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darwin-as-an-old-man-337-450-17The New Yorker has a piece up, Same but Different: How epigenetics can blur the line between nature and nurture, which I think on the balance is pretty good. It introduces epigenetics to a broader audience in a manner that’s more than just a catch-phrase, and, cautions that people shouldn’t over-hype what is a legitimately interesting field of science.

But there’s a major factual problem which I mentioned when it came out, and, which some friends on Facebook have been griping about. I’ll quote the section where the error is clearest:

…Conceptually, a key element of classical Darwinian evolution is that genes do not retain an organism’s experiences in a permanently heritable manner. Jean-Baptiste Lamarck, in the early nineteenth century, had supposed that when an antelope strained its neck to reach a tree its efforts were somehow passed down and its progeny evolved into giraffes. Darwin discredited that model….

It is true that in Neo-Darwinian evolution, the modern synthesis, which crystallized in the second quarter of the 20th century, genes do not retain an organism’s experiences in a permanently heritable manner. But this is not true for Charles Darwin’s theories, which most people would term a “classical Darwinian” evolutionary theory. This is because first, Darwin worked in the pre-genetic era. He did not posit particulate inheritance, and had no genetic model. Second, though it is correct that Charles Darwin’s deemphasized the role of acquired characteristics, he himself was quite open to Lamarckianism in some cases. This openness persisted into the early 20th century, Ernst Mayr started his career as a Lamarckian!

In the least The New Yorker should have had someone with a background in evolutionary biology read the draft. The error is pretty obvious, and easy to fix.

 
• Category: Science • Tags: Lamarckianism 
    []
  1. AG says:

    Unfortunately, Darwin is treated like scientific Jesus by general public. His words are holly, and unchallengeable.

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  2. utu says:

    “Darwin is treated like scientific Jesus by general public. His words are holly, and unchallengeable.” – Not just by general public. Science popularizers are responsible for it. But it is even worse with Einstein.

    Read More
    • Replies: @AG

    Science popularizers are responsible for it.
     
    Agree.

    People believe God created human. But it is really that human created God (in their heads). The priests (popularizers) job is to keep the image of God holly perfect. Any flaw about God could shake the foundation of faith entirely in general public. Hopeless situation.

  3. aeolius says:

    Pot calls the kettle black?
    Darwin’s On the Origin of Species proposed natural selection as the main mechanism for development of species, but did not rule out a variant of Lamarckism as a supplementary mechanism.[11] Darwin called his Lamarckian hypothesis pangenesis, and explained it in the final chapter of his book The Variation of Animals and Plants under Domestication (1868), after describing numerous examples to demonstrate what he considered to be the inheritance of acquired characteristics. Pangenesis, which he emphasised was a hypothesis, was based on the idea that somatic cells would, in response to environmental stimulation (use and disuse), throw off ‘gemmules’ or ‘pangenes’ which travelled around the body (though not necessarily in the bloodstream). These pangenes were microscopic particles that supposedly contained information about the characteristics of their parent cell, and Darwin believed that they eventually accumulated in the germ cells where they could pass on to the next generation the newly acquired characteristics of the parents. Darwin’s half-cousin, Francis Galton, carried out experiments on rabbits, with Darwin’s cooperation, in which he transfused the blood of one variety of rabbit into another variety in the expectation that its offspring would show some characteristics of the first. They did not, and Galton declared that he had disproved Darwin’s hypothesis of pangenesis, but Darwin objected, in a letter to the scientific journal Nature, that he had done nothing of the sort, since he had never mentioned blood in his writings. He pointed out that he regarded pangenesis as occurring in Protozoa and plants, which have no blood. (wiki-Lamarckism)

    Read More
  4. pyrrhus says:

    Oddly enough, this same error came up in a panel discussion, with some big names at the UA’s Science of Consciousness Conference here in Tucson, which is ongoing. But the error was promptly corrected by one of the panelists, Prof. Rudolph Tanzi of Harvard Med School….

    Read More
  5. AG says:
    @utu
    "Darwin is treated like scientific Jesus by general public. His words are holly, and unchallengeable." - Not just by general public. Science popularizers are responsible for it. But it is even worse with Einstein.

