Wednesday, May 10, 2017

Debating philosophers: Pierrick Bourrat responds to my criticism of his paper

I recently criticized a paper by Lu and Bourrat on the extended evolutionary synthesis [Debating philosophers: The Lu and Bourrat paper]. Pierrick Bourrat responds in this guest post.


by Pierrick Bourrat
Research Fellow, Department of Philosophy
Macquarie University
Sydney, Australia

Both Qiaoying Lu and I are grateful to Professor Moran for the copious attention he has bestowed on our paper. We are early career researchers and didn’t expect our paper to receive so much attention from a senior academic in a public forum. Moran claims that our work is out of touch with science (and more generally works in philosophy of biology), that the paper is weakly argued and that some of what we write is false. But in the end, he puts forward a similar position to ours.

Before delving into the substance, I would like to make some general comments, starting first with the claim that philosophers are out of touch with science. Once upon a time, some areas of philosophy had limited contact with science. But philosophy of science, a special sub-field of philosophy, has always had some engagement. These days, especially in philosophy of biology, the norm is to be very engaged. Both of us (authors of the paper) have biology degrees (evolutionary biology in my case) as well as philosophy ones, and we make a considerable effort to be in touch with issues in evolutionary biology, specifically evolutionary theory and models. Theory and philosophy are not that far apart, when one thinks about it a bit. We think it must be the case that Moran likes only some interpretations of evolutionary biology, and that his objections to us are based on how well we do or don’t fit these favourite interpretations. Moran likes non-adaptive evolutionary theory, and especially Michael Lynch’s promotion of it. We do too. It is great to see such blanket endorsement of non-adaptive evolution, and perhaps another time we’ll find an evolutionary topic that requires us to address it in detail (rather than the small mentions we made of it in the current paper).

In his second post, Moran reproaches us for talking about three extensions of the modern synthesis that aren’t significant in comparison to the modifications of evolutionary theory coming from neutral theory and the increased emphasis on genetic drift. We only took the term “modern synthesis” to be one way to characterise some core principles that people tend to agree with. It would be naïve not to recognize that from one evolutionary biologist or school of thought to another there will be some variation in what they mean by “modern synthesis”. Following Gould, Moran thinks the Modern Synthesis is dead. It is one way to interpret what happened in evolutionary theory over the last sixty years or so. Nevertheless, whether some features of current evolutionary theory should be regarded as extensions of the Modern Synthesis or as parts of a different theoretical apparatus is a mere semantic point. What matters is to be clear about what one means.

But the problem with Moran’s criticism is that neutral theory and the increased emphasis on genetic drift are aspects of evolutionary theory that are quite distinct from the main topic of our paper. The core aim of our paper addresses issues surrounding epigenetic inheritance, rather than which aspect(s) of the modern synthesis have been the most challenged by recent theoretical developments and empirical discoveries.

In his third post, Moran claims that we confuse the terms “allele” and “gene”. I recognize that in some parts of the manuscript we could have been more careful and used “allele” instead of “gene”. That said, Moran doesn’t notice that we define the terms “epigene” and “epiallele” precisely in order to avoid the analogous confusion between “allele” and “gene”. It is also fair to note that the confusion between “gene” and “allele” is encountered in various places, including evolutionary biology textbooks. For instance, Moran uses a slide from Pearson Education in which one can read “[t]hree major factors alter allele frequencies […] gene flows” (my emphasis). Note also that Futuyma, in his textbook extensively quoted by Moran, uses the expression “gene flows”. Following Moran’s own point (with which I largely agree), it would be more appropriate to use “allele flows” instead of “gene flows”. Many other textbooks (e.g., Ridley’s Evolution) do not consistently make the distinction between “gene” and “allele” when referring to changes in frequency. Thus, at best, Moran’s point is minor and could be equally attributed to biologists (including some theorists) in addition to philosophers.

In the fourth post Moran accuses us of equating natural selection with evolutionary change. Moran regards our definition of the evolutionary gene as problematic because it “only recognizes genes that cause a difference in phenotype and that such differences are subject to selection” and that we don’t “seem to be aware of neutral or nearly-neutral alleles whose frequency is strongly influenced by random genetic drift”. It is actually not the case that we regard phenotypic differences as necessarily due to selection. We mention trait variation, which is different from selection. We even wrote elsewhere in our article that “our focus here is the concept of the gene, rather than gene selectionism.” The important point here is that we define the phenotype of a gene as “everything [it] makes a difference to when compared to another evolutionary gene.” A difference in phenotype can be a difference in DNA sequence with no other observable difference. For an example of this use see the chapter 6 of Sean Rice’s 2004 book Evolutionary Theory. Thus, the claim that our definition is incompatible with neutral evolution is incorrect.

