Saturday, April 23, 2016

Proponents of the Extended Evolutionary Synthesis (EES) explain their logic using the Central Dogma as an example

There's a group of biologists who think that the current version of evolutionary theory is insufficient. They want to create an extended evolutionary synthesis that incorporates evo-devo, plasticity, niche construction, evolvability, epigenetics, and other things.

You might be wondering how these things could be incorporated and what that would do to "classic" evolutionary theory. Fortunately, we have a road map provided by Massimo Pigliucci and Gerd Müller in chapter one of Evolution: The Extened Synthesis. They help us out by providing an analogy.
As we will see in the rest of this volume, several of these tenets [of the Modern Synthesis] are being challenged as either inaccurate or incomplete. It is important, however, to understand the kind of challenge being posed here, in order to avoid wasting time on unproductive discussions that missed the point of an extended evolutionary synthesis. Perhaps a parallel with another branch of biology will be helpful. After Watson and Crick discovered the double-helix structure of DNA, and the molecular revolution got started in earnest, one of the first principles to emerge from the new discipline was the unfortunately named "central dogma" of molecular biology. The dogma (a word that arguably should never be used in science) stated that the flow of information in biological systems is always one way, from DNA to RNA to proteins. Later on, however, it was discovered that the DNA > RNA flow can be reversed by the appropriately named process of reverse transcription, which takes place in a variety of organisms, including some viruses and eukaryotes (through retrotransposons). Moreover, we now know that some viruses replicate their RNA directly by means of RNA dependent RNA polymerases, enzymes also found in eukaryotes, where they mediate RNA silencing. Prions have shown us how some proteins can catalyze conformational changes in similar proteins, a phenomenon that is not a case of replication, but certainly qualifies as information transfer. Finally, we also have examples of direct DNA translation to protein in cell-free experimental systems in the presence of ribosomes but not of mRNA. All of these molecular processes clearly demolish the alleged central dogma, and yet do not call for the rejection of any of the empirical discoveries or conceptual advances made in molecular biology since the 1950s. Similarly, we argue, individual tenets of the Modern Synthesis can be modified, or even rejected, without generating a fundamental crisis in the structure of evolutionary theory—just as the Modern Synthesis itself improved upon but did not cause rejection of either Darwinism or neo-Darwinism.
I thank Pigliucci and Müller for giving us a clear idea of the logic behind their attack on the Modern Synthesis.

... I must correct a wrong idea that has been spreading for the past three or four years. It was discovered some years ago that in some cases, the transcription step from DNA to RNA works in the reverse direction. That is nothing surprising. ... it could be predicted that such events could occur. They do occur, indeed, but this must not be taken to mean that information from protein could possibly go back to the genome. ... I am ready to take any bet you like that this is never going to turn out to be the case.

Jacques Monod (1974) p.394
The original, and correct, version of the Central Dogma of Molecular Biology was stated clearly by Francis Crick in 1958. Crick restated the Central Dogma of Molecular Biology in a famous paper published in 1970 at a time when the premature slaying of the Central Dogma by reverse transcriptase was being announced (Crick, 1970). According to Crick, the correct, concise version of the Central Dogma is ...
... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)
Jim Watson published the well-known, but incorrect, version in his 1960s textbook but anyone who does even a little bit of research will discover that the Crick version is the original [see: The Central Dogma of Molecular Biology].

Here's the summary provided by Francis Crick in his 1970 Nature paper.

Fig. 1. Information flow and the sequence hypothesis. These diagrams of potential information flow were used by Crick (1958) to illustrate all possible transfers of information (left) and those that are permitted (right). The sequence hypothesis refers to the idea that information encoded in the sequence of nucleotides specifies the sequence of amino acids in the protein.
This is important because whenever someone attacks the Central Dogma you can get a good idea of their academic ability by seeing if they understand the concept they attack. In this case, there's a question about proponents of the extended evolutionary synthesis and whether they have a sufficient grasp of evolutionary theory to be challenging it. Pigliucci and Müller have tried to convince us that they know what they are talking about by giving us an analogy; namely, the "demolition" of the Central Dogma of Molecular Biology.

They didn't do their homework. That doesn't inspire confidence in their ability to overthrow modern evolutionary theory.


Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163. [PDF]
Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]
Monod, J. (1974) "On the Molecular Theory of Evolution" reprinted in Mark Ridley (editor) Evolution (1997) p. 389

96 comments :

  1. Disappointing, because Pigliucci makes a distinction that most are unaware of, between the modern synthesis and neodarwinism. Presumably his distinction is correct, since the term was coined long before the modern synthesis or even the rediscovery of Mendel's work.

    -jaxkayaker

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    1. DEFINITION OF NEODARWINISM. George Romanes in his 1893 text An Examination of Weismannism defines neodarwinians as "Those who believe that natural selection has been the only modifying influence in the evolution of species, and that the material for its action has been only plasmogenetic characters." The latter characters are "Variations due to admixtures of germ plasm in acts of sexual fertilization (and therefore present at birth), as distinguished from somatogenetic characters - variations which have been acquired independently of germ-plasm."

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    2. RE: Revisiting Neo-Darwinism!?

      George Romanes in his 1893 text An Examination of Weismannism defines neodarwinians as "Those who believe that natural selection has been the only modifying influence in the evolution of species, and that the material for its action has been only plasmogenetic characters." The latter characters are "Variations due to admixtures of germ plasm in acts of sexual fertilization (and therefore present at birth), as distinguished from somatogenetic characters - variations which have been acquired independently of germ-plasm."

      I thought the above quoted definition of Neo-Darwinism is correct by the conventional Darwinian philoscientific and geo-biomorphic sense, or natural phenomenology; whereas it is biologically and physiologically inaccurate nor testable by any consequent Darwinists or neo-Darwinists (including Galton, Darwin and Romanes themselves) since the 1860s, and even today!?

      As a consequence, Weismann’s germline theory of heredity -- as opposed to Darwin’s gemmules theory of heredity -- was correct; as it was eventually observed and tested in the modern developmental biology of embryology, physiology, and Mendelian genetics of the 1860s, and beyond.

      Thus, the Modern Synthesis of Neo-Darwinism -- without consideration nor incorporation of Weismannism -- since the early 20th century, is now under a foundational challenge -- not another extension -- of its rhetorical evolutionism life of over a century past!? Caveat lector!

      Best wishes, Mong 4/26/16usct11:05; practical public science-philosophy critic (since 2006).

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    3. I think readers should be warned that the term "Neodarwinism" is changing its meaning, in fact reverting to its original meaning. It has been used a lot in the last 50 years as a synonym for the views of the Modern Synthesis. But as people like Donald Forsdyke have pointed out, it was the label proudly adopted by a group of biologists just after Darwin who maintained that natural selection was the explanation for the evolution of adaptations. They defined themselves in opposition to a diverse set of Lamarckians, advocates of orthogenesis, and saltationists who accepted common descent but did not think that natural selection was important in explaining adaptation.

      So people are gradually ceasing to refer to the Modern Synthesis as "Neodarwinism".

      PS I do not understand Mong H. Tan's argument, given above.

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    4. Hi Joe,

      regarding: I think readers should be warned that the term "Neodarwinism" is changing its meaning,...

      exactly correct, even though Wikipedia in both German and in English continue to conflate those two meanings.

      August Weismann was the first to coin the phrase "Neodarwinismus" even though Weismann himself apparently did not embrace the implications of so-called Mendelism.

