Culture Darwinism Science

Defending Darwinism: The Stumpire strikes back

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Where are those people who said no one believes classical Darwinism any more? How be:

Qiaoying Lu Pierrick Bourrat, Br J Philos Sci axw035. The Evolutionary Gene and the Extended Evolutionary Synthesis: DOI: https://doi.org/10.1093/bjps/axw035 20 April 2017:

Abstract: Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance. The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient. We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate. Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘gene’, ‘environment’, and ‘phenotype’ in a way that makes them consistent with gene-centric evolutionary theory. We argue that the evolutionary gene, when being materialized, need not be restricted to nucleic acids but can encompass other heritable units such as epialleles. If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance. More.

This is breathtaking in its duplicity: “If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance.”

Understanding it the new way is the most major conceptual change since Origin of Species. And long overdue.

Jonathan Wells’Zombie Science seems relevant somehow.

See also: Darwinism: Replacement or extension?

Hat tip:Pos-Darwinista

20 Replies to “Defending Darwinism: The Stumpire strikes back

  1. 1
    Jon Garvey says:

    Interesting. So if Lamarck turned out to be right, and acquired characteristics can be consolidated by use and inherited, then Lamarckism is actually Darwinism.

    And if Eve Jablonka’s theory of cultural evolution is true, then new behaviours worked out by parents and passed on to offspring and so inherited by imitation, rather than gentics, are actually evolutionary genes. Learning is actually Darwinism.

    You thought that antique clock was a family hearloom – it’s really a gene!

  2. 2
    News says:

    Jon Garvey at 1: How about, Darwinism is in such disarray that its proponents are co-opting anything that actually works, like people in a wreckers’ yard looking for possibly useful parts for a unique item they are trying to repair.

  3. 3
    kmidpuddle says:

    It always amuses me when evolution opponents think that epigenetics is somehow a death knell for evolution. Epigenetics is nothing more than the same gene having more than one expression of the same gene. As such, it is still fuel for selection.

  4. 4
    Phinehas says:

    kp:

    While what amuses you could be amusing, we are currently being amused by how some Darwinists think that epigenetics somehow is Darwinism.

  5. 5
    Latemarch says:

    K-puddle@3
    Evolution is fundamentally a change in gene frequency in a population.

    Oops! The epigenetic control of the underlying gene results in either suppression, normal expression, or enhanced expression. Thus fitting the organism for its environment. This is plasticity, even if selected for, results in no underlying change in the gene frequency.

  6. 6
    wd400 says:

    Oops! The epigenetic control of the underlying gene results in either suppression, normal expression, or enhanced expression. Thus fitting the organism for its environment. This is plasticity, even if selected for, results in no underlying change in the gene frequency.

    Except for the genes that control the expression…

  7. 7
    Latemarch says:

    WD400@6

    Except for the genes that control the expression…

    There’s a reason it’s called epigenetics….the control genes don’t change in frequency either.

  8. 8
    wd400 says:

    Epigenetics is an extremely ill-defined term, so you will have to point to some specific research. I don’t know of any examples where a gene-environment interaction has been “selected for” but no genes have changed frequency.

    It is possible there example of an epiallele that is stably inherited and reaches high frequency. But then you would have a hertiable variant that increases frequency due to its effect on a host. That is not wildly different than standard evolutionary biolgy, is it?

  9. 9
    Latemarch says:

    WD400@8

    I don’t know of any examples where a gene-environment interaction has been “selected for” but no genes have changed frequency.

    That’s because we’re talking about epigenetic-environment interactions not gene-environment interactions.

    It is possible there example of an epiallele that is stably inherited and reaches high frequency. But then you would have a hertiable variant that increases frequency due to its effect on a host. That is not wildly different than standard evolutionary biolgy, is it?

    Epialleles are at best metastable which means that it can be lost inside of one generation by an environmental bump. No mutation required. But whether or not it changes, there is by definition no change in the underlying genetic information. I refer you back to the definition of evolution that I started with….yes, epigenetic interactions do seem wildly different from standard evolutionary biology.

  10. 10
    wd400 says:

    Well, you’ll have to tell me what makes an “epigenetic-environment interaction” different than a gene-environment interaction (epigenetics refers to changes in gene expression after all). But my point stands, I don’t know of an “epigenetic-environment interaction” that has been “selected for” but is not the result of changing allele frequencies.

    The wider point you are missing is that epigenetic changes are largely the result of larger genetic networks. When an epigenetic response is selected for it is through changes in the frequency of alleles for those genes.Unless you have some evidence to the contrary?

  11. 11
    Latemarch says:

    Well, this thread is settled to my satisfaction./s

  12. 12
    wd400 says:

    Well, you made the claim that gene expression changes could be selected for without a change in allele frequencies. It’s really up to you to support that claim.

  13. 13
    Latemarch says:

    Epigenetic Gene Regulation in the Bacterial World

    Here go educate yourself.
    The part you should be interested in is pili regulation in E.coli. A epigeniticly heritable condition related to environment that reverts based on environmental conditions with no underlying change in the DNA. No change in allele frequency.
    It is only a small part of the amazingly complex epigenetic control system that you somehow think comes about by random mutations and natural selection.
    You’ve done your best to obfuscate, use words imprecisely and engage in logical fallacies. I’m done with you.

  14. 14
    kmidpuddle says:

    WD400 is correct. The phenotypes expressed by the epigenetically affected gene (is that the correct term?) are open to selection. If the environment changes the expression of a gene such that it is more fit that those with an allele that is not affected in the same way, it will increase in frequency. Or decrease in frequency if it is less fit. Classic “Darwinism”.

  15. 15
    Latemarch says:

    kmi@14

    Let’s do a little thought experiment. This particular experiment has its counterpart in reality but this way we can avoid all the acronyms.