The second point Moran makes in this fourth post is basically the same as the one he makes in the previous one, namely that we should have used “allele” instead of “gene”. Yes, perhaps David Haig using the term “strategist gene” should have used the term “strategist allele” and perhaps making the distinction would make clearer the point that the two concepts are different. But this is for the great part a semantic point, not a conceptual one. I also note that David Haig and George Williams, on whom we relied for our definition, are acclaimed evolutionary biologists.

Moran’s fifth post is making yet another semantic point. He claims that our definition of the molecular gene is wrong and should be substituted with his definition. The two definitions are very similar, with one emphasizing what a gene typically is, while the second aims for generality, something Moran does not acknowledge. In fact, we clearly write that our definition (which we owe to Griffiths and Stotz) is a stereotyped one. Like any stereotype, it will have exceptions, and in particular contexts it will not be applicable. Rather Moran concludes: “[t]he Griffiths and Stotz definition is wrong because it excludes all DNA sequences that lack an open reading frame and this means that tRNA genes aren't genes by their definition”. At the same time, like us, he recognizes that there is no consensus on the definition of the molecular gene.

In the sixth post, Moran finally presents our main thesis about epigenetic inheritance and whether it can be accommodated within current evolutionary theory. Moran concludes: “it's safe to say that most experts in evolutionary biology do not see epigenetics as a threat to current evolutionary theory, with its heavy emphasis on population genetics, and they do not see any need to shift paradigms”. Clearly, therefore, his conclusion does not contradict in any way what we argue in our paper. Accommodation is our point.

Overall, we are delighted that Moran agrees with us that contemporary evolutionary theory can accommodate heritable epigenetic change, and grateful he took so very much time to echo the exact point of our paper.


49 comments :

  1. Semantics is the study of meaning and that's a very important part of philosophical argument. I taught with two different philosophers and both of the emphasized the importance of precision when it comes to definitions.

    I suspect that Pierrick is using the word in its more pejorative sense to mean "trivial."

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    1. Here's what Lu and Bourrat write in the abstract of their paper.

      We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate.

      I agree that a thorough discussion of the meaning of the word "gene" would be an interesting topic for a paper in the philosophy of biology. That's why I criticized their paper.

      Similarly when Pierret Bourat says above that ...

      Nevertheless, whether some features of current evolutionary theory should be regarded as extensions of the Modern Synthesis or as parts of a different theoretical apparatus is a mere semantic point. What matters is to be clear about what one means.

      I think it's really important to have a thorough discussion about the meaning of the term "Modern Synthesis" and what exactly the proponents of EES are attacking. The title of the Lu and Bourrat paper refers to the "Extended Evolutionary Synthesis" so I assume they agree that interpretations of evolutionary theory are important.

      I don't understand why Pierret says this is "merely semantics,"

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    2. RE: How to differentiate ”Semantic” (rhetoric) vs “Scientific” (empiricist) philosophy debates and defences!?

      Preamble: Since I have proclaimed in this series of “Debating philosophers” before, that RE: There can be no debates but withdrawal of the flawed Evolutionary Theory in Biology of the 20th century past!?; I shall now further present more argumentations that I think which are relevant to the LAM’s brief response above on “semantic” rhetoric point.

      Obviously, the LAM serial criticisms of the Lu and Bourrat paper have been under close scrutiny and rebutted vigorously by one of the defendant (aka neo-darwinist) philosophers (Pierrick Bourrat), with whom LAM must have communications, while articulating their many a philoscientific issues on the evolutionary theory in biology expressed, in and by, the varied points and counterpoints (debates and defences) as referenced above.

      Accordingly, with the currency of our mutual 21st-century multiplinary readings, understandings, definitions, and standards in and of the philoscientific literature in biology, I shall now try to quote and refute the 5 key neo-Darwinism-biased fallacies or defences, that Bourrat has had made in the above “semantic” vs “scientific” philosophies debates and defences, as follows:

      1) "Theory and philosophy are not that far apart, when one thinks about it a bit." -- On the contrary, I thought this statement may be true only if, it is specifically applied in those non-life physical sciences, such as physics, physical laws, mathematics, or even chemistry as well as “physicalist, reductionist philosophy” (or neo-Darwinism). Whereas it would be absolutely detrimental, if it is casually applied to any living subjects in biology (ot behaviourism). This is because all living entities (or organisms) and their behaviors -- which are unlike non-life matters -- can only be sustained or subscribed to their own life-dynamisms, including life multidisciplinary systems, and inquiries, in and by their own multidimensional systems of biological empiricism, physiology, empiricist theory, and/or philosophy, etc, namely the physicalist theoretical ideas in quantum computers may not be equated to the empiricist life-theory or philosophy of organic cells.