      That would mean the original incarnation of Neo-Darwinism" was by no means identical to the Modern Synthesis.

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    5. Weismann’s prescient Germ Plasm Theory was the first modern incarnation of what is sometimes called “Hard Inheritance” (or “Hard Heredity”) articulating categorically that offspring are never affected by characteristics secondarily acquired during a parent’s lifetime. The champions of “Soft Inheritance” (or “Soft” Heredity”) countered that at least some acquired characteristics (due to environment interactions) were in fact heritable.

      Some modern Social Scientists still employ Ernst Mayer’s relatively recent “Hard vs. Soft” terminology unfamiliar to most modern Biologists. Weismann and his contemporaries instead had employed the terms “neo-Darwinism” and “neo-Lamarckism” to distinguish the between “Hard” and “Soft” heredity.

      Understandably, historical debate can become understandably confused. Weismann and others made matters even worse by resorting to “short cuts” when employing scientific jargon.

      The so-called “Soft Inheritance” of “Neo-Lamarckism” was often identified simply as “Lamarckism” and its antithesis (i.e. the Hard Inheritance of “neo-Darwinism”) as “Darwinism”, just so.

      Textbooks have perpetuated this confusion ever since. The “Hard” vs. “Soft” debate actually persisted well into the 20th Century and was far removed from the original theories first proposed by Darwin and Lamarck. Later versions of Neo-Lamarckism even embraced Natural Selection as “Nature’s sieve”, disputing only the initial mechanism generating heritable variation.

      Even today, Epigenetics is confusedly considered by some as a “Lamarckian” exception to current “Darwinian” Theory.

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    6. PS I do not understand Mong H. Tan's argument, given above.

      There was an argument? I thought it was Shakespearean, specifically Macbeth: "[F]ull of sound and fury, signifying nothing."

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    7. RE: Differentiating Darwinism from Neo-Darwinism!?

      But as people like Donald Forsdyke have pointed out, it was the label proudly adopted by a group of biologists just after Darwin who maintained that natural selection [NS] was the explanation for the evolution of adaptations [by gradual modifications, mutations or variations, which Darwin had modelled on the process of Charles Lyell’s geological anamorphism that I first analyzed and presented as geo-biomorphic “tree of life” as geo-biomorphism here: https://whyevolutionistrue.wordpress.com/2009/12/02/matthew-cobb-reviews-two-evolution-books/#comment-15762 and “natural phenomenology” as ortho-Darwinism here: http://philipball.blogspot.com/2011/12/darwin-not-guilty-shock-verdict.html ]. -- (Mong’s edits and links in parenthesis).

      These were the original Darwinists, whose purpose was only to seek and propagate the reading, interpreting, and understanding of Darwinism as presented in Darwin’s treatise “The Origin of Species” (1859); or the classical Darwinists, who defined themselves in opposition to a diverse set of Lamarckians, advocates of orthogenesis, and saltationists who accepted common descent [by acquired hereditary] but did not think that natural selection was important in explaining adaptation [and/or variation, modification, mutation, etc which were all not in the scope of their observations or imaginations]. -- (Mong’s edits in parenthesis).

      So people are gradually ceasing to refer to the Modern Synthesis as "Neodarwinism".

      No, this is a misreading of the neo-Darwinists history and the Modern Synthesis that neo-Darwinists would have had hoped younger generations of biologists to erase from their reading and training since the 1970s, with the worldwide publications of the 2 most renowned, influential, inferential as well as controversial neo-Darwinist, reductionist books: “Sociobiology: The New Synthesis” and “The Selfish Gene” that at once popularized the gene-centric narrative of the modern biology as “evolutionary biology”!?

      1) By modern definitions: the neo-Darwinists are those scholars who have had tried to extend Darwinism into all fields of scientific inquiry: by manufacturing an overarching theory of evolutionism (by superimposing Darwinism over Mendelism as their reductionist rhetoric, consensus, and synthesis) that they called the Modern Synthesis in the 1930s-40s; which in effect has at once become an unfalsifiable evolutionary theory by empiricism ever since in the Western scientific literature and philoscientific thinking since Darwin!?

      2) By historical analysis: Darwin and Romanes (including Galton) did try to expand the NS theory into the gemmules theory of heredity; but in vain, so they never published their related works since 1860s!? -- To be continued below:

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    8. -- Continued from above:

      3) Whereas Galton -- the then leading polymath cum neo-Darwinist -- had continued to implicate (but not empirically proven) the NS theory of gemmules (or geniuses) in his 3 most influential and detrimental reductionist books “Hereditary Genius” (1869), “Inquiries into Human Faculty and Its Development” (1883) and “Natural Inheritance” (1889); with which, the subsequently eager Darwinists and neo-Darwinists alike, have had used the Galtonism as their guiding light, so as to launch and disseminate the unproven Eugenics movements and programs in both Americas and Europe; especially in Germany where the Nazis had had used all of their own physico-biological reductionist, positivist, and selectionist ideologies, so as to justify and intended to exterminate all of their deemed undesirable people from the face of their Fatherland: namely the Holocaust of the 20th century past!?

      PS I do not understand Mong H. Tan's argument, given above.

      So, it is my hope that the younger generations of biologists and historians will be able to clearly differentiate and decouple the neo-Darwinism from Darwinism; and the Mendelism from ortho-Darwinism, etc in the 21st century!? And let the Darwinism of 1859 be what it originally purported to be: A natural philosophy; a philoscientific naturalism; or a natural phenomenology -- by the 21st-century biological and physiological understandings and definitions; and not being continuously hijacked and ditched by the physical reductionists, neo-Darwinists, since the early 20th century past!?

      Best wishes, Mong 4/28/16usct16:11; practical public science-philosophy critic (since 2006).

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  2. Larry, can you recommend a book on history of molecular biology?

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    1. I can: "The Eighth Day of Creation", Horace Freeland Judson

      THE definitive tome on the history & build out of the subject, eloquently written by the drama writer of the London Times.

      http://www.amazon.com/Eighth-Day-Creation-Revolution-Commemorative/dp/0879694785/ref=sr_1_1?s=books&ie=UTF8&qid=1461579033&sr=1-1

      2nd edition preferred.

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  3. "What could possibly go wrong?" I smiled, reading the headline. And what went wrong was exactly what I expected, well trained by earlier Sandwalk posts.

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  4. Jacques Monod lost his bet. These days, genetic engineers can reverse-engineer gene sequences from dinosaur proteins extracted from dinosaur bones, and then splice the resulting DNA into chickens - a pretty clear violation of the central dogma. So much for this 'never' being the case.

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    1. Yes, that's clearly a violation of the central dogma, except of course that it's not, because Crick, Monod and even Watson were talking about what happens in cells, not in reaction tubes and well plates.

      -jaxkayaker

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    2. Also, due to the degenerate nature of the genetic code, you can't learn exactly what the original codon is from the amino acid it coded for, unless the amino acid is tryptophan. (But it usually isn't.)

      So the reverse-engineering may work when you're referring to the proteins, but it doesn't really reconstruct the DNA.

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    3. If Crick really meant that the dogma only applies under certain circumstances, they he could easily have said so. Instead, he made an impossibility claim that has proven to be mistaken. Such transfers of sequential information are indeed possible in the present day organisms that Crick said he was talking about: Crick was mistaken.

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    4. So you think Crick believed it would never be possible for human beings to determine the chemical structure of a protein and, from that, determine the genetic sequence that led to its synthesis? I somehow don't think he was that stupid.

