Sunday, January 04, 2015

A lesson on genetic load

The genetic load argument is one of the five things you should know if you are going to participate in the junk DNA debate.

Dan Graur has written an excellent summary of the genetic load argument from the perspective of population genetics. He links to it from his blog: If @ENCODE_NIH is right, each of us should have 7 x 1045 children.

Read it.


27 comments :

  1. A gaur is a large bovine native to south and southeast Asia. Not a starling.

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  2. By the way, Romanian graur comes from Latin grāculus, which means 'jackdaw' rather than 'starling'. In some other Romance languages the same bird name has eventually stuck to various corvids (Romanian is an exception): crows, ravens, rooks, and choughs (sometimes to more than one in the same dialect). Speakers of Vulgar Latin seem to have been little good as ornithologists or birdwatchers, but their ignorance made room for a lot of semantic evolution.

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    1. Does "grackle" fit into this somewhere?

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    2. Yes, of course, though it's a modern Neo-Latin coinage, anglicised in the 18th century, unlike the Romance words that have been inherited "vertically" from colloquial Latin: dialectal French grolle, Italian gracchio, etc.; Spanish grajilla still retains the original meaning of 'jackdaw'.

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    3. P.S. [second thoughts]: grajilla is a sort of diminutive of grajo 'rook', which is the actual reflex of grāculus in Spanish, so we are not dealing with simple retention here. The "official" Classical Latin terminology represents the usage of learned naturalists like Pliny the Elder, to whom the difference between a jackdaw and a rook (let alone a starling) was obvious and important. To the vast majority of the population, a grāculus was, I suppose, any crow-like bird that went "grah-grah" (starlings don't, but the Romanian development is unique).

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    4. This turns out to be more interesting and complicated than I had originally thought. It appears that the word "grackle" was originally coined from a genus of myna (Gracula). One would assume that it originally referred to some group of mynas and/or starlings, but I can't so far find confirmation of that. So when and how was it transferred to a group of icterids?

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    5. According to the Oxford English Dictionary:

      Etymology: Anglicized form of the generic name Gracula, a modern Latin feminine corresponding to Latin grāculus jackdaw.

      The earlies examples:

      1772 Forster in Philos. Trans. (Royal Soc.) 62 400 The Gracula Quiscula, Linn. or shining Gracule.
      1782 J. Latham Gen. Synopsis Birds I. ii. 455 Gracula religiosa, Minor Grakle.
      1782 J. Latham Gen. Synopsis Birds I. ii. 457 Gracula calva, Bald Grakle.

      And a longer quote explaining the terminological confusion:

      1893 A. Newton Dict. Birds Grackle..a word..restricted to members of the Families Sturnidæ (starling) belonging to the Old World, and Icteridæ belonging to the New. Of the former those to which it has been most commonly applied are the species variously known as Mynas, Mainas and Minors of India..and especially the Gracula religiosa of Linnæus... In the New World the name Grackle has been applied to several species of the genera Scolecophagus and Quiscalus... The best known are the Rusty Grackle, S. ferrugineus..and Q. purpureus, the Purple Grackle or Crow-Blackbird.

      It seems Linnaeus originally classified the common grackle in the genus Gracula, taking it to be a kind of myna. Who can blame those Vulgar Latin speakers for confusing one blackish bird with another?

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  3. Very informative paper Professor Moran, thanks for that. BTW, the 3 founding fathers of population genetics are supposed to be Fisher, Wright, and Haldane, but I keep coming across reference to papers by Kimura for very basic and important results. Should Kimura be counted as a 4th founding father, or am I missing something?

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    1. Kimura was too late to be a founding father of population genetics, but he gets to be one of the two founding fathers of the neutral theory.

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    2. If you have access to it, I'd recommend Michael Dietrich's paper from 1994 if you'd like to know how Kimura's work fits into the context of the foundational population genetics from Fisher, Wright and Haldane.

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    3. Fischer is not usually thought of as one of the founders of the Modern Synthesis. The key players were those at the Princeton Conference of 1947 and they included Haldane and Wright but also Dobzhansky, Mayr, Huxley, Simpson, Stebbins, Muller and several others. The most important books were those by Julian Huxley, Bernard Rensch, and George Gaylord Simpson. The founding fathers were those who saw and understood the connections between population genetics and the other fields of evolutionary biology.

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    4. Of course there is no right answer as to who gets to be called "founder". Although Hardy and Weinberg and some others worked earliest in theoretical population genetics, Fisher [not spelled Fischer -- he was English, not German], Wright, and Haldane made such a massive contribution that they are universally acclaimed as the major figures in the establishment of theoretical population genetics. Kimura was the most important theoretical population geneticist in the last half of the 20th century.

