which is not science (nor scientific,) from experimental (falsifiable) science, which is the real thing. If you think of science as a way of finding out how things really are by experience instead of analysis, as I do, this is a particularly mystifying distinction.

      As to the Modern Synthesis, I can only speak to popularizations. Random genetic drift gets much more than the occasional lip service. All traits are deemed to be adaptations due to natural selection by default, and the default is rarely questioned. Neutral theory is occasionally mentioned as some exotic add-on, trivial in effect like niche construction (though admittedly no one ever asks if niche construction might be more important after mass extinctions.) As for population genetics, popularizations hold that the gene is the unit of selection, therefore the genome is adapted. (I must say that my reading of Gillespie's intro left me with the distinct impression this is a bold conclusion even from gene selection, but perhaps I should re-read?)

      In popularizations, gene selection is usually presented as the modern evolutionary theory. In popularizations, gene selection and the pervasive power of natural selection to perfect the genome effectively stand in for very old ideas of perfection of design. Eons of time in effect often substitute for God the Creator. The more secular versions appear to read adaptationism with old ideas about genetic determinism/the pervasive power of heredity/scientific racism investing a certain content in ostensible pure science. See Evolutionary Psychology. Most proposals for an EES in popularizations appear to be aimed at the latter kind of thinking, while aiming for a more benign, Godly kind of adaptationism.

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    6. (I think my post got lost, so I'm trying again)

      Larry, when you say that the Neutral Theory was incorporated into modern evolutionary theory, this is problematic. By "modern", I assume you mean "contemporary". Kimura's Neutral Theory of Molecular Evolution is the specific conjecture that the *majority* of molecular changes are due to random fixation of neutral alleles. To my knowledge, this conjecture has not been established. It certainly isn't a consensus among evolutionary geneticists.

      But I want to set that aside, and suppose that what you really mean to say is that extensive neutral evolution is an established part of a contemporary understanding of how evolution works. It sounds like you are supposing that there is an automatic process of consensus-building in evolutionary biology, and you are just taking the pulse of the field and reporting back to us that neutral evolution is now accepted.

      OK, even if we accept that, what is your basis for calling it "evolutionary theory"?

      Also, I do not believe that there is such a process. We have a process of negotiating novel ideas in evolution, but it is completely broken as anyone can see from the 2014 Nature debate. I have consulted the greatest living authorities on evolution, and both Bill Nye and Jerry Coyne say that Darwin discovered the mechanism of evolution, which is natural selection. How does that leave any room for neutral evolution? I quoted Mayr's solution above: random fixation of neutral alleles may occur, but this isn't "evolution", which involves changes in phenotypes.

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    7. @Arlin: By "modern", I assume you mean "contemporary". Kimura's Neutral Theory of Molecular Evolution is the specific conjecture that the *majority* of molecular changes are due to random fixation of neutral alleles. To my knowledge, this conjecture has not been established. It certainly isn't a consensus among evolutionary geneticists.

      I disagree. If you mean the majority of changes in the genome, including the great proportion of it which is junk DNA, I'd say it is uncontroversial among molecular evolutionists and other evolutionary geneticists.

      But if you go from that rather obvious point to the conclusion that the majority of changes in coding sequences and in their nearby upstream and downstream control sequences are neutral, there is certainly no consensus there.

      Do you mean to make that jump? I get the impression from many if Larry's statements that he means to make it.

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    8. If you mean the majority of changes in the genome, including the great proportion of it which is junk DNA,...

      Sounds like the human genome. Not all genomes carry that much nonfunctional DNA. Most of them don't.

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    9. ...because most genomes are eubacterial?

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    10. True that pufferfish don't contain much junk DNA, nor do Drosophila. But mammalian genomes have lots of it, and as for salamanders and lungfish ...

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    11. ...because most genomes are eubacterial?

      I believe the argument extends to many unicellular eukaryotes as well, but yes.