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    5. Regarding codon ambiguity, a few ambiguous codons are surely permitted by "detailed residue-by-residue transfer of sequential information". Detailed sequence information is still transferred, even if there are a few mistakes due to codon ambiguity. Crick wasn't asserting something that was trivial and stupid.

      That the central dogma has been overtaken by modern technology is well recognized in the tech community, I believe. For example, here's James Gardner (1999): "to a degree that is largely unappreciated by orthodox theoretical biologists, the ongoing revolution in biotechnology renders the central dogma obsolete. The fact is that information can and does flow upstream into the genome". No doubt evolutionary biologists will cotton on to protein reverse engineering in due course.

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    6. No, I don't think that Crick was stupid. Maybe that has to do with why he called it a "dogma". It was plausibly true back when he wrote his paper. Crick didn't speculate about the possible impact of technological progress on the dogma - instead just saying that he intended it to apply to "present-day organisms". So, the dogma was true back then, and is not true any more. Such is often the fate of dogmas.

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    7. It would be helpful to go back and look at the historical period in which Crick was speaking. Remember, until Oswald Avery's experiments in the 1940's, everybody who was anybody in science "knew" that genes were made of proteins. There was even an elaborate hypothesis, the tetraneucliotide hypothesis, that DNA was just a boring scaffold for the histones that were the real carriers of genetic material. Even after Avery's work, many scientists strongly resisted the idea that nucleic acids, not proteins, were the true genetic material. So there were all kinds of ideas floating around, about how maybe proteins coded back for genes in DNA, or maybe this, maybe that....
      In that context, Crick's message was, "hang it up, guys. The issue is settled. The game is over. The fat lady has sung. Genes are not made of protein, full stop."
      I'm pretty sure that's really all he was trying to say. I think people have so consistently confused the Central Dogma because it's hard even to imagine now just how vague and confusing ideas about genes were at the time. Crick cut to the chase and got people to concentrate on the big challenge of the time, which was working out the genetic code, instead of still trying to prove proteins were providing some kind of genetic material.
      Dissing Crick because he didn't foresee protein reverse engineering is like dissing the guy who increased speed of transport by inventing the horse collar because he didn't invent the 747.

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    8. I'm not dissing Crick, respect to Crick. If there's a problem, it is more with modern day defenders of the central dogma, who refuse to acknowledge that there could be anthing wrong with it. The fact is that these days, detailed sequence information can flow from protein to DNA, RNA and protein in the way that the central dogma prohibits. Genetic engineering probably wasn't on Crick's mind back when he wrote his papers, or he might have phrased thing differently. These days we know about genetic engineering, and I think that we need to acknowledge that certain information transfer dogmas from a byegone era are now out-of-date.

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    9. Tim Tyler,

      The fact that we can genetically engineer sequence information does not really violate the Central Dogma, except insofar as we systematically use such technologies to alter the evolutionary trajectories of a species. I suppose this is possible. The modern day defenders of the Central Dogma correctly point out that there is no naturally occurring (i.e., without human intervention) violation of the CD as defined by Crick.

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    10. So far, I haven't seen anyone offer much of a defense - advocates just seem to ignore the whole issue. It's true that violations are currently rare and confined to interventions by humans. I wouldn't say that humans are "unnatural", though - that would be an unscientific definition of "nature": humans are an unusual species, but not one divided from the rest of nature.

      Unfortunately, the central dogma is quite "dogmatic". It says information cannot flow in ways that it clearly can. The moral of the story seems to be that it's best to avoid making proclamations about how information cannot flow without being very careful with your conditions and caveats. Crick could easily have avoided this whole issue with a bit more foresight.

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  5. I have a web page of Rants and Diatribes on my departmental machine. It is a constant struggle of evolutionary biologists to fight all the people who want to rename the evolutionary synthesis. Here is what I say about it there:


    Rant #5: The Modern Synthesis has not been replaced. Sure, all sorts of new phenomena have come along since the 1940s: neutral mutation, lateral gene transfer, symbiosis, evo-devo, epigenetics, etc. And we could declare the death of the current Synthesis each time one came along. But here's why we shouldn't do that:

    1. Otherwise every time John Blotz pointed out a new phenomenon he could strut around publicizing the fact that he, the great Blotz, had invalidated the evolutionary synthesis, and now we had (ta-da!) the Blotzian Synthesis. But he would be shocked a year or two later when Jane Schmerz came along and invalidated the Blotzian Synthesis in favor of the new Schmerzian Synthesis. And so it would go, synthesis after synthesis, until everyone was totally confused, and most people were several syntheses behind.

    2. Meanwhile the public would be continually told that all that stuff they learned in secondary school, about mutation and natural selection and some other evolutionary forces, was all wrong, because now we had the Blotzian (er, oops, actually the Schmerzian) Synthesis instead.

    It would be (temporarily) great for Blotz's and Schmerz's careers and egos, but a disaster for everyone else.


    We may expect Blotz and Schmerz, and maybe Larry too, to be featured in Pigliucci and Müller's book.

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    1. Oops, link to Rants and Diatribes just goes back to this post. here is a working link.

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    2. If you put a label on your particular version of evolutionary theory then it has to mean something. It has to distinguish your concept of how evolution works from other concepts. That's what evolutionary biologists did in the 1940's and 1950's when they came up with the Modern Synthesis version of evolutionary theory.

      They deliberately excluded certain mechanisms and deliberately emphasized others. The modern view of evolutionary theory is quite diifferent from the one promoted by Ernst Mayr and others back then. It makes sense to refer to it as "modern evolutionary theory" but it makes no sense to refer to it as the "Modern Synthesis" since that version of evolutionary theory meant something very different in the past.

      I agree with Gould that the Modern Synthesis is effectively dead. It died in the 1970s. That's why it's so bizarre to see modern evolutionary biologists trying to resurect it so they can "extend" it.

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    3. You don't agree with Gould, because Gould did not in fact state that the Modern Synthesis was effectively dead. He worte a response to Mayr and Mayr had put forward this view:
      The proponents of the synthetic theory maintain that all evolution is due to the accumulation of small genetic changes, guided by natural selection, and that transspecific evolution is nothing but an extrapolation and magnification of the events that take place within populations and species. (Mayr.E. 1963, "Animal Species and Evolution", Cambridge: Belknap Press of Harvard University Press.). The quote from Gould is
      [..]if Mayr's characterization of the synthetic theory is accurate, then that theory, as a general proposition, is effectively dead[..] (Gould, SJ. "Is a new and general theory of evolution emerging?" Paleobiology 6: 119-130.)
      So Gould is arguing against the specific points made by Mayr. It's worth noting that Mayrs claim itself is somewhat suspect, because quite a few of the scientists we include in the Synthesis held views that did not agree with at least some part of his characterization (Wrights shifting balance, Simpsons views on quantum evolution to give two examples). Mayr quite regularly employed this as a rethorical device: State his own opinion on some matter, then declare it central to the Synthesis (see his advocacy for evolutionary classification over both phenetics and phylogenetic systematics - try to find an argument in there that does not boil down to "I'm Ernst Mayr and I'm right because I was part of the Synthesis and Hennig wasn't", which becomes even more ridiculous when you consider that Hennigs views were first made popular by Dobzhansky).
      Also note Goulds discussion of his quote in the Structure:
      [..]I do not claim that the synthetic theory of evolution is wrong, or headed for complete oblivion in the ashheap of history

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    4. There is abundant evidence that Mayr's characterization of the Modern Synthesis was correct. That's what a majority of evolutionary biologists believed. (However, I do agree with your general characterization of Mayr. He just happened to be correct on this one.)