      As far as the Modern Synthesis is concerned, the effect of theoretical population genetics was crucial -- without it, there could be no synthesis. So Fisher's work counts even if he didn't make it to Princeton in 1947. (Of course as someone trained as a theoretical population geneticist, I may be biased).

      Kimura's theoretical papers in the international literature start to have an impact in 1954. To my mind that makes him too late to be called a "founder".

      But your mileage will vary -- maybe someone who publishes next year will be the real founder of the field.

      And we seem to be discussing two issues here: who is a founder of theoretical population genetics, and who is a founder of the Modern Synthesis.

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    5. John H: One other person who founded the neutral theory is Richard Lewontin. In the famous Lewontin and Hubby 1966 paper on the high level of genetic variability seen using electrophoresis on proteins, there is a very good discussion towards the end of the paper, written I am sure by Dick. In it he raises the possibility that the variability could be explained by neutral mutation.

      You may protest that the paper by Kimura and Crow 1964 has priority there. The math is there in that paper (Jim Crow told me he wrote that section). But it was there only as a null case for their consideration of how much variability could be maintained by overdominance with many alleles. There was no advocacy in the 1964 paper of the use of neutrality to explain electrophoretic variability -- for the simple reason that the variability wasn't known yet! Kimura's advocacy starts with his famous 1968 Nature paper. Lewontin did not nail his flag to the mast -- he just said it was a possible explanation. But I think he should be credited with the first clear explanation of the possible role of neutral mutation in explaining genetic variation within species.

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    6. Joe: Speaking as a person who contrived to make it through the University of Chicago without a single course in population genetics, I bow to your wisdom. It was indeed Jim Crow I was thinking of.

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    7. O/T you don't hear much about Rensch. Anybody know anything about him?

      I'm wondering, was Rensch anti-Nazi or what? Yeah, it's off topic, but I get sick of hearing from creationists that "Hitler was a Darwinist", so I compile lists of who's pro-Darwinist and anti-Nazi, who's anti-Darwinist and pro-Nazi (a lotta guys), and their converses.

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    8. Wikipedia:
      He [Rensch] joined the zoological museum of the University of Berlin as an assistant in 1925... In 1937 he was forced to leave the museum because he refused to join the Nazi party, and took a position at a zoological garden in Münster.[1] In 1940 he was recalled for military service, but was discharged for medical reasons in 1942.[4]


      Ref. 1 is to Ernst Mayr's memoriam for Rensch.

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    9. Not every paleontologist was a founder of the Modern Synthesis even though paleontology and macroevolution were key parts of the synthesis. Similarly, not every field biologist and ecologist were founders even though these were also part of the synthesis. Not every population biologist was a founder even though population biology was one important discipline that became part of the synthesis.

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    10. I think the "founders" terminology has outlived its usefulness. It arose from a deliberate mid-20th-century exercise in empire-bulding by Mayr, et al., resulting in an organized discipline of "evolutionary biology" with a society, a journal, a set of fixed doctrines, and a deity (Darwin) along with mythic heroes (Weissman, Fisher) and villains (Bateson, de Vries, et al).

      In reality, evolutionary theory is not static and is not all built on the same foundation, and the foundations do not all come from the alleged "founders". There are different branches of theory that have different starting points. To the extent that the starting point is nearly always discrete genetics, we must thank the early geneticists who preceded Fisher. As Dave McCandlish and I wrote recently, post-synthesis developments in theoretical population genetics notable for their wide use include the theory of kin selection (Hamilton 1964), evolutionary game theory (Maynard Smith and Price 1973), the coalescent (Kingman 1982), and the multivariate generalization of quantitative genetics (Lande and Arnold 1983). Our paper was about an equally important innovation-- origin-fixation models-- which began in 1969 (King, Jukes, Kimura, Maruyama) and which corresponds to a mutationist view of evolution contrary to the stated views of Fisher, et al.

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    11. It arose from a deliberate mid-20th-century exercise in empire-bulding by Mayr, et al., resulting in an organized discipline of "evolutionary biology" with a society, a journal, a set of fixed doctrines, and a deity (Darwin) along with mythic heroes (Weissman, Fisher) and villains (Bateson, de Vries, et al).

      Exactly. That's what the Modern Synthesis was all about.

      In reality, evolutionary theory is not static ...

      That's also correct. It's why we need to move beyond the Modern Synthesis.

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    12. Hi Larry,

      Forgive my presumption and thanks in advance for your indulgence, but I still don’t get it.

      When I look back at what you wrote here: http://sandwalk.blogspot.ca/2014/10/nature-criticizes-science-hyperbole-and.html?showComment=1417808999992#c4727783262835368592

      And what even Darwin himself (much less what the Modern Synthesists said)

      I can only reiterate what I said before.