      Consequently, many a physicalist methods that doesn’t bring-up, concern, and/or sustain life-viability or vitalism issues in the purely reductionist theoretical processes will not suffice; and that all purely physicalist theories or philosophies will also not enable any hard-headed, neo-darwinist philosophers so as to appreciate and comprehend the whole process of life-viability or vitality inquiry issues, including the many an evolutionary dynamisms of biomolecular composites or cellular component bits and parts, and their inactive and connected network within their dynamic operating milieu and/or the organism’s real world environments, or ecology, etc. Thus, any biological theory or philosophy in biology must concern itself with the empiricist witness and awareness of being able to predict, attain, and sustain the proofs of life-viability in biologist philosophy or physiology, etc; and not merely by applying the physicalist, reductionist, or evolutionist theory or philosophy alone in biology as well as developmental genetics and embryology!?

      -- [To be continued below] --

      Delete
    3. -- [Continued from above] -- RE: How to differentiate ”Semantic” (rhetoric) vs “Scientific” (empiricist) philosophy debates and defences!?

      Although the gene-centric evolutionary theory (gcET) -- which doesn’t even represent or consider any gene being viably motivated or sustained in its real component or nutrient milieu -- has had only been pursued rhetorically (but not physiologically nor empirically since 1976) by most physicalist, reductionist, neo-darwinist, evolutionist, theorist philosophers; gcET in itself is Not a falsifiable geneticist, empiricist theory or philosophy at all. At best, gcET may be deemed as a linearly static (non-life) physicalist, reductionist (or at worst) anthropomorphised neo-darwinist, eugenicist, evolutionist (rhetorically-flawed) theory, philosophy, or the pseudo-genetic self-determinism of the 20th century past (please see more arguments below)!?

      2) "Nevertheless, whether some features of current evolutionary theory [ET] should be regarded as extensions of the Modern Synthesis [MS] or as parts of a different theoretical apparatus is a mere semantic point." -- Wrong! As our world history has shown: When the neo-darwinist, natural (or reductively-modified as gene-centric version of) selectionist MS of the detrimental ET that once had been ill-conceived, misunderstood, and hubristically applied in and to our Humanity issues (such as, the Holocaust in Europe and the Eugenics in Americas, etc) further been dictated in and to the Agriculture policies (such as the Lysenko case in the now-defunct USSR), a mere semantic point of misconceived argumentation or philosophical trivialization issues -- the sheer reductionist tactical semantic aversion and/or diversion of the truly-deep philoscientific debates, enquiries into such a complex, multidimensional, biological or genetical empiricism, realism, as well as ethical imperative -- can have many a severe, intractable, as well as deadly consequences!

      3) “What matters is to be clear about what one means.” -- That is exactly why in any deep philoscientific debates, one must justify argumentations to be based on advanced scientific empiricism or empiricist philosophy; and not to be alone arguing in or by invoking “semantic” rhetorical issues. As such, intellectually, this latter type of argumentation tactic somehow reminds me of the fact that these rhetorical defences on “semantic” evolutionary issues, have had been deployed and exhausted by both the world renowned British evolutionists, neo-darwinists, and bio-reductionists William D Hamilton (1936-2000) and Richard Dawkins before, especially in the 1970s-80s past (please see more arguments below)!?

      -- [To be continued below] --

      Delete
    4. -- [Continued from above] -- RE: How to differentiate ”Semantic” (rhetoric) vs “Scientific” (empiricist) philosophy debates and defences!?

      4) “The core aim of our paper addresses issues surrounding epigenetic inheritance, rather than which aspect(s) of the modern synthesis have been the most challenged by recent theoretical developments and empirical discoveries.” -- I think the core aim of the paper is trying to persuade incorporating the discovery of epigenetic inheritance into the now-defunct illy-conceived MS of the biological ET: whether by extension or assertion by semantic means, while neglecting the fact that epigenetics was actually uncovered by the means of developmental geneticist empiricism, theory, and philosophy; the developmental, molecular genetics (not the gcET as refuted in arguments 1 - 3 above) that has been increasingly pursued since 1970s-80s; especially at a time when the precision biotechnology and methods, have begun to proliferate and accelerate in varied research and development programs that have been actively applied in and to the many a revitalized disciplines of developmental cell and molecular biology, genetics, biomedicine, etc: but definitely not arisen in or from the field of physicalist, reductionist, neo-darwinist, and theorist evolutionary biology!?

      Therefore, food for thought: There will be No more of any physicalist theoretical developments or syntheses that can resuscitate or revive the semantic defences of the gcET or the MS of the ET, whether by extending revision, insertion, or reduction in the current static state of evolutionary biology (as one that has had been rhetorically-formalized in 1930s-40s and further modified in 1960s-70s past) in the 21st century and beyond!? -- [Please see Featured issue: May 2016 see the beginning of an end to the hubristic neo-Darwinist narrative of “evolutionary pseudogenetics” -- “The Selfish Gene” meme narrative, RIP (1976-2016)*, that is!? Etc.]