      See: Is the "Modern Synthesis" effectively dead?

      A substantial minority of biologists still act as if they believe that all evolution is due to random mutation guided by natural selection. And a majority still believe that macroevolution is just lots and lots of natural selection on individual traits.

      Simon, you are nitpicking again. If you think that the Modern Synthesis included Neutral Theory and a major role for random genetic drift, especially in molecular evolution, then please provide documentation from leading evolutionary biologists in the 1960s.

      You might want to consult ...

      King, J. L., and Jukes, T. H. (1969) Non-darwinian evolution: Most evolutionary change in proteins may be due to neutral mutations and genetic drift. Science, 164:788-798. doi: PDF

      They are attacking the prevailing view of evolution in the 1960s. I suspect they had a better understanding of that prevailing view in 1969 than you do in 2016.

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    5. That's what a majority of evolutionary biologists believed.
      Irrelevant. The question here is whether it is what the architects of the modern synthesis believed, because if you want to understand what the view of synthesis was, there are readily available primary sources. I don't need to look at Mayr to tell me what Wrights position was on anything, because Wright did produce quite a body of work in which he clearly states his view.

      If you think that the Modern Synthesis included Neutral Theory and a major role for random genetic drift, especially in molecular evolution

      This is so bloody anachronistic it blows my mind. The modern synthesis laid the foundation for neutral theory though. The Fisher-Wright model for allele changes under selection and drift is still as central to understanding this process as it ever was. In the early 60s Kimura used mathematical tools that weren't available to Fisher, Wright and Haldane when they developed the theory to produce an approximation that gave clear results for cases which were previously intractable, because they were to computationally heavy. But Kimuras model is simply a continuous approximation of the discrete Fisher-Wright process. But it tells us what the FWP would tell us about fixation probabilities, substitution rates and the expected amount of polymorphic loci in a population. It's worth noting that Kimura was inspired by Wrights papers to go into population genetics and when he went to graduate at the University of Wisconsin, Wright coincidentally also moved there. Before Kimura submitted his manuscript for his hallmark 1968 paper to Nature (published prior to King and Jukes, Kimura arrived at the same result independently) he sent a copy to Wright and Wright replied:
      I agree with your "main thesis that neutral or nearly neutral mutations are occurring at a very high rate and that random drift, due to finite population numbers, is extremely important in forming the genetic structure of biologic populations".

      By the time the data on which Kimura based his paper became available Haldane and Fisher had both died already. Stebbins thought that the evidence Kimura and later King and Jukes presented wasn't conclusive (but he did not think there was good enough evidence against neutral theory either - his view can be summed up as "further research is needed"). Mayr and Dobzhansky were openly hostile towards it - Mayr because it was based on mathematics, Dobzhansky because he had been in an argument with Kimura over classical vs. balance selection for a decade (it's worth noting here with a nod to the other blogpost that Lewontin took the same view as Dobzhansky and by the time he cowrote the spandrels paper had come so far as to view neutral theory as at least worth discussing - but that's a decade after it had been formulated).

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    6. They are attacking the prevailing view of evolution in the 1960s

      Here's my problem with this. The synthesis was pretty much done by the end of WWII. Huxley coined the term in 1944 and only Stebbins published his "big book" after that. Joe puts the end in the 1940s as well in his post above. When I think of the synthesis, I think primarily of the mathematical treatments of population genetics by Wright, Fisher and Haldane. Between them and the 1960s you have the second generation synthesis starting with Dobzhansky (who at least understood the mathematical underpinnings) and the people who epitomize the dictum that every formula reduces readership by half. It's well worth re-reading Haldanes defense of bean-bag genetics. And after that you had people that were resurrecting Weismann, like Williams and Maynard-Smith (whose "The theory of evolution" starts with a chapter on adaptation, which is supplemented by the following chapter on selection, followed by Heridity and then a Chapter on Weismann - Dawkins cites this as the first book in which he was informed of evolution). And of course they understood the maths - but anything intended for a broader audience would go to verbal arguments with drift pretty much omitted. I think there's a general problem in that drift can not be adequately explained without putting down at least some equations. There never has been - and I doubt there ever will be - a popular science book that gets drift right. And even textbooks, unless they are specifically aimed at students in a math-intensive population genetics course will usually be horrible.

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    7. There never has been - and I doubt there ever will be - a popular science book that gets drift right.

      With some trepidation, I ask as a layperson whose understanding or lack of same comes from "popular science:" What is so difficult about understanding that sampling in the real world is imperfect?

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    8. This is so bloody anachronistic it blows my mind.

      We are discussing whether the standard view of the Modern Synthesis back in the 1960s is the same as the current view of evolutionary theory. The proponents of the extended synthesis are attacking the Modern Synthesis as though it were the prevailing theory today. That's the theory they want to extend by incorporating niche construction, plasticity, epigenetics, evo-devo, etc.

      You are arguing that it is because a few of the founders of the Modern Synthesis knew about random genetic drift. I am arguing that the Modern Synthesis isn't modern isn't because ...

      1. those few founders vastly underestimated the role of random genetic drift

      2. most of the other proponents of the Modern Synthesis ignored drift, they were strong adapatationists

      3. the fundamentals of Neutral Theory were developed after the Modern Synthesis.

      There's nothing anachronistic about my claim. You, on the other hand, are projecting the modern view of evolutionary theory onto biologists who knew nothing about it.

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    9. Dick Lewontin actually was more friendly to neutral theory than noted above. In his famous 1966 paper with Jack Hubby he wrote the section on possible explanations for the high level of electrophoretic polymorphism (at least, it sounds like him and reflects grasp of the population-genetic theory and his broad knowledge of evolutionary biology). In it he lists several possibilities, one of which was neutral mutation. This is really the first presentation of neutral theory for polymorphism; it does not discuss divergence between proteins of different species. It is 2 years before Kimura's 1968 paper and 3 years before King and Jukes's paper. However Lewontin does not commit himself to neutrality as the explanation so he didn't get the credit for advocating neutrality. But his extremely clear and cogent discussion was undoubtably influential in allowing readers to understand the effect of neutrality.

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    10. @Joe: By the time Kimura as well as King and Jukes had published he did think neutral theory was empirically vacuous. The main thing to note there is that Lewontin did not see the fundamental question as "what is the relative importance of drift vs selection", but "is selection generally acting to remove heterozygosity via fixation or is it generally acting to preserve heterozygosity through overdominance". Kimura had maintained that overdominance played a relatively minor role during the 60s and the epirical conclusion from this would be that there should be little polymorphism. So when there was evidence for more polymorphism than one would expect and neutral theory was proposed, Lewontin thought this to be ad hoc to save a hypothesis that had failed in its main prediction. I think this position was absolutely justifiable at the time and he abandoned it when there were results that neutral theory could explain that the balance view could not.

      @Laurence: We are discussing whether the standard view of the Modern Synthesis back in the 1960s is the same as the current view of evolutionary theory.

      No, we're not. At least I haven't. In Joes post that opened this subdiscussion he ends the Synthesis in the 1940s. I agree with that view and think it is anachronistic to project the views of biologists in the 1960s back on biologists in the 1930s and 1940s.