    Science popularizers are responsible for it.

    Agree.

    People believe God created human. But it is really that human created God (in their heads). The priests (popularizers) job is to keep the image of God holly perfect. Any flaw about God could shake the foundation of faith entirely in general public. Hopeless situation.

    Read More
  6. Sean says:

    Well written article, and interesting about how it was the supposed science of Marxism that the original theorist of epileptics CH Waddington was inspired by. His commie convictions produced wild speculation about genetic plasticity, which turned out to be correct.

    this is not true for Charles Darwin’s theories, which most people would term a “classical Darwinian” evolutionary theory.

    “Classical”, which the overachieving author of the piece uses more than once, is a useful word. For instance

    Robert F. Kennedy issued a statement saying his brother “does not now nor has he ever had an ailment described classically as Addison’s disease.” [...] Robert Kennedy’s semantic dodge rested on the point that in the disease as originally described by Thomas Addison in 1855, the adrenals were destroyed by tuberculosis; John Kennedy, whose Addison’s disease was caused by unknown factors, did not have tuberculosis.

    I suppose like the “scientific” bias of the forties, when almost every intellectual was some kind of a Marxist, riding the current Zeitgeist to universal acclaim requires tagging as nineteenth century Darwinist, any belief in genetic immutability.For what the TED talking writer calls “classically Darwinist” is actually the modern evolutionary synthesis. But I’m sure he knew that. No lack of fact checking, it’s hermeneutic skill within what are real constants on how genetics can be written about in the mainstream media.

    Read More
  7. DEFINITION OF NEODARWINISM.

    At Darwin’s (his mentor’s) behest, George Romanes went beyond Galton in experimenting to validate the aspect of the pangenesis hypothesis concerning movement to the gonads. While there is now some evidence for this (e.g. ancient retroviral genes in the germline), the enduring feature of pangenesis is the quantal nature of the pangens (“gemmules”; see de Vries’ Intracellular Pangenesis (1889) and My 2001 speciation text).

    One should be careful about the term “neodarwinism,” when considering what some call “the modern synthesis.” In his 1893 An Examination of Weismannism Romanes 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.” He is here branding Weismann and Wallace as neodarwinians. We would today see epigenetic characters as sometimes capable of either plasmogenetic or somatogenetic inheritance.

    Read More
  8. BogiT says:

    If I remember this correctly Fleeming Jenkin challenged Darwin on his pangenesis theory of inheritance, stating that simple blending inheritance would lead to loss of variation. Darwin responded by modifying his work, so that environmental cues could affect gemmules dispersed throughout the body prior to reproduction. These modifications of gemmules by environment are then inherited by offspring.

    I am bringing this up because I’m not really sure what you meant by saying “open to Lamarckianism in some cases.” I always thought that Lamarckism was an integral component of Darwin’s view of inheritance. Did I misunderstood something?

    Read More
  9. Chad says:

    The New Yorker article fell into the same trap of watering down the definition of epigenetics.

    Read More
  10. @Chad
    The New Yorker article fell into the same trap of watering down the definition of epigenetics.

    How so?

    Read More
    • Replies: @Chad
    Waddington originally coined the term to describe how cell types became locked into a set state of differentiation and how they passed that state on mitotically to new cells. Implicit in this was that this state of differentiation was not temporary or transient, but stable and heritable across generations of those cells.

    Robin Holliday in the 1970s continued this definition, but also included the ability of transgenerational epigenetics, where these states were not only inherited within cell lineages, but across generations of the organism. Again, inherent in this definition is the idea that it is not transient or a mere means of gene regulation, but something that is stably passed on across generations (of an organism or a cell).

    The environment is not necessary or inherent in either definition. The regulation of gene expression can be dynamic, transient, is typically genetically encoded, and typically not heritable.

    Only recently, in the last few years as "epigenetics" has become one of the latest buzz terms, do you suddenly see it widely used to describe everything from gene x environment interactions to mere gene expression changes. This is to render the term meaningless and detract from these other areas, which have long been their own fields.

    The New Yorker, typically uses this expanded language, so that "epigenetics" literally means everything the cell is doing....including a lot of things that are actually genetic.