      5) Last but not least: "But this is for the great part a semantic point, not a conceptual one. I also note that David Haig and George Williams, on whom we relied for our definition, are acclaimed evolutionary biologists." -- Once again I think this is clearly a self-defeatist, parasite philosophy of evolutionary biology, parroting rhetorical semantic point from the flawed physicalist, reductionist, selectionist, neo-darwinist ET authority of the 20th century past!? As such, if “one thinks about it a bitscientifically, empirically, and above all, biologically and ethically: Such argumentation rhetoric invoking any semantic point(s) is just too philo-scientifically a 19th-20th-century rhetorical or self-defeatism-biased defence, whether evolutionary or degradingly in philoscientific debates since the rise and fall of neo-Darwinism past (please see arguments 1 - 4 above)!?

      Best, Mong 5/14/17usct01:39; practical public science-philosophy critic (since 2006).

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    5. RE: Corrections: I would like to make some spelling corrections in the 3 continuous posts [RE: How to differentiate ”Semantic” (rhetoric) vs “Scientific” (empiricist) philosophy debates and defences!?] above, as follows:

      Post 1, paragraph 3, sentence 1 should read: “Accordingly, with the currency of our mutual 21st-century multi[disci]plinary readings, understandings, definitions, and standards in and of the philoscientific literature in biology, I shall now try to quote and refute the 5 key neo-Darwinism-biased fallacies or defences, that Bourrat has had made in the above “semantic” vs “scientific” philosophies debates and defences, as follows:”

      Post 1, paragraph 4, sentence 3 should read: “Whereas it would be absolutely detrimental, if it is casually applied to any living subjects in biology (o[r] behaviourism).”

      Post 1, paragraph 5, sentence 1 should read: “Consequently, many a physicalist methods that doesn’t bring-up, concern, and/or sustain life-viability or vitalism issues in the purely reductionist theoretical processes will not suffice; and that all purely physicalist theories or philosophies will also not enable any hard-headed, neo-darwinist philosophers so as to appreciate and comprehend the whole process of life-viability or vitality inquiry issues, including the many an evolutionary dynamisms of biomolecular composites or cellular component bits and parts, and their in[ter]active and [inter]connected network[s] within their dynamic operating milieu and/or the organism’s real world environments, or ecology, etc.”

      Post 2, paragraph 1, sentence 1 should read: “Although the gene-centric evolutionary theory (gcET) -- [one] which doesn’t even represent or consider any gene being viably [ac]tivated or sustained in its real component or nutrient milieu -- has had only been pursued rhetorically (but not physiologically nor empirically since 1976) by most physicalist, reductionist, neo-darwinist, evolutionist, theorist philosophers; [the] gcET in itself is Not a falsifiable geneticist, empiricist theory or philosophy at all.”

      -- [To be continued below] --

      Delete
    6. -- [Continued from above] -- RE: Corrections:

      Post 2, paragraph 1, sentence 2 should read: “At best, [the] gcET may be deemed as a linearly static (non-life) physicalist, reductionist (or at worst) anthropomorphised neo-darwinist, eugenicist, evolutionist (rhetorically-flawed) theory, philosophy, or the pseudo-genetic self-determinism [par excellence] of the 20th century past (please see more arguments below)!?”

      Post 2, paragraph 2, sentence 3 should read: “As our world history has shown: When the neo-darwinist, natural (or reductively-modified as [the] gene-centric version of) selectionist MS of the detrimental ET that once had been ill-conceived, misunderstood, and hubristically applied in and to our Humanity issues (such as, the Holocaust in Europe and the Eugenics in Americas, etc) [and] further been dictated in and to the Agriculture policies (such as the Lysenko case in the now-defunct USSR), a mere semantic point of misconceived argumentation or philosophical trivialization issues -- the sheer[ly] reductionist tactical semantic aversion and/or diversion of the truly-deep philoscientific debates, enquiries into such a complex, multidimensional, biological or genetical empiricism, realism, as well as ethical imperative -- can have many a severe, intractable, as well as deadly consequences!”

      Post 3, paragraph 1, sentence 2 should read: “I think the core aim of the paper is trying to persuade incorporating the discovery of epigenetic inheritance into the now-defunct illy-conceived MS of the biological ET: whether by extension or assertion by semantic means, while [completely] neglecting the fact that epigenetics was actually uncovered by the means of developmental geneticist empiricism, theory, and philosophy; the developmental, molecular genetics (not the gcET as refuted in arguments 1 - 3 above) that has been increasingly pursued since 1970s-80s; especially at a time when the precision biotechnology and methods, have begun to proliferate and accelerate in varied research and development programs that have been actively applied in and to the many a revitalized disciplines of developmental cell and molecular biology, genetics, biomedicine, etc: but definitely not arisen in or from the field of physicalist, reductionist, neo-darwinist, and theorist evolutionary biology!?”