      On your 3 points:
      1. Can you elaborate on this? It's worth noting that neutral theory is the neutral theory of molecular evolution. Can you give examples on estimates of the role of drift in molecular evolution in the 1940s? Again, my charge is anachronism. Your claim is akin to saying that Newton underestimated the half-life of 232U. He didn't. He didn't estimate the half-life of 232U at all, because he was completely unaware of radioactive decay. Moreover nothing in Newtonian mechanics is in any way tied to the half-life of 232U.

      2. This is just plain false. Nothing in the modern synthesis makes sense without drift and the founders of the synthesis understood that just fine. The number of offspring an individual produces is a random variable and its fitness is the expected value of that variable. If reproduction was deterministic and thus the RVs were dirac-distributed, you could not have small differentials in fitness. Throw out drift and you have saltationism.

      3. What are the fundamentals of Neutral Theory in your opinion. Both Fisher and Wright derived results for the propagation of neutral alleles. That in a diploid population the probability of fixation for a novel allele was 1/2N (and for haploids 1/N) was well known at the time.

      @Judmark: The key issue is that just saying drift is sampling error doesn't tell you a lot about what effects it has. Trying to describe this in detail suffers from one key problem: Drift is somewhat of a negative space. There are relatively easy to understand models of evolution under selection and drift. You simplify them further using a law of large number approximation and get something you can easily explain without using any formula. But drift then is the difference between your approximation and the full model and that gets very obtuse very quickly. Imagine having a regular heptagon. Then imagine cutting out a parallelogram from the middle. A heptagon is easy to understand. So is a parallelogram. Now try to describe the shape you get when you take out the parallelogram from the heptagon. Oh, and do so without saying "it's a heptagon with a parallelogram cut out". Drift is population resampling minus a law of large numbers approximation of population resampling.

      Delete
  6. With regard to prions falsifying the Central Dogma, Dan Graur writes:

    "A prion is a protein that can fold in multiple, structurally distinct ways, at least one of which is transmissible to other prion proteins. Does this structural “contagiousness” really contradicts the central dogma. I fear not. Francis Crick defined information in the context of information flow as “the sequence of amino residues in a protein or the sequence of nucleotides in DNA or RNA.” According to this definition, a prion does not transmit protein-to-protein information."

    http://judgestarling.tumblr.com/post/121925270966/dna-makes-rna-makes-protein-is-not-the-central

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  7. Its irrelevant how you call the mechanism that explains evolutionary novelties. Relevant is the fact that we live in exiting times where the black box is being opened successively, and completely different mechanisms are brought to light that direct body development and form. We know that its not just one, but several work in a orchestrated way, and not only genetics, but several other ones are involved. The key is information at various levels.

    Dembski and J.Wells: The design of life, general notes, page 16:

    What Besides DNA Controls Development? If DNA does not control development, what does? Actually, there is good evidence for the involvement of at least two other factors in the developing egg: the cytoskeleton and the membrane. Every animal cell contains a network of microscopic fibers called a cytoskeleton. These fibers include microtubules, which are known to be involved in patterning embryos. For example, one of the gene products involved in head-to-rear patterning of fruit fly embryos is delivered to its proper location by microtubules; if the microtubules are experimentally disrupted, the gene product doesn’t reach its proper destination and the embryo is grossly deformed. Microtubules consist of many identical protein subunits, and each subunit is produced according to a template in the organism’s DNA. What matters in development is the organization of microtubule arrays, and the organization of a microtubule array is not determined by its subunits any more than the layout of a house is determined by its bricks. Instead, microtubule arrays are formed by organelles called centrosomes, which are inherited independently of an organism’s DNA. Centrosomes play a central role in development: a frog egg can be induced to develop into a frog merely by injecting a sperm centrosome—no sperm DNA is needed. Another non-genetic factor involved in development is the membrane pattern of the egg cell.

    Cell membranes are not merely featureless bags, but highly complex structures. For example, a membrane contains specialized channels that pump molecules in and out of the cell, enabling it to control its interactions with the external environment. An egg cell membrane also contains “targets” which ensure that molecules synthesized in the nucleus reach their proper destinations in the embryo. The gene product, which is involved in head-to-rear patterning of fruit fly embryos and which depends on microtubules to deliver it to its proper location, also needs a target molecule to keep it in place after it arrives. The target is already there, embedded in the membrane. Experiments with single-celled animals show that membrane patterns are determined by pre-existing membranes, not by DNA. Like microtubule subunits, the proteins embedded in a membrane are produced according to templates in the organism’s DNA; but like the form and location of microtubule arrays, the patterns of those embedded proteins are inherited independently of the organism’s DNA. So the control exercised by microtubule arrays and membrane patterns over embryonic development is not encoded in DNA sequences. This does not mean that we now understand developmental programs. Far from it! But it is quite clear that they cannot be reduced to genetic programs, written in the language of DNA sequences. It would be more accurate to say that a developmental program is written into the structure of the entire fertilized egg—including its DNA, microtubule arrays, and membrane patterns—in a language of which we are still largely ignorant.

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  8. The work will centre on what has become known as the 'extended evolutionary synthesis' in which the genome does not have privileged control over development and heredity. In addition to genetic influences, the organism plays active, constructive roles in its own development as well as that of its descendants. This imposes directionality in evolution that is not accounted for by natural selection, and allows for multiple routes to the adaptive fit between organisms and environment.

    http://www.st-andrews.ac.uk/news/archive/2016/title,458706,en.php


    Directionality in evolution???

    So that's why the EES Project is not sitting well with the proponents of random, unguided and undirected evolutionary processes like Larry, Coyne, PZ Myers, Dawkins and others...

    Directionality in evolution could implicate supernatural and that is just plainly unacceptable no matter what the evidence will reveal.

    ReplyDelete
    Replies
    1. So if we can show you one example of evolution changing course or backtracking, will you openly concede that there is no supernatural designer?

      Delete
    2. If you can show an instance of several consecutive mutations being reversed, I would suspect some sort of intervention.

      Delete
    3. TOJ,

      I don't believe in directed evolution. I only believe in change within kinds that you often call evolution. However, I am willing to consider any evidence, both scientific and biblical, that there could have been a "directed evolution" within kinds after the flood. My company funded a research into this and both sides came up empty-handed. So, I have no proof either way.

      The change within kinds, that you refer to as evolution, could very well be random, or it could be designed in such a way so that there is only a limited number of changes or limited randomness of changes that are allowed within kinds or that the changes can only happen within the designed setup of limitations. I just don't know but it is possible.

      BTW: To openly concede that there is no supernatural designer, you would have to provide loads of evidence starting with how information and first replicating organism (s) arose out of chaos. Until then, no evolution can happen either Darwinian or modern. If you think that this gap can just be overlooked to support your unfounded religion of atheism, you are wrong. Any attempt to skip this fundamental part out of the many missing parts, and the many more gaps just because of your belief, just ain't gonna happen. However, if you think it can be done, you also have to consider the fact that religious blindness can and has been attributed to both sides of the spectrum just in case you didn't know...

      Delete
    4. Eric,

      What's a kind? How do you tell if two species belong to the same kind or different kinds? And if you can't tell, how do you know if evolution is only within kinds?

      Delete
    5. how information and first replicating organism (s) arose out of chaos

      Well you see, the universe cannot produce anything as complex as a virus or amoeba, so we must therefore believe it produced something infinitely more complex, intelligent and powerful than humans first.

      In other words, if a tornado in a junkyard cannot produce a 747, the only alternative answer is to say it produced New York City instead.

      Follow my/your logic? Didn't think so.