    For example, just because it involves a change in a histone modification, doesn't make it "epigenetic". Certain histone modifications are quite dynamic with changing gene expression. And do not represent the stable heritable sort of state that Waddington or Holliday referred to when they used the term.
  11. Twinkie says:

    Jean-Baptiste Lamarck, in the early nineteenth century, had supposed that when an antelope strained its neck to reach a tree its efforts were somehow passed down and its progeny evolved into giraffes. Darwin discredited that model….

    NOOOOOOOOOOOO! Frank Herbert says otherwise!

    Read More
    • Replies: @gruff
    I read Dune recently and was astounded that I had never, in years of reading about the novel, watching the movie etc., heard anyone mention the underlying message of the book: that humanity has become genetically stagnant and requires a massive upheaval (= interstellar war) to mix the populations and reinvigorate the species. Beginning this star jihad is the real role of the Kwisatz Haderach, and the plan is deeper than even the Bene Gesserit know: it comes from the human genome itself. The deliberate association of this coming destabilizing conflict with religion, and specifically with Islamic jihad, not to mention the idea of increased intermarriage expected to take place due to large population flows, is eerily prescient of current world events.

    I was also struck by how much attention Herbert pays to phenotypes. Good characters are almost all dark haired, and bad ones (Shaddam, Irulan, most Harkonnens apart from Feyd, the Sardaukar officer corps) are blond or redheaded. The Sardaukar are described in terms that make clear they are "Aryan space Nazis"; and in the final pages Herbert dwells in some detail on Irulan's icy blonde beauty and, in the same passage, her coming forced chastity and failure to reproduce.

    He also uses the phrase "race consciousness" at least once in the book.

    TLDR: Nobody talks about how Dune is about HBD.
  12. Chad says:
    @RaceRealist88
    How so?

    Waddington originally coined the term to describe how cell types became locked into a set state of differentiation and how they passed that state on mitotically to new cells. Implicit in this was that this state of differentiation was not temporary or transient, but stable and heritable across generations of those cells.

    Robin Holliday in the 1970s continued this definition, but also included the ability of transgenerational epigenetics, where these states were not only inherited within cell lineages, but across generations of the organism. Again, inherent in this definition is the idea that it is not transient or a mere means of gene regulation, but something that is stably passed on across generations (of an organism or a cell).

    The environment is not necessary or inherent in either definition. The regulation of gene expression can be dynamic, transient, is typically genetically encoded, and typically not heritable.

    Only recently, in the last few years as “epigenetics” has become one of the latest buzz terms, do you suddenly see it widely used to describe everything from gene x environment interactions to mere gene expression changes. This is to render the term meaningless and detract from these other areas, which have long been their own fields.

    The New Yorker, typically uses this expanded language, so that “epigenetics” literally means everything the cell is doing….including a lot of things that are actually genetic.

    For example, just because it involves a change in a histone modification, doesn’t make it “epigenetic”. Certain histone modifications are quite dynamic with changing gene expression. And do not represent the stable heritable sort of state that Waddington or Holliday referred to when they used the term.

    Read More
  13. RCB says:

    I see the error, but it’s a pretty esoteric topic. The distinction is between the beliefs of people who might call themselves “Darwinists” and the beliefs of “Darwin” himself – which surely the majority of readers don’t and needn’t care about. Anyone who spends more than 5 minutes griping about this on facebook probably should get a life. :)

    That said, maybe it’s time we just replaced “Darwinian” with “Fisherian” (or, for those who fear Fisher’s politics, you could call yourself a “Wrightist”… but that’s a bit self-defeating). If we all more-or-less accept the Modern Synthesis (apart from the few annoying “extended synthesis” authors like Kevin Laland) as the foundation of evolutionary theory, why not use the name of someone who was actually involved in it?

    Read More
    • Replies: @Sean
    The New Yorker piece misrepresents as nineteenth century a view that was not fully in place until (after a few expedient funerals) the 40's. Moreover, German racial hygienists did not believe in the immutability of genes, that is why they were opposed to X rays, pollution, tobacco and sugar. Even Mein Kampf has a passage railing against the lifechanging effects of child abuse (here).