      Best, Mong 5/14/17usct10:32; practical public science-philosophy critic (since 2006).

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    7. Dr. Moran-
      I found the use of the term ‘semantic’ to be off putting in this case. (Is ’snide’ appropriate?)
      The reply seems quite defensive.

      After analyzing the situation, the authors deemed epigenetic does not create a difficulty for modern evolutionary theory.

      I wonder if you had spent more time acknowledging the accomplishment and where they agree with you before getting into the details of the disagreements things might have gone differently.

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    8. @Jack Jackson

      In my opinion, epigenetics is uninteresting form an evolutionary perspective because it does not contribute to changes in the genetic characteristics of a population. I don't think Lu and Bourrat agree with me. They believe that epigenetics is important in evolution and all you have to do to remove any controversy is tweak the definitions of "gene" and "evolution" to smooth things over.

      We all agree that there's no paradigm shift under way but our reasons are quite different.

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    9. Dr. Moran-
      When I read your critique, I understood there was some very basic differences, but most of the material is over my head.
      Now I see the differences are even more basic than I thought.

      It’s hard to find agreement where there is so little.

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    10. Yes. When someone is almost completely correct, and the other almost completely wrong, there is not much room for agreement. Your job, then, is to become informed enough to determine which is which. Or, at very least, stop talking about the subject until you correct your ignorance.

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  2. "We think it must be the case that Moran likes only some interpretations of evolutionary biology, and that his objections to us are based on how well we do or don’t fit these favourite interpretations."

    What they can't seem to understand is that models are accepted or rejected because of the data, not someone's preference. This is the disconnect that our lovely host, Dr. Moran, is talking about.

    Who cares how you define epigenetics or genes. It really doesn't matter in the long run. Just define what you mean by epigenetics or genes, and get on with it.

    The problem scientists face is explaining the data. As it turns out, all of the evidence points to the fact that things like DNA methylation and histone packaging has little to no effect on long term evolutionary trends. Epigenetics isn't a challenge to the current evolutionary model because it has an almost insignificant effect on the evolution of species. That's what they can't seem to understand.

    You can also define genes however you like. Doesn't matter. What matters is your model. The current model states that evolution proceeds through changes in the DNA sequences of genomes, though not all (and probably a majority) DNA sequence changes will cause phenotypic evolutionary change. If you want to group DNA sequences into things you call genes, then fine. The basic concept is still there, that evolution occurs through changes in DNA sequence.

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    1. "Who cares how you define epigenetics or genes. It really doesn't matter in the long run. Just define what you mean by epigenetics or genes, and get on with it."

      If only it were that simple! The history of science shows that the structure of our taxonomies, the way we categorise things, the way those concepts relate together in our models is essential to our both empirical progress and fruitful communication. Experimental science leads to progress precisely it helps us to bring our hypothetical constructs (and how they relate in models) into line with the actual constructs and relations in the world.

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    2. The problem scientists face is explaining the data. As it turns out, all of the evidence points to the fact that things like DNA methylation and histone packaging has little to no effect on long term evolutionary trends..

      All of the evidence also indicates that things like DNA methylation and histone packaging may have a considerable impact on standing heritable variation and short-term evolutionary responses. Unless you want to trivialize those findings by restricting evolution to "long term trends", it really is important to conceptually accomodate epigenetic heritable variation.

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    3. Mt. Analogue,

      "
      If only it were that simple! The history of science shows that the structure of our taxonomies, the way we categorise things, the way those concepts relate together in our models is essential to our both empirical progress and fruitful communication."

      However, semantic arguments divorced from reality don't further progress. Models are derived from DATA, not definitions in a dictionary. The more you criticize a model by quibbling about definitions the more divorced you are from the practice of science.

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    4. Corneel,

      "All of the evidence also indicates that things like DNA methylation and histone packaging may have a considerable impact on standing heritable variation and short-term evolutionary responses."

      That really isn't true either. Nearly all epigenetic factors are wiped out during gamete production. Very little of the parent's DNA methylation patterns make their way into their offspring. Almost all DNA methylation in your genome occurs after conception.

      The concept that biologists are trying to deal with is why species look different from each other. Humans and chimps are different from each other because of primary sequence differences found between the respective genomes. Those differences are not due to different heritable DNA methylation patterns or heritable histone packaging patterns.

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    5. 'Semantic arguments divorced from reality don't further progress.'

      You are making a semantic claim with lots of non-operationalised terms that is unfalsifiable.