      Delete
    6. Eric,

      "To openly concede that there is no supernatural designer, you would have to provide loads of evidence starting with how information and first replicating organism (s) arose out of chaos."

      No, Eric, that is just an argument from ignorance. Because science cannot explain everything does not mean some supernatural designer did what cannot currently be explained. When people without sufficient knowledge said that the Sun was carried across the sky in a magical chariot driven by a god, they were making the same argument you are here.

      "If you think that this gap can just be overlooked to support your unfounded religion of atheism, you are wrong."

      Stop projecting, Eric. You are the one trying to fill in the gaps with your god, for which you have ZERO evidence. Atheism is not a religion, it is simply the provisional conclusion that there are not gods, based on the complete lack of evidence for them. Not beleiving in gods is no more a religion than not believing ion the Tooth Fairy. Learn and absorb this concept, Eric.

      Delete
    7. When people without sufficient knowledge said that the Sun was carried across the sky in a magical chariot driven by a god, they were making the same argument you are here.

      The critical difference being the lack of sufficient knowledge in the past was due to it not being available in the world, whereas with Eric it's proud resistance to readily available knowledge.

      Delete
    8. Eric spake thus; I don't believe in directed evolution. I only believe in change within kinds that you often call evolution.

      What about a multicellular animal that went back to being something mistakable as an amoeba? Would that be an evolutionary U-turn? Something that a directional supernatural being would be unlikely to do?

      Delete
    9. John Harshman, when you say

      What's a kind? How do you tell if two species belong to the same kind or different kinds? And if you can't tell, how do you know if evolution is only within kinds?

      ... you overlook the obvious: a "kind" is a set of species that has the property that evolution can result in them, from a common ancestor. From this we can conclude that evolution cannot result in organism of different "kinds" from a common ancestor.

      You are obviously blinded by your religious commitment to evolutionism when you fail to see the power of this argument. No one can possibly contradict it.

      Delete
    10. Eric said: However, I am willing to consider any evidence, both scientific and biblical, that there could have been a "directed evolution" within kinds after the flood. My company funded a research into this and both sides came up empty-handed. So, I have no proof either way.

      Wow, someone should inform the shareholders of this company, whatever it is, as to what was done with their investments.

      Delete
    11. Eric,

      "that there could have been a "directed evolution" within kinds after the flood. My company funded a research into this and both sides came up empty-handed."

      There was no world wide flood as described in Genesis, so you were bound to come up empty-handed.

      Delete
    12. Joe, Do you think there can be horizontal transfer between kinds? If not, we have evidence that bacteria and eukaryotes are the same kind.

      Delete
    13. It doesn't matter what Joe and you think. Don't you get it.?You will NOT get a free pass anymore!

      It only matters what you can prove. The BS thinking has ended. It is now the era about what you can prove, I hope.

      You and Joe will have a really hard time with proving your shit, which is expected when you make claims without one piece of shitty evidence.

      Welcome to the new world of science. This world requires evidence and not evolutionary bull-shit.

      Halleluyah!!!

      Delete
    14. Chris B,

      Too bad you don't have any evidence for your claims...

      But, you must have had at least some evidence that proves that life originated on its own. Just give it to me and I will settle it only after only 1 (one) scientific experiment that proves how life has come about on it's own. It must be so easy since the belief is so strong...It seems...

      Delete
    15. Eric, thanks for dropping by. Would you mind answering my questions?: What's a kind? How do you tell if two species belong to the same kind or different kinds? And if you can't tell, how do you know if evolution is only within kinds?

      Delete
    16. Eric,

      "Too bad you don't have any evidence for your claims..."

      You are the one claiming that there was a Noah's flood as described in Genesis. You are the one making ridiculous claims, so you provide the evidence. It's not my job to prove each of your delusional religious fantasies false.

      But for the record, there is no geological or archaeological evidence that the world was destroyed in a massive flood around 6000 years ago. Or any evidence from any other discipline of human knowledge. Eric, when you make truth claims of this nature, there are consequences to what you claim.

      For example, in order for the earth to be flooded to the mountaintops would require a volume of water greater than currently exists on the earth. For that much water to be deposited on the earth's surface over forty days and nights and the attendant energy, any 'ark' floating on the surface would be completely obliterated.

      Noah et al. would have to care for many thousands of multicellular species and all of their food/waste requirements for several months, while they didn't kill or eat each other. What about the plants? They could hardly turn up at the ark on their own, could they? Noah et al. would also have to rescue many of the species' pathogens who could not survive such a time period without killing a host. Why didn't Noah just let these things go extinct and save humanity unfathomable amounts of misery, pain and death? Did he have shelves of petri dishes and suitable media to save them all? Or did god intelligently design all those horrors after the flood to inflict the remnants of humanity with? Noah could have at least left the ticks and Congo floor maggots behind to drown with all the rest of creation, and humans, including unborn babies, infants and children. Which of the eight human ark passengers incubated the human bot flies to repopulate the world with?

      Which brings up another point. Noah's flood claims that the human population was reduced to eight people, three of whom were full male siblings of two of the other eight. I don't recall the Bible mentioning that Mr. and Mrs. Noah had any more children after the flood, so apparently three full sib brothers and one mate each repopulated the earth. No human population genetic and genomic evidence supports such a scenario.

      Noah released his many wards on the flanks of Mount Ararat, to repopulate the world. Absolutely nothing about the distribution of plants and animals on the earth is even remotely consistent with such a scenario. The predators would have killed prey off immediately, dooming both to extinction. If they all went their separate ways and did not start consuming each other until prey population numbers had risen to supportable levels, most predators would have died in the mean time. That's all assuming there was a lush landscape of plants to give herbivores a chance, unlikely after a deluge destroyed all life on the planet.

      I could continue, but why?

      Delete
    17. Eric,

      "But, you must have had at least some evidence that proves that life originated on its own."

      First, this has nothing to do with Noah's flood.

      Second, this is an argument from ignorance/god of the gaps logical fallacy combo, a favorite of ID/creationists and for which you have been schooled many times. Why do you continue to reiterate it as if it were at all relevant?

      "Just give it to me and I will settle it only after only 1 (one) scientific experiment that proves how life has come about on it's own. It must be so easy since the belief is so strong...It seems..."

      Your belief is apparently strong enough and I won't even require you actually physically do it. Just describe to us, Eric, how you will settle it after just one experiment. What experiment on the "origins of life" will disprove all of evolutionary theory?

      Delete
    18. It only matters what you can prove. The BS thinking has ended. It is now the era about what you can prove, I hope.

      You and Joe will have a really hard time with proving your shit, which is expected when you make claims without one piece of shitty evidence.


      Sorry Eric, you lose. The evidence (for example, amino acids in meteorites) shows "organic" (i.e., carbon-based) chemistry that forms complex building blocks of life is relatively common even in the unfriendly vastness of space. There is absolutely nothing precluding the chemistry necessary to originate life that's been found in all the research that's been done over hundreds of years. It all points the other way (toward the formation of life being possible without any special guidance), from the Wohler synthesis onward.

      Your preferred fairy tales, on the other hand, have been shown to be scientifically impossible on multiple grounds, a small handful of which Chris B alluded to.

      Thus on your own criterion (evidence) you're done.

      Thanks for playing, and I hope you enjoy the home version of our game.

      Delete
  9. Larry,

    I'd be interesting to know how Crick came up with his central dogma Was it based on lack of contradictory evidence, or evolutionary considerations, or some thermodynamic first principles? It seems to be that if we ever completely master protein design...say a few centuries hence, we could design some macromolecular complex that could extract information in peptides and convert it to DNA. It wouldnt be easy but it cant be ruled out as impossible

    ReplyDelete
    Replies
    1. You could read the papers Larry linked to above (specifically the Crick 1970 article).