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    12. True that pufferfish don't contain much junk DNA, nor do Drosophila. But mammalian genomes have lots of it, and as for salamanders and lungfish ...

      I guess that at the time when Kimura suggested his neutral theory, he was probably dealing with protein polymorphisms in animals and plants. I just wanted to point out that modern evolutionary theory should be a little more inclusive of microbes.

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    13. I believe the argument extends to many unicellular eukaryotes as well, but yes.
      What proportion of unicellular eukaryotes have less junk DNA than humans? I don't know myself. But that's probably the wrong question. What proportion have significant amounts of junk, which we might characterize roughly as anything over 0.3pg for a haploid genome? How does that compare with multicellular eukaryotes?

      Now, if the population size theory of junk control is correct, we might expect the average protist to have a smaller genome than the average large, multicellular organism. Is it true?

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    14. @Joe, I have not done a current review of the evidence, so I do not have a fixed position on this issue. I could be convinced one way or the other.

      In the old days, theories were proposed with macroscopic animals and sometimes vascular plants in mind, and other organisms were not generally considered. Given that, and given the bloated genomes of most macroscopic animals and plants, we can look favorably on your argument.

      But if we consider that the biosphere has been dominated (until recently, when plants took over) by prokaryotes with slim genomes, then this argument doesn't fly.

      Furthermore, many of the actual arguments offered by Kimura, King and Jukes were based on protein comparisons. For instance, a familiar argument of the neutralists was that K = u implies a constant rate, and K = 4Nus implies a variable one, therefore the observation of an approximate clock for protein evolution is evidence of neutrality. In retrospect, this is a loose argument that should not carry much weight, but my point is simply that the argument refers to protein sequence evolution rather changes in non-coding regions.

      This is all tangential to the point that I would like to discuss, which is this issue of talking about revisions to evolutionary theory or the Modern Synthesis when no one can agree what these are. A point rarely considered is that the explanans of evolutionary biology has changed. Mayr continued happily declaring the unification of biology in the 1980s when there was clearly a massive molecular-organismal schism. But Mayr, et al. did not need a theory for molecular evolution, which they considered unimportant.

      By contrast, most of what we want to explain today in evolutionary biology involves discrete molecular characters. We have no use for a Darwinian theory that literally reduces creativity (the origin of novelty) to infinitesimal shifts in quantitative characters. This gives us no help in understanding how introns or mitochrondria first arose.

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    15. ah, @corneel has already made part of this point, to the effect that the explanans has changed to include microbes. One might add that the whole argument about the totipotent "gene pool", which in the Modern Synthesis automagically soaks up and maintains variation so that selection can respond to any change in conditions, does not apply in prokaryotes, which generally lack the conditions that give the gene pool its mojo (recessivity, heterosis, sexual mixis, recombination, etc).

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    16. All right, let me be the one to restrict the discussion to multicellular eukaryotes. If we look only at those, and omit those that have little junk DNA, it is fair to say that most evolutionary geneticists accept that the majority of changes in the genome are neutral.

      (I am not saying that we should ignore all the others, just that I'm thinking of the views of evolutionary geneticists about organisms such as multicellular eukaryotes that have a fair amount of junk DNA).

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    17. @joe, sure. It is useful to make such taxonomic distinctions. The neutral theory applies as intended in certain groups.

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    18. @John

      What proportion have significant amounts of junk, which we might characterize roughly as anything over 0.3pg for a haploid genome? How does that compare with multicellular eukaryotes?

      Oof, that I cannot answer. I based my statement on Lynch, who showed a plot of genomic content against genome size in his book. It is figure 1 of this paper (It's behind a paywall, but I think you can manage that). All unicellular eukaryotes in that figure have proportions of coding DNA above that of humans. We both know that there are exceptions, this being biology and all, right?

      Now, if the population size theory of junk control is correct, we might expect the average protist to have a smaller genome than the average large, multicellular organism. Is it true?