    I suppose Mukherjee is setting up a Mendelian Darwin consensus as inspiration of the Third Reich with essentialist overtones, to show Allis's research as refuting an implacable genetic destiny.

    Darwin was impressed with the amount of small continuous variation and gradual change, not the large effects of a particular gene that Mendel happened to have got with his well chosen peas, so Darwin's personal legacy or school of thought was on the other side of a Hopeful Monsters debate to German scientists like Otto Schindewolf.

    The New Yorker piece portrays Waddington, who was the canalization or robustness man, as something quite different, and if Chad is correct and I read him aright, this is yet another "classic" semantic dodge by Mukherjee, because Waddingtom coined "epigenetics" not to mean on/off toggling, but rather permanent assimilation .


    “The remarkable thing about workers and gamergates,” Yan told me, “is that they are almost genetically identical.” The gene sequence before and after the transition is the same. Yet, as DNA methyl groups or histone modifications get shifted around those gene sequences, the worker transforms into a gamergate, and virtually everything about the insect’s physiology and behavior changes. “We’re going to solve how the change can have such a dramatic effect on longevity,” Reinberg said. “It’s like one twin that lives three times longer than the other”—all by virtue of a change in epigenetic information.
     
    Nice upgrade, and he muses "The ant chooses a life between its genes and its epigenes—inhabiting one self among its incipient selves."

    The worker ant's epigenetic lane changing happens as a result of the ants being well cared for when young, not being abused or given too little sustenance (or being coked out of their exoskeleton)? Not really, the ants become queenly by means of an epigenetic jackpot awarded to the winner of a Battle Royal.


    When the queen is removed from the colony, the workers, sensing opportunity, launch a vicious, fight-to-the-death campaign against one another—stinging, biting, sparring, lopping off limbs and heads, until a few workers win and become queenlike.
     
    And then they lord it over all remaining workers.

    Now it seems to me that as the ants are identical genetically, those who come out on top in the deathmatch are the ones whose phenotype most faithfully, most robustly, reflects the genetic master plan for an unbeatable ant. When the contenders all have an identical genotype and the epigenetic queening comes after they win, what else but developmental stability of each individual participant could be selected in a fight?

    Note that Mukherjee also seems to be describing something similar when talking about his mother's identical twin:-


    My mother was boisterous. She had a mercurial temper that rose fast and died suddenly, like a gust of wind in a tunnel. [...] Tulu was gregarious. She made friends easily. She was impervious to insults. Bulu was reserved, quieter, and more brittle.
     
  14. Sean says:
    @RCB
    I see the error, but it's a pretty esoteric topic. The distinction is between the beliefs of people who might call themselves "Darwinists" and the beliefs of "Darwin" himself - which surely the majority of readers don't and needn't care about. Anyone who spends more than 5 minutes griping about this on facebook probably should get a life. :)

    That said, maybe it's time we just replaced "Darwinian" with "Fisherian" (or, for those who fear Fisher's politics, you could call yourself a "Wrightist"... but that's a bit self-defeating). If we all more-or-less accept the Modern Synthesis (apart from the few annoying "extended synthesis" authors like Kevin Laland) as the foundation of evolutionary theory, why not use the name of someone who was actually involved in it?

    The New Yorker piece misrepresents as nineteenth century a view that was not fully in place until (after a few expedient funerals) the 40′s. Moreover, German racial hygienists did not believe in the immutability of genes, that is why they were opposed to X rays, pollution, tobacco and sugar. Even Mein Kampf has a passage railing against the lifechanging effects of child abuse (here).

    I suppose Mukherjee is setting up a Mendelian Darwin consensus as inspiration of the Third Reich with essentialist overtones, to show Allis’s research as refuting an implacable genetic destiny.

    Darwin was impressed with the amount of small continuous variation and gradual change, not the large effects of a particular gene that Mendel happened to have got with his well chosen peas, so Darwin’s personal legacy or school of thought was on the other side of a Hopeful Monsters debate to German scientists like Otto Schindewolf.

    The New Yorker piece portrays Waddington, who was the canalization or robustness man, as something quite different, and if Chad is correct and I read him aright, this is yet another “classic” semantic dodge by Mukherjee, because Waddingtom coined “epigenetics” not to mean on/off toggling, but rather permanent assimilation .