      Models aren't derived from data, they are interpretations that seek to help us interpret and explain the data we see. There is no direct correspondence between DATA and models, hust as meaning ins't in the words, in in the sentences they make. That is why the same DATA can correspond to different models (e.g. Newtonian physics vs relativistic physics). It is our models that generate hypotheses, and provide empirical predictions, not the DATA. As such, models depend robust and clearly defined explanatory concepts and models, which allow us to interpret the results of our experiments.

      I agree that our terms and concepts should be falsifiable and generate clear hypotheses. Philosophy of Science can help to clarify those terms, and thus make empirical tests easier to interpret.

      You may not like it, but listen to any top biologist, and you will see they have gone beyond the positivist idea that DATA = PROGRESS

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    6. Eric said:
      Nearly all epigenetic factors are wiped out during gamete production.
      Yet epigenetic variation has been proven to contribute to heritable variation. See for example this study

      The concept that biologists are trying to deal with is why species look different from each other.
      I am a biologist and I can assure you this does not concern me at the moment. I also know from first hand that many evolutionary biologists study changes WITHIN lineages on ecological timescales. Epigenetic variation often plays a significant role in that.

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    7. Corneel said:
      Yet epigenetic variation has been proven to contribute to heritable variation. See for example this study

      From that study:

      "We demonstrate that several of these differentially methylated regions (DMRs) act as bona fide epigenetic quantitative trait loci (QTL(epi)), accounting for 60 to 90% of the heritability for two complex traits, flowering time and primary root length"

      Like I said, pretty insignificant stuff when you look at the whole.

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    8. Mt. Analogue writes:
      "Models aren't derived from data, they are interpretations that seek to help us interpret and explain the data we see. There is no direct correspondence between DATA and models, hust as meaning ins't in the words, in in the sentences they make. "

      That is really just more semantics. The point I am talking about is that scientists deal with the data, and construct models with the data in had. Philosophers don't seem to have a handle on that data, and that is why their criticisms fall short.

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    9. Corneel,

      «All of the evidence also indicates that things like DNA methylation and histone packaging may have a considerable impact on standing heritable variation and short-term evolutionary responses.»

      Depends on what you mean by evolutionary responses. I doubt that epigenetics contributes to speciation, and thus I would not even worry about accounting for such a thing when talking about evolution. I'd leave it as a confounding factor though. One that might mislead evolutionary studies.

      «Unless you want to trivialize those findings by restricting evolution to "long term trends", it really is important to conceptually accomodate epigenetic heritable variation.»

      I doubt there's any trivialization. I think that the discussion is not about the importance of epigenetics as a biological phenomenon, but whether it should be considered in evolutionary theory.

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    10. @Eric
      Like I said, pretty insignificant stuff when you look at the whole

      I get exactly the oppposite impression from that paragraph.
      Apart from the fact that flowering time is a major fitness component, I would have expected you to realise that if epigenetics conditions phenotypic variation in these traits, it is very likely to apply to any complex trait (fitness!). Especially since you have been lecturing about the use of models.

      @Gabriel Moreno-Hagelsie
      Depends on what you mean by evolutionary responses

      From this very website:

      "Evolution is a process that results in heritable changes in a population spread over many generations."

      In my book, this includes changes WITHIN species. Hence, focusing on evolutionary processes at and above the level of speciation (macro-evolution) amounts to delibarately restricting the definition of evolution to exclude changes in epigenetic variation.

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    11. Corneel -

      Two questions from a layperson:

      - Am I correct that (1) it is very rare for epigenetic changes to span multiple generations, and (2) even those that do span a handful of generations go away before what we might think of as "evolutionary time" has passed?

      - If so, even within species, how significant would epigenetic changes lasting a few generations be, except as a non-repetitive contingent occurrence that can simply be considered with all other contingencies?

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    12. Hi Corneel,

      Hum, then I doubt that we can agree on this one. I doubt that epigenetics can even give us varieties within a species (besides it being reversible), and I don't think that my understanding of evolution is made explicitly to exclude epigenetics. It's just that the changes that happen because of epigenetic phenomena are very far from what I have always understood as evolution, even before I heard about epigenetics. But to each their own.

      Best,
      -G

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    13. @judmarc
      It is true that "epimutations" are unstable and most of these revert rather quickly. As has been remarked several times in this thread it is very unlikely to contribute to any substantial variation among evolutionary lineages.
      Your final question is an important one and to be honest, I don't know the answer. As far as I know nobody has ever quantified the contribution of epigenetic variation relative to genetic variation. Still, I think it has been demonstrated that it could be considerable, and that it can contribute to short-term evolutionary change (adaptation and drift), so let's not dismiss it out of hand.