      Delete
  10. Dana,
    Yeah, but I'm at work and cant spare the time- I think it entirely possible I wont find my answer there anyway. Plus asking it publicly would lead to interesting discussion

    ReplyDelete
    Replies
    1. Too busy at work to click on the pdf, but not to read and comment on blogs. Got it.
      You may think you won't find your answer but you're wrong, which is why I specifically directed you to that reference.
      It didn't lead to an interesting discussion.

      Delete
  11. John HarshmanTuesday, May 12, 2015 11:30:00 AM
    I don't think gnomon's problem bears any resemblance to Denton's. His essential contention, as I understand it, is that most pairwise comparisons of protein sequences are saturated, i.e. randomized by multiple hits. And that differences in protein-sequence distances among species arise because more "complex" organisms have reduced numbers of residues free to vary. Thus humans are closer to chimps than orangutans not because a longer time has elapsed since their common ancestor but because chimps and humans are more complex than orangutans and have more invariant residues, thus reducing the maximum possible sequence difference at saturation. Which is crazy, but a different crazy from what you think."

    I just got a chance to respond to this comment of yours from sometime ago on another thread. I must say it is quite a relief to see you have got my point very well simply by reading my papers. The vast majority simply cannot due to lack of expertise on the topic.

    However, that you found the point crazy is puzzling to me. That human is the most complex and tolerates the least amount of randomness within its body, i.e., having the lowest amount of genetic errors or genetic diversity, is just objective observational fact. That chimp is in turn more complex or has more reasoning power than orangutan is also a fact(ref below). These facts also makes sense. How is acknowledging the plain obvious crazy? How is paying a price for rise in complexity less sensible than getting it for free?

    Sequence identity could mean at least two things: time since common ancestor and shared building parts. The field has ignored or neglected to consider the second point. Bacteria within species seq divergence could be as high as 30% whereas human 0.1%. This is because human can only be built by more precise parts. Any more divergence than that would only make human sick.

    E. Herrmann, et al., Humans have evolved specialized skills of social cognition: the cultural intelligence hypothesis, Science 317 (2007) 1360–1366.

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    Replies
    1. Abstract

      Humans have many cognitive skills not possessed by their nearest primate relatives. The cultural intelligence hypothesis argues that this is mainly due to a species-specific set of social-cognitive skills, emerging early in ontogeny, for participating and exchanging knowledge in cultural groups. We tested this hypothesis by giving a comprehensive battery of cognitive tests to large numbers of two of humans' closest primate relatives, chimpanzees and orangutans, as well as to 2.5-year-old human children before literacy and schooling. Supporting the cultural intelligence hypothesis and contradicting the hypothesis that humans simply have more “general intelligence,” we found that the children and chimpanzees had very similar cognitive skills for dealing with the physical world but that the children had more sophisticated cognitive skills than either of the ape species for dealing with the social world.

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    2. However, that you found the point crazy is puzzling to me.

      Shouldn't be. It's crazy. You're forcing the data to fit a preconceived conclusion. I suppose you think chimps and humans are just a little bit more complex than gorillas, which are a bit more complex than orangutans, which are a bit more complex than gibbons. But if you look at the data from another direction with the same reasoning, you come to the conclusion that gibbons and siamangs are more complex than great apes. You can start the genetic similarity chain at any point on the tree and decide that any species is the complexity champion, based on the sort of data you use.

      In short, you are a crank.

      Delete
    3. Let’s follow your logic through. Suppose bacteria are the most complex, yeasts a bit less, worms a bit further less, etc. Based on my rule that the distance between low and high complexity species is purely determined by the low one, one would get that worm is equidistant to bacteria and yeast. But the fact is worm is closer to yeast. Or as in your examples, if gibbon is the most complex, with orang less and human further less, then human would be equidistant to gibbon and orang. But the fact is that human is closer to orang than to gibbon whereas gibbon is equidistant to human and orang, suggesting gibbon is the least complex of the three, which happens to fit with all data known.
      So, I am afraid that your reasoning, if I understand it correctly, is not true. Sorry.

      Delete
    4. Your own logic doesn't work with your own example. It all depends on picking particular species and ignoring the rest. Try doing it with all the species of gibbons, humans, and a monkey. You will find that one species of gibbon is the most complex, followed by various other gibbon species, then human, then monkey. This only works if the tree you pick is what the literature calls a ladder.

      Delete
    5. Not so. Certainly, the closest to a particular gibbon species would be another gibbon that happens to diverge most recently, where distance between them has yet to reach saturation. However, the distance between two most diverged (based on anatomy or fossil data etc) gibbons would represent the saturated distance, and that distance is equal to that between either one of them with human. Same logic and same fact, you would see distance between fission and fusion yeasts to be the same as either with human.

      One has to acknowledge the coexistence of both linear and maximum distance. It seems that you are not separating the two. It is very easy to do. Just count the number of hotspots or saturated sites or overlapped mutant sites.

      Delete
    6. The MGD of a species (human species has 6 billion individuals) is equal to the distance between two most diverged individual. The MGD of a kind or type of organisms with multiple species (monkey has ~300 species) is equal to the distance between two most diverged species.

      Delete
    7. Insights into the dN/dS ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity

      A newly published paper confirming the MGD theory by another group. Three of their highlights:
      Highlights

      Brain-specific genes (BSGs) show lower dN/dS ratio than widely expressed genes (WEGs) in different species.

      Difference between dN/dS ratio of BSGs and WEGs increases as the complexity of the compared pair decreases.

      This difference in dN/dS ratio of BSGs and WEGs among diverse species supports the MGD theory over the universal molecular clock hypothesis.

      Delete
    8. gnomon: "However, that you found the point crazy is puzzling to me. That human is the most complex and tolerates the least amount of randomness within its body, i.e., having the lowest amount of genetic errors or genetic diversity, is just objective observational fact. That chimp is in turn more complex or has more reasoning power than orangutan is also a fact(ref below). These facts also makes sense. How is acknowledging the plain obvious crazy? How is paying a price for rise in complexity less sensible than getting it for free?"

      Could you clarify what the universal metric of "complexity" is, such that humans are objectively at the apex as you assert? You seem to be alluding to some aspect of neural function in the above paragraph, but why not things like metabolic pathways or substrate utilization, or cell type number, or any other measure that varies in the number of components between species (which begs the question of whether or not the number of parts is relevant to an assessment of "complexity")?

      Delete
    9. where distance between them has yet to reach saturation

      ?

      Delete
    10. There is no universal molecular clock hypothesis, and the MGD theory is not the preferred alternative. Unfortunately I can't break through the Elsevier paywall to see anything other than the abstract. But how did the authors of that paper measure the complexity of the compared pair? Sorry, but a difference in dN/dS doesn't tell you that changes are saturated; it may tell you there have been multiple hits (but not necessarily to saturation) at synonymous or non-synonymous sites in some taxa, it may tell you that there has been positive or purifying selection at synonymous or non-synonymous sites in some taxa.

      You appeal to different phenomena to explain the same patterns of genetic distance whenever it suits you. Results that don't fit your model are due to divergence, results that do are due to saturation. And yet there's no objective difference.