    “The remarkable thing about workers and gamergates,” Yan told me, “is that they are almost genetically identical.” The gene sequence before and after the transition is the same. Yet, as DNA methyl groups or histone modifications get shifted around those gene sequences, the worker transforms into a gamergate, and virtually everything about the insect’s physiology and behavior changes. “We’re going to solve how the change can have such a dramatic effect on longevity,” Reinberg said. “It’s like one twin that lives three times longer than the other”—all by virtue of a change in epigenetic information.

    Nice upgrade, and he muses “The ant chooses a life between its genes and its epigenes—inhabiting one self among its incipient selves.”

    The worker ant’s epigenetic lane changing happens as a result of the ants being well cared for when young, not being abused or given too little sustenance (or being coked out of their exoskeleton)? Not really, the ants become queenly by means of an epigenetic jackpot awarded to the winner of a Battle Royal.

    When the queen is removed from the colony, the workers, sensing opportunity, launch a vicious, fight-to-the-death campaign against one another—stinging, biting, sparring, lopping off limbs and heads, until a few workers win and become queenlike.

    And then they lord it over all remaining workers.

    Now it seems to me that as the ants are identical genetically, those who come out on top in the deathmatch are the ones whose phenotype most faithfully, most robustly, reflects the genetic master plan for an unbeatable ant. When the contenders all have an identical genotype and the epigenetic queening comes after they win, what else but developmental stability of each individual participant could be selected in a fight?

    Note that Mukherjee also seems to be describing something similar when talking about his mother’s identical twin:-

    My mother was boisterous. She had a mercurial temper that rose fast and died suddenly, like a gust of wind in a tunnel. [...] Tulu was gregarious. She made friends easily. She was impervious to insults. Bulu was reserved, quieter, and more brittle.

    Read More
    • Replies: @another fred

    Note that Mukherjee also seems to be describing something similar when talking about his mother’s identical twin:-

    My mother was boisterous. She had a mercurial temper that rose fast and died suddenly, like a gust of wind in a tunnel. [...] Tulu was gregarious. She made friends easily. She was impervious to insults. Bulu was reserved, quieter, and more brittle.
     

     
    Twins struggle for place in the womb. One usually establishes itself as dominant.
  15. j mct says:

    I’d say that maybe the next time one reads the New Yorker about something one doesn’t know all that much personally about, to update one’s priors on holding what the article says is true. I’d say that the best most journalists do when they write a story is that about half of the factual assertions are actually factual. Obviously, if one knows about the topic of the article you can figure out which is which, or grade it as a paper, and as a school paper most journalism would flunk given that a 50% is usually flunking. The problem is with articles about stuff one doesn’t know all that much about. At least half of the article will be bass ackwards wrong, but if it’s about something one doesn’t know about one cannot tell which half.

    Read More
  16. @Sean
    The New Yorker piece misrepresents as nineteenth century a view that was not fully in place until (after a few expedient funerals) the 40's. Moreover, German racial hygienists did not believe in the immutability of genes, that is why they were opposed to X rays, pollution, tobacco and sugar. Even Mein Kampf has a passage railing against the lifechanging effects of child abuse (here).

    I suppose Mukherjee is setting up a Mendelian Darwin consensus as inspiration of the Third Reich with essentialist overtones, to show Allis's research as refuting an implacable genetic destiny.

    Darwin was impressed with the amount of small continuous variation and gradual change, not the large effects of a particular gene that Mendel happened to have got with his well chosen peas, so Darwin's personal legacy or school of thought was on the other side of a Hopeful Monsters debate to German scientists like Otto Schindewolf.

    The New Yorker piece portrays Waddington, who was the canalization or robustness man, as something quite different, and if Chad is correct and I read him aright, this is yet another "classic" semantic dodge by Mukherjee, because Waddingtom coined "epigenetics" not to mean on/off toggling, but rather permanent assimilation .