    We have a population of organisms, all are genetically alike. They are also all epigenetically alike as well.

    One organism wanders into a new environment where an environmental stimulus results in a change in the epigenetic histones which turns on (or off, it doesn’t really matter in our thought experiment) the expression of the underlying gene. The organism is now phenotypically different from its original population.

    This phenotype allows the organism to thrive in its new environment. Now because the histone pattern is heritable all the children of this organism will express the same phenotype. There is no waiting for an environmental condition that turns it on.

    Now one day one of these phenotypically different organisms wanders back to the old environment. It doesn’t function quite as well in the old environment but continues to pass on it’s histone pattern. It doesn’t reproduce at quite the same rate and after a few generations that phenotype dies out.
    So in summary we have a heritable phenotype that shows selection with no change in the underlying DNA.

    In the real world organism it is possible to flip the histone switch back off though it is harder to turn it off than on ie it is metastable.

    Now my take on this is that it counters the usual Evolutionary mechanism of descent with modification as there is no modification of the underlying genome. The organism is (so to speak) going nowhere.

    This stuff goes on a lot more than we originally realized. I suspect that a lot of what is termed microevolution will turn out to be epigenetic in origin.

    I’m not denying that genetic variation exists and can be selected for. It’s certainly not all epigenetics!

  16. 16
    kmidpuddle says:

    LM, in your example, there is no genetic variation with respect to this gene. As such, selection is not possible. Whether or not the gene is epigenic or not is irrelevant. A gene that does not have any variability (alleles) in the population cannot change its frequency. We all understand this.

    But if an epigenic gene has one or more allies within the population, even if they are all epigenic, natural selection can act on them.

  17. 17
    Latemarch says:

    kmi@16:

    LM, in your example, there is no genetic variation with respect to this gene. As such, selection is not possible.

    Perhaps this is why you are having difficulty. Selection doesn’t happen to genes it happens to phenotypes.

    Whether or not the gene is epigenic or not is irrelevant.

    A second confusion. The epigenome is not the genome. There is no such thing as an epigenic gene. It’s a pattern of histones that is heritable. I know that the literature has taken to tossing around epiallele to define these patterns. Don’t mistake them as interchangeable.

    Here’s a definition from the literature that invites the same confusion but notice the genetically identical part as well: The bold is mine.

    Metastable epialleles are alleles that are variably expressed in genetically identical individuals due to epigenetic modifications established during early development and are thought to be particularly vulnerable to environmental influences.
    Pediatric Research

    Why is this distinction important. Because you can select all day for the phenotypic variation caused by the epigenetic control but you never change the underlying gene frequency. This is the point of the argument.

    But if an epigenic gene has one or more allies within the population, even if they are all epigenic, natural selection can act on them.

    This is pretty garbled. I think that I know what you’re trying to say. Rather than me guessing if you could rephrase this then maybe I could respond.

  18. 18
    kmidpuddle says:

    LM:

    Perhaps this is why you are having difficulty. Selection doesn’t happen to genes it happens to phenotypes.

    Yes, I am aware of this.

    A second confusion. The epigenome is not the genome. There is no such thing as an epigenic gene. It’s a pattern of histones that is heritable.

    The pattern of histones alone does nothing. Without the gene it cannot express any phenotype. Its heritability would be as non functional as junk DNA. Referring to an allele as an epigenic allele, or a potential epigenically affected allele, is an appropriate term (although I am not sure about the spelling).

    Why is this distinction important. Because you can select all day for the phenotypic variation caused by the epigenetic control but you never change the underlying gene frequency. This is the point of the argument.

    And this is the flaw in your argument. You are assuming that this epigenic gene is only present as one allele within the population. This may be true in some rare instances but most genes in a population will be present as two or more alleles, each which may express a different phenotype. Let’s assume that there are five alleles in a population, dominated by an epigenic allele who’s expressed phenotype affords a reproductive advantage over the others. The environment changes and the epigenic allele is expressed differently. If this new expression affords a reproductive advantage that is lower than any of the other alleles, the allele frequency will change. Natural selection in action.

  19. 19
    Latemarch says:

    kmi:

    LM said:
    A second confusion. The epigenome is not the genome. There is no such thing as an epigenic gene. It’s a pattern of histones that is heritable.

    kmi said:
    The pattern of histones alone does nothing. Without the gene it cannot express any phenotype. Its heritability would be as non functional as junk DNA. Referring to an allele as an epigenic allele, or a potential epigenically affected allele, is an appropriate term (although I am not sure about the spelling).

    You do know that argument cuts both ways. Without its pattern of histones the gene cannot express itself. I think that we can agree that a control system needs something to control and without control a system doesn’t function.

    As per the fourth sentence as long as we agree that allele is not the same as epigenic allele or epiallele.

    And this is the flaw in your argument. You are assuming that this epigenic gene is only present as one allele within the population.

    Yes I did. And I showed how selection happens. This is what the original argument was about.

    This may be true in some rare instances but most genes in a population will be present as two or more alleles, each which may express a different phenotype.

    Irrelevant. Even a rare instance is sufficient to prove the point. However it is in fact not rare. The populations that I frequently deal with, bacteria, frequently have solitary alleles that control phenotypic expression. One should not just frivolously exclude the dominate life form on the planet.

    And this is why Lenski’s long term evolution of E.coli still only has E.coli (with degeneration due to harmful mutations) after more than 66,000 generations. If the information isn’t there in the first place no novel phenotypes appear.

  20. 20
    rvb8 says:

    If he environment doesn’t ‘select’ the gene mutation (however that mutation may have arrisen), then the mutation is not inherrited.

    Classic Darwinian selection at work.

    epigenetics-schempigenetics:)

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