      Delete
    11. at the cellular phenotype level, complexity can be measured by the number of cell types, especially neuronal cell types, which is similar to the number of epigenetic programs or ways of using DNA.
      at the lowest building parts or DNA level, it can be measured by the precision of the parts or MGD.
      These are my working definitions. I have not seen anything better.
      at the common sense level, complexity also has two measures, the architectural map and the precision of building parts.

      Delete
    12. Those aren't working definitions; they're Rorschach blots. You can get whatever cellular complexity you want by dividing cell types finer and finer. How many more cell types do humans have than rats do, and how did you count it? As for "precision of the parts", you seem to be assuming what you want to show; no, you can't measure complexity by pointing to the result you think is correlated with complexity.

      Delete
    13. John, If there is no universal clock (I am glad to see you acknowledging that), how do you explain the fact that the distance between fission and fusion yeasts is similar to that between either and human?

      Delete
    14. We can in most cases use common sense to make a pretty good judgement of complexity. There are things in Nature that you can not precisely measure but you know it when you see it. Things like beauty etc. My measurement may not be perfect but it works or solves puzzles like the question about yeast above. It is way better or scientific than simply ignoring the complexity issue as if it does not exist or does not need to be taken account for by evolutionary theory.

      Delete
    15. No reply is really necessary, now that you have compared your measure of complexity to beauty; that's just an admission that complexity, like beauty, is subjective and personal.

      Delete
    16. Someone please tell me that gnomon isn't being paid by some university for writing crap like this.

      Delete
    17. John Harshman,

      In this paper:
      Insights into the dN/dS ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity

      the assumed increasing order of complexity is:

      mouse ~= rat < orang < chimpanzee < human

      There is no specific method given for determining this, in fact 'complexity' does not even appear in the Methods section.

      Delete
    18. Why don't all say that you don't like the scientific evidence presented by Gnomon? I think that I know what the problem is...

      I don't like the science that does one thing and then is forces many scientists to interpret the findings of their experiments in the acceptable way to the Darwinian-bully-"scientists".

      What kind of science is that? If you, as a scientist, can't publish the actual results of your experiments if they are not in line with the bullies from the Darwinian religion? Is this really science?

      Some people may think it is, actually...

      Delete
    19. Chris,

      Thanks. How do people manage to publish such shoddy work? Don't answer that.

      Hey, look, Gnomon has a groupie.

      Delete
    20. Eric,

      Explain hoe Gnomon's interpretation is a problem for evolutionary theory.

      In scientific terms, please, not according to your victimhood fantasies/pathologies where there exist "Darwinian bullies".

      BTW, how's that defense of Noah's flood as historical fact coming along?

      Delete
    21. Axioms are subjective and human specific. Therefore all mathematics and physics are subjective but they work in describing nature, much more precise than those soft sciences claiming to have more objective assumptions.

      Delete
    22. If one can publish papers with the assumption that complexity does not matter or exist, why cannot someone else publish with the opposite assumption? If neither has hard evidence, one at least is consistent with common sense. And common sense is the foundation of hard sciences.

      Delete
    23. Therefore all mathematics and physics are subjective but they work in describing nature, much more precise than those soft sciences claiming to have more objective assumptions.

      Good thing then that the biochemistry we are talking about is based in quantum physics. Biochemistry, like all chemistry, has to do with orbital electrons and energy states, which are governed by quantum physics.

      As for evolution, there is plenty of mathematics there. I'm sure you know all about the pertinent population genetics equations, right?

      Delete
    24. Why don't all say that you don't like the scientific evidence presented by Gnomon?

      We may, if he gives us the chance by presenting any.

      Delete
    25. gnomon,

      "And common sense is the foundation of hard sciences."

      I have to disagree with you here. Science is designed to safeguard against the easy, seductive false knowledge of common sense. Common sense suggests hypotheses (which I learned in grade school as "educated guesses"). These educated guesses are then evaluated in well-controlled empirical experiments, where they are objectively tested.

      Countless declarations of 'common sense' have been proven wrong by empirical testing.

      Delete
    26. first, all truths are common senses although the reverse is not necessarily true.
      second, common senses may have at least two types, one is self evident by logic with its opposite position being obviously absurd. all truth and axioms are of this type. the other is really just common observations whose opposite may not be absurd. earth is flat. but its opposite, earth is round, also makes sense or can explain the apparent flatness that one observes.

      The whole thing of science is nothing more than a refinement of everyday thinking.
      -Albert Einstein

      Even for the physicist the description in plain language will be the criterion of the degree of understanding that has been reached.
      -Werner Heisenberg

      Delete
    27. Honey, can you get some milk when you do the shopping? - Albert Einstein

      Hmm what?? Oh yes, I'll put the garbage out in a minute, just need to finish this nice quote - Werner Heisenberg

      Regardless how much I bend the truth to fit my own religious believes, my failed attempts at logic still shine through - gnomon

      Delete
    28. Sure, things getting heavier and shorter as they move faster, and stuff like quantum entanglement and collapse of wave functions under measurement or observation are intuitively obvious, right?

      Delete
    29. I knew when I said all laws of nature are axioms or self evident intuitions, someone will always bring up quantum mechanics. But I have a ready answer for them. No one really understands quantum mechanics and it is too dearly to tell. It is too close to the God question.

      I think I can safely say that nobody understands quantum mechanics. ~ Richard Feynman

      Quantum mechanics, that mysterious, confusing discipline, which none of us really understands but which we know how to use. It works perfectly, as far as we can tell, in describing physical reality, but it is a ‘counter-intuitive discipline’, as social scientists would say. Quantum mechanics is not a theory, but rather a framework, within which we believe any correct theory must fit.
      Murray Gell-Mann,

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    30. John:



      'Beauty is truth, truth beauty,' - that is all ye know on earth, and all ye need to know.' John Keats

      Truth is in a way like beauty also subjective. The vast majority of people consider a truth objectively true not because they can see it for themselves but because a small circle of experts, sometimes just 1 or 2 person, have said so. Also, few can appreciate a law the way the inventor of the law did. So, does this subjective nature of truth or beauty makes truth or beauty non real in this world?

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    31. Chris B:
      "In this paper:Insights into the dN/dS ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity

      the assumed increasing order of complexity is:

      mouse ~= rat < orang < chimpanzee < human

      There is no specific method given for determining this, in fact 'complexity' does not even appear in the Methods section."

      Okay. Let's grant you that we don't have evidence for mouse < human (in fact we do, by measurable MGD). but so what? Why cannot I just say so or assume so? After all, millions of papers got published in the past 100 years assuming human = mouse = bacteria. have they described methods and results for saying or assuming so?

      In the final analysis, what works counts! The results presented in this paper, as well as the genetic equidistance phenomenon and the century old riddle of what determines genetic diversity, simply have no explanation unless you grant the obvious that mouse or bacteria have lower complexity than human. Do you prefer to have no answer to mystery? Then stay away from science!

      So, perhaps someone is purposely making a point by not describing in the paper the methods/results on measuring complexity even if they could do it. No one ever did and no one ever made a noise.

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    32. it is too early to tell. It is too close to the God question.

      Yes, after all, it has only been around 116 years, and confirmed by more experiments than any other scientific theory, so we clearly don't know enough about it and must fall back on some imaginary deity.

      :rolleyes:

      No, I don't think we must, Gnomon. I think it is people whose imaginations are too small to be scientists and who hold to some crank theory of their own against all the weight of the evidence, who think this.

      Delete
  12. Well, how about that...

    There can be occasion when John and I actually agree on something!

    ReplyDelete