      Eyeballing that figure, it certainly seems that way. Since that theory is pushed by Lynch, you may not be surprised to find that information in his paper. The paper is pretty old BTW, so many genomes have probably been added. Somebody more knowledgeable than me will have to enlighten us about those

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    19. Also: werent't you a taxonimist? Are you still allowed to use the term "protist"?

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    20. You can say "protist" all you want, just as you can say "tree" or "ungulate". Just don't call them taxa.

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    21. I like to say "prokaryote", just to offend Woesians. I can't wait until "Archaea" turns out to be a paraphyletic group. Will they disband their cult, or find someway to reinterpret the words of the founder?

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    22. Hasn't "Archaea" already turned out to be paraphyletic? Still not a problem, though. Just don't call it a taxon any more. "tree" and "ungulate" are polyphyletic, "tree" massively so. Or you could retain the taxon by putting eukaryotes within Archaea, if we suppose that the eukaryote genome originated from an archaeal genome by descent plus a buttload of horizontal transfer from eubacteria.

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    23. I'm OK with that John! The first step would be to follow your practice with "tree" and "ungulate", and stop capitalizing "archaea".

      Ooh, this is going to be fun. I think we should go back to the original name archaebacteria, which was a Freudian slip for "our key bacteria", i.e., the bacteria whose uniqueness must be exaggerated in order to continue a funding stream.

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  4. Müller makes this distinction when he argues that the "fact that innovative evolutionary mechanisms have been mentioned in certain earlier or more recent writings does not mean that the formal structure of evolutionary theory has been adjusted to them".

    So, I don't quite understand (or don't agree) with what you are suggesting when you seem to refer to an automatic process of "addition to evolutionary theory".

    Is there a current formal canonical evolutionary theory? If someone asked, where would you tell him or her to look?

    If not, how else are new ideas incorporated besides an informal "automatic" process?

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  5. I had what is being called the ‘old-fashioned’ view of evolutionary theory until fairly recently. But if almost all the people at the conference have that view, then ‘common contemporary’ might be the more accurate word to describe the situation.

    My attempt to remedy the situation—

    https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0338-2

    Koonin states
    “Null models are standard in physics but apparently not in biology. However, if biology is to evolve into a “hard” science, with a solid theoretical core, it must be based on null models, no other path is known.”

    and-
    “The time for naïve adaptationist “just so stories” has passed. Not only are such stories conceptually flawed but they can be damaging by directing intensive research toward intensive search for molecular functions where there is none.”

    This link is from a Jan. 02, 2017 post of Sandwalk.

    When Koonin’s view is the norm, then it will be OK to call the adaptationist view ‘old-fashioned’.
    Until then, I’m afraid it is the common contemporary view.

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  6. Larry claims that the Modern Synthesis was old-fashioned adaptationism that was replaced by modern evolutionary theory, particularly Neutral Theory and random genetic drift. This is bullshit and Larry obviously do not know his history. Genetic drift was a strong part of the Modern Synthesis, largely due to the influence of Sewall Wright (who discovered it and formalized it) and Dobzhansky (who studied it in Drosophila). It is simply dishonest to claim that genetic drift was ignored in the Modern Synthesis and it is poor scholarship to equate genetic drift with Neutral Theory. But Larry is not an evolutionary biologist, so this lack of scholarship is not entirely surprising.

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    1. My view is similar to Gould's - I believe that Stephen Jay Gould was a card-carrying evolutionary biologist. My view is also similar to that of Douglas Futuyma, who I also believe counts as an evolutionary biologist.

      Futuyma presented a paper at the meeting and you can read it by following the link above. The opening sentence of the abstract says,

      Evolutionary theory has been extended almost continually since the evolutionary synthesis (ES), but except for the much greater importance afforded genetic drift, the principal tenets of the ES have been strongly supported.

      Like most knowledgeable evolutionary biologists, Futuyma recognizes that the original Modern Synthesis dealt almost exclusively with natural selection. Lip service was paid to random genetic drift but it was never an important part of the thinking of people like Ernst Mayr.