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    14. Gabriel Moreno-Hagelsieb said
      It's just that the changes that happen because of epigenetic phenomena are very far from what I have always understood as evolution

      Hi Gabriel

      Sorry, but that I don't believe. The changes we are talking about are shifts in the population mean of continuous characters or the frequency of discrete traits. Think of responses to selection on height or flowering time or the spread of a resistance phenotype. This stuff is considered genuine evolutionary change by most biologists, and I doubt that you would argue with that if we were talking about genetic alleles.
      But somehow, now we are talking about epimutations, the bar has been raised to (sub)speciation and interspecies variation, otherwise it doesn't count as evolution.

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    15. Hey Corneel,

      As I said, I see epigenetics as a confounding factor in evolutionary studies, rather than evolution. In my mind, at least, as changes in those characters happen, we get such divergence that species split, then genera, then families, etc. There's something going on that can go on and on. Epigenetics doesn't look that way (come to think of it, epigenetics might be a quasi-sympatric isolation factor, but I'm not sure, it just occurred to me).

      (I might end up convincing myself that you're right, as I argue, but it doesn't seem that way)

      Best,
      -Gabo

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    16. epigenetics might be a quasi-sympatric isolation factor

      That's along the lines of what I was picturing, but since the isolation factor wouldn't last over evolutionary time scales, I conceive of it as something that might contribute on a contingent basis to survival of, but not a change over time in, a population. So for example an epigenetically controlled earlier time to flower and seed might enable some members of a plant population to survive a fire or flood while the part of the population still in flower dies. But then this remnant, if it successfully establishes there or elsewhere, won't carry that earlier flowering and seeding characteristic more than a handful of succeeding generations if at all. So it "smells like" a founder effect, but the epigenetic characteristics of the founder(s) aren't passed on in the population.

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    17. There's something going on that can go on and on.

      I see where you are coming from, but hopefully you can see that that is a requirement of evolution that you have added yourself. Many evolutionary processes will not result in diversification of lineages, e.g. gene flow which accomplishes exactly the opposite.

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    18. @judmarc

      That's along the lines how I think of it as well. But as I see it, the transient nature of the epigenetic variation does not disqualify the selection event you've described from being an evolutionary change.

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    19. Hi Corneel -

      But when you talk about evolutionary change, what is the *change* in the population? You have the same population at a new location, yes?

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    20. 1. change takes a long time 2. change occurs from constant environmental pressure(s). 3. im not sure the religious mind is capable of comprehending this, as pretty every story in the bible talks as though everything is immediate, instantaneous- when in fact science proves absolute the process of evolution is almost as unique as the individual species that have gone through and continue to go through varying processes of evolution- as we all are and will continue to do- remember, evolution does NOT happen within a single lifetime, that is known as adpatation- btw- how about this for common sense, doesnt HOT air rise? and cool/cold air sink? so why isnt Heaven HOT and Hell cold?

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    21. @judmarc,

      Epimutations aren't as stable as genetic mutations, but neither do they revert immediately. I expect the selection response to be sustained for, say a few dozens or maybe hundreds of generations. In addition, if the selection pressure persists the response may be sustained in mutation-selection balance for somewhat longer. I guess that on even longer timescales, processes like genomic rearrangements, expansion of TEs or mutations of the methylation machinery, will completely wreck any previous contribution of epigenetic variation to adaptation and lineage divergence but that is a different story.
      But I am really no expert in this, just been exposed to it by Frank Johannes and his group when he still was in Groningen. I see they have a nice review up here.

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    22. @Corneel,

      I'd only seen discussion of epimutations lasting up to a couple of dozen generations (in the materials for one of the speakers at the seminar Larry went to on extending the evolutionary synthesis). The paper you linked to talks about thousands of generations. Big difference. O_o

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  3. They quite mad. They don't seem, willing to correct themselves on any important point(s). No good criticisms at all?!

    'early career researchers". Well then youth should be open more then others to correction if there is some! They are in the big leagues now and would parade this paper for position.

    anyways the cool thing was thier claim that INTERPRETATION was at essence here and Mr Moran's was the origin for his criticisms.
    Well creationists always say interpretation of the data is a issue but we are accused of rejecting the data. We also accuse that interpretation becomes dogma too quickly.
    Would these folks admit creationists can complain/be suspicious that interpretation of data is a defence?? YES i hope they do.
    It is all interpretation of data because nothing is witnessed. Its not like sciences where existing processes can be witnessed.

    Its a good lesson for everyone about contentions.
    Creationists can contend, even if wrong or done poorly, about origins and are not rejecting or opposing science. Its dumb lame for us to be accused so!
    Creationism is as scientific as the paper writers here and the criticism of same.
    Everybody is trying to be scientific. wrong answers is not equal with NOT SCIENCE. Call the judges back to the bench once more.!

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  4. A difference in phenotype can be a difference in DNA sequence with no other observable difference

    That's the first time I see a definition of "phenotype" that is indistinguishable of the definition for "genotype".