      I agree that the original "synthesis" was very naïve compared to today's version. But I fail to discern any fundamental contradiction of the original... "expansion" yes, but "contradiction" no.

      Neutral Theory is not as different from the Modern Synthesis as say Relativity is different from Newtonian Physics.

      Here is what Darwin himself said which to my ears sounds strikingly similar to what Laurence Moran says today:

      The foregoing remarks lead me to say a few words on the protest lately made by some naturalists, against the utilitarian doctrine that every detail of structure has been produced for the good of its possessor. They believe that very many structures have been created for beauty in the eyes of man, or for mere variety. This doctrine, if true, would be absolutely fatal to my theory. Yet I fully admit that many structures are of no direct use to their possessors… But by far the most important consideration is that the chief part of the organisation of every being is simply due to inheritance; …many structures now have no direct relation to the habits of life of each species.
      http://darwin-online.org.uk/Variorum/1860/1860-199-c-1859.html

      Pretty insightful for a Dude who had no inkling of modern Genetics. In other words, Darwin himself was not a strict “adaptionist”.

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  4. I'm surprised no one has mentioned Thomas Jukes in the context of neutral evolution -- I would have thought his contribution was as great as Lewontin's, though both were far less important (in this context) than Kimura, who is one of my heroes, but I agree with those who say he came too late to be a "founder". If we believe Wikipedia Jukes was English (I didn't know that) and got his PhD at the U of T (I didn't know that either, and suspect that our host may not know it either).

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    1. Of course I knew. Thomas Jukes got his Ph.D. in my department (Biochemistry) in 1933. I've mentioned this several times.

      More importantly, the development of Neutral Theory and the enhanced importance of random genetic drift were seen as contrary to the standard view of evolution at the time. That view was the Modern Synthesis. That's why the King and Jukes paper is about "non-Darwinian" evolution.

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    2. OK. Sorry. I think I missed your mentioning of it several times.

      I don't understand your more important point, however. I expect King and Jukes used a different name from "neutral evolution" because that name wasn't current when they wrote their paper. In any case, do you disagree with my more important point, that King and Jukes deserve to be mentioned in the context of the origins of the neutral theory?

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    3. The King and Jukes paper is Non-Darwinian Evolution. It begins with, "Darwinism is so well established that it is difficult to think of evolution except in terms of natural selection." They are referring to the Modern Synthesis view of evolution that was common at the time. In 1979 we see Jukes writing to Crick and saying ... [Jukes to Crick on Junk DNA]

      I am sure that you realize how frightfully angry a lot of people will be if you say that much of the DNA is junk. The geneticists will be angry because they think that DNA is sacred. The Darwinian evolutionists will be outraged because they believe every change in DNA that is accepted in evolution is necessarily an adaptive change. To suggest anything else is an insult to the sacred memory of Darwin.

      He was well aware of the fact that Neutral Theory was an affront to the prevailing view of most evolutionary biologists.

      As for your important point ... yes, King & Jukes usually get credit for developing Neutral Theory along with Kimura. See Neutral Theory on Wikipedia and the relevant sections of all evolutionary biology textbooks.

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    4. King and Jukes are often ignored in preference to Kimura. This is partly because Kimura went on to play such a prominent role in defending and promoting his view for 25 years. However, they clearly co-proposed the neutral theory, on a rather different basis than Kimura-- on the basis of empirical patterns of sequence divergence, rather than esoteric arguments about load.

      I think the debate over molecular evolution would have been quite different if King had survived longer and played a leading role, rather than Kimura with his focus on strict neutrality. King saw something about the big picture that Kimura did not seem to see, which was that (1) the whole "molecular evolution" view emerging in the 1960s treated evolutionary change as a Markov process of mutation-and-acceptance and (2) this was *not* the Modern Synthesis view, which had insisted that evolution is not a process of fixing mutations one at a time, is not limited by mutation, and that selection does not act as a filter or editor. Importantly, the distinctiveness of the former view is not tied to neutrality, something that King saw but no one else seemed to see.

      I continue to be surprised as to how this key point has gotten lost in the debate over neutrality. The distinction between origin-fixation models of evolutionary dynamics (which King & Jukes co-proposed), and models that are based on standing variation is emphasized in a recent review (http://www.ncbi.nlm.nih.gov/pubmed/25195318) where we argue that these are essentially 2 different theories of evolution.

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  5. "I am sure that you realize how frightfully angry a lot of people will be if you say that much of the DNA is junk. The geneticists will be angry because they think that DNA is sacred. The Darwinian evolutionists will be outraged because they believe every change in DNA that is accepted in evolution is necessarily an adaptive change. To suggest anything else is an insult to the sacred memory of Darwin. "

    Hah that's a great quote! Jukes was quite a guy!

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