      Futyuma goes on to say,

      The abundant evidence of natural selection and the development of optimality models for characters that almost unquestionably affect fitness may have led to a broadly held view of selection as an almost exclusive factor of evolution. But the all-important role of selection was challenged by interpretations of molecular polymorphism and evolution in neutralist terms, and the ‘neutralist–selectionist’ debate ultimately resolved itself into rendering unto Kimura and unto Darwin those provinces of variation that each best explains.

      Futuyma thinks that the Modern Synthesis simply added Neutral Theory and an increased emphasis on drift but it didn't change substantially. This is where I part company with him. I think those changes in point of view and emphasis were substantial - important enough to spell the end of the version of evolutionary theory known as the "Modern Synthesis."

      That version is dead. It has been replaced with an more up-to-date version exemplified by people like Michael Lynch.

      I discussed this with Futuyma. He admits that he's a bit uneasy with his position. He realizes that the changes that occurred in the late 1960s were as close as you could get to being a "paradigm shift." Nevertheless, he remains convinced that the basics of evolutionary theory advocated by the founders of the Modern Synthesis are sound and all additions are easily incorporated into that framework.

      I do not equate Neutral Theory with random genetic drift. Dawkins does that but I don't. Although fixation of neutral and nearly-neutral alleles requires drift, it's important to note that drift also affects fixation of deleterious alleles and beneficial alleles.

      It is very poor scholarship to accuse someone (e.g. me) of something they didn't do.

      Is the "Modern Synthesis" effectively dead?

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    2. This discussion is about the scientific theory "Modern Synthesis", not the personality cult. As Müller (2017) points out, the "fact that innovative evolutionary mechanisms have been mentioned in certain earlier or more recent writings does not mean that the formal structure of evolutionary theory has been adjusted to them".

      The structure of the MS is not hard to figure out if one knows what to look for. Everyone says it is based on population genetics. Yet, when Mayr, Simpson and others supposedly showed that the MS applies across biology, they were not doing any population genetics. They were crafting verbal explanations for observed patterns using verbal theories blessed by Dobzhansky, Fisher and Haldane. The theory that became popular and that ordinary evolutionists used is not a set of equations or models, but a set of verbal principles telling us how high-level causes account for evolution.

      The principles were things like (1) rapid adaptation is likely because natural populations have abundant variation, (2) variation-induced trends are impossible because mutation rates are too small, and (3) adaptation proceeds by infinitesimal shifts because this is most likely. The MS further simplified evolution by assigning stereotypic roles to factors, e.g., variation is merely a source of raw materials, recombination is the proximate source of variation for selection, selection supplies the direction in evolution, and so on.

      Provine (1971) dissected the population-genetic basis of this view. The sine qua non of evolution is the ability of selection to shift the phenotypic value outside its original range without new mutations, as shown by Castle's hooded rats. "Evolution" in this theory is "shifting gene frequencies": upon a change in environment, selection shifts the frequencies of small-effect alleles at many loci simultaneously, going from the old optimum to a new optimum.

      This the foundation of the verbal theories applied by Mayr, et al. Wright's uses of genetic drift were not part of the theory. Obviously, it can't have been part of some standard orthodoxy if most scientists hadn't heard of it. Wright himself wasn't invited to the 1959 synthesis party.

      Today, the original MS has been forgotten, and the concept of a "Modern Synthesis" is defended with an endless stream of bait-and-switch arguments. Eventually this is all going to come crashing down on Futuyma, et al. If the MS seems like a mere "framework" today, that is because its corpse has rotted away, leaving only the bones. The bones can be reassembled into various shapes that directly contradict the verbal theories of Mayr, et al.

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  7. I saw a person with a tattoo that said “survival of the fittest”.
    That tautology seems to be the basic concept behind adaptationist thinking. It is also something a person can believe in.

    I have yet to see a person with a tattoo that says ‘random genetic drift’ and I doubt I will.
    Somehow I think adaptationist thinking is with us to stay for a while yet.

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