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    1. Not indistinguishable. It makes genotype a subset of phenotype.

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    2. I agree with their definition. After all, many structural (phenotypic) features of organisms have been used to infer evolutionary relationships and in many modern analyses differences or similarities between the fine structures in the jaw or teeth or limb bones (for example) have been replaced with the fine structures of genes or proteins (ie either their nucleotide or amino acid sequences) without regard to the actual activities that might be associated with those genes or proteins. DNA sequence is itself a phenotype, even if the terminology seems odd for obvious reasons.

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    3. @Jim Menegay and SRM
      Yes, it makes genotype a subset of phenotype ...which is a silly thing to do. The reason why Johannsen coined the terms was to distinguish between genetic and environmental effects on trait variation. Of course, you can define a DNA sequence as a phenotype with Vp = 0, but to me this seems to defeat the purpose.

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    4. a phenotype with Vp = 0
      That should be Ve = 0, of course.

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    5. The proponents of EES make a big deal about phenotype in all their publications. In fact, they believe that modern evolutionary theory tends to ignore phenotype.

      The reason they want to place such an emphasis on phenotype is that they have an adapationist view of evolution that relies heavily on the role of natural selection.

      On first reading of the Lu and Bourrat paper, I assumed they knew this and that's why they placed such a strong emphasis on phenotype in their definition of a gene.

      Now they are saying that various alleles of a gene may be entirely neutral with no observable effect on the fitness of an organism and no visible effect other than nucleotide difference and that still counts as a "phenotype."

      That makes no sense in any context and certainly makes no sense in the context of EES. As pointed out above, it makes the word "phenotype" useless and that's the exact opposite of what EES proponents want.

      Not only that, Lu and Bourrat write as though the only significant source of evolution is through changes in "genes". This seems to rule out any nucleotide differences in much of the genome since it doesn't correspond to molecular genes.

      I'd like to ask Pierret whether SNPs in junk DNA correspond to "genes" by his definition. What about allelic differences in sites like origins of replication or centromeres that might have real phenotypic effects? Are they "genes"?

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  5. This comment has been removed by a blog administrator.

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    Replies
    1. The skills are; Communication, Critical thinking, Developed logic, and Ability to deal with various angles of one issue.

      I agree that in an ideal world philosophy courses should develop these skills in their students. That's why I favor making a course like "Introduction to Logic" a required course for first year students.

      On the other hand, I do not agree that teaching these skills is "unique" to philosophy. Lot's of other disciplines emphasize critical thinking. logic, communication etc.

      As a matter of fact, there seem to be lots of humanities students these days who are notoriously deficient in these basic skills and lot of professional philosophers who lack them as well.

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    2. One sure way for a student to not develop critical thinking skills is to have one's papers written by companies like the one being promoted by the lovely "Marlene Saffan."

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    3. It's really quite distressing to see how openly these fraudsters are able to advertise themselves. As the parent of two university students it's maddening to know that they are competing against so many cheaters. I can't imagine how frustrating it must be to professors.

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  6. In my opinion, Pierrick Bourrat fail to argue consistently in several aspects.

    First, there are no different kinds of evolution, one adaptive and one non-adaptive. All evolutionary factors like mutation, drift, selection, draft, recombination and so on interacts, so they shaping genomes only together. They certainly have very different relative influences upon different bases or regions, but this is another story.

    Second, if one like to say something meaningful about an issue like „modern synthesis“, one have to tell a reasonable definition of this term before that. And no, semantics is very important, especially for epistemology, which should be the main topic for philosophers of biology.

    Third, an existing confusion over the usage of the terms „gene“ and „alleles“ in the literature is no argument to confuse even more.

    Fourth, gene products are the essential connection between genotype and phenotype. To dispose an empirical verified gene definition (see transgenes) in favor of the here discussed „evolutionary gene“ means to strip this term from some important scientific content. That should not be tolerated. To say that also DNA sequences are phenotypes is formally correct, however, misses the point. DNA sequences could only become evolutionary if they express a gene product, become express as a gene product or interfere with the expression of a gene product.

    Fifth, I doubt that Lu and Bourrat need novel terms like „evolutionary gene“ and „epigene“ to came to a similar conclusion on heritable epigenetic changes as Larrry Moran, that is, such changes have not yet shown to be really important for evolution. As Heard and Martienssen [1] has pointed out „Thus, although the notion of adaptive epigenetic inheritance retains considerable appeal, concrete evidence from model systems is still lacking.“

    [1] Edith Heard and Robert A Martienssen: Transgenerational epigenetic inheritance: myths and mechanisms. Cell, 2014 vol. 157 (1) pp. 95-109, doi: 10.1016/j.cell.2014.02.045

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