    “The remarkable thing about workers and gamergates,” Yan told me, “is that they are almost genetically identical.” The gene sequence before and after the transition is the same. Yet, as DNA methyl groups or histone modifications get shifted around those gene sequences, the worker transforms into a gamergate, and virtually everything about the insect’s physiology and behavior changes. “We’re going to solve how the change can have such a dramatic effect on longevity,” Reinberg said. “It’s like one twin that lives three times longer than the other”—all by virtue of a change in epigenetic information.
     
    Nice upgrade, and he muses "The ant chooses a life between its genes and its epigenes—inhabiting one self among its incipient selves."

    The worker ant's epigenetic lane changing happens as a result of the ants being well cared for when young, not being abused or given too little sustenance (or being coked out of their exoskeleton)? Not really, the ants become queenly by means of an epigenetic jackpot awarded to the winner of a Battle Royal.


    When the queen is removed from the colony, the workers, sensing opportunity, launch a vicious, fight-to-the-death campaign against one another—stinging, biting, sparring, lopping off limbs and heads, until a few workers win and become queenlike.
     
    And then they lord it over all remaining workers.

    Now it seems to me that as the ants are identical genetically, those who come out on top in the deathmatch are the ones whose phenotype most faithfully, most robustly, reflects the genetic master plan for an unbeatable ant. When the contenders all have an identical genotype and the epigenetic queening comes after they win, what else but developmental stability of each individual participant could be selected in a fight?

    Note that Mukherjee also seems to be describing something similar when talking about his mother's identical twin:-


    My mother was boisterous. She had a mercurial temper that rose fast and died suddenly, like a gust of wind in a tunnel. [...] Tulu was gregarious. She made friends easily. She was impervious to insults. Bulu was reserved, quieter, and more brittle.
     

    Note that Mukherjee also seems to be describing something similar when talking about his mother’s identical twin:-

    My mother was boisterous. She had a mercurial temper that rose fast and died suddenly, like a gust of wind in a tunnel. [...] Tulu was gregarious. She made friends easily. She was impervious to insults. Bulu was reserved, quieter, and more brittle.

    Twins struggle for place in the womb. One usually establishes itself as dominant.

    Read More
    • Replies: @Sean
    Well I got a bit mixed, because it seems the ants fighting to be queen are midway between fraternal and identical human siblings. But I still think superior robustness or canalisation may be the recipe for a champion ant.

    One of the ants leaped out of the Tupperware box onto my shirt. There was a momentary commotion—“They bite,” Yan said, matter-of-factly—and then we found the ant on my shoulder, making a desperate break for my ear.
     
    Aaargh! https://en.wikipedia.org/wiki/Harpegnathos_saltator
  17. gruff says:
    @Twinkie

    Jean-Baptiste Lamarck, in the early nineteenth century, had supposed that when an antelope strained its neck to reach a tree its efforts were somehow passed down and its progeny evolved into giraffes. Darwin discredited that model….
     
    NOOOOOOOOOOOO! Frank Herbert says otherwise!

    I read Dune recently and was astounded that I had never, in years of reading about the novel, watching the movie etc., heard anyone mention the underlying message of the book: that humanity has become genetically stagnant and requires a massive upheaval (= interstellar war) to mix the populations and reinvigorate the species. Beginning this star jihad is the real role of the Kwisatz Haderach, and the plan is deeper than even the Bene Gesserit know: it comes from the human genome itself. The deliberate association of this coming destabilizing conflict with religion, and specifically with Islamic jihad, not to mention the idea of increased intermarriage expected to take place due to large population flows, is eerily prescient of current world events.

    I was also struck by how much attention Herbert pays to phenotypes. Good characters are almost all dark haired, and bad ones (Shaddam, Irulan, most Harkonnens apart from Feyd, the Sardaukar officer corps) are blond or redheaded. The Sardaukar are described in terms that make clear they are “Aryan space Nazis”; and in the final pages Herbert dwells in some detail on Irulan’s icy blonde beauty and, in the same passage, her coming forced chastity and failure to reproduce.

    He also uses the phrase “race consciousness” at least once in the book.

    TLDR: Nobody talks about how Dune is about HBD.

    Read More
  18. Sean says:
    @another fred

    Note that Mukherjee also seems to be describing something similar when talking about his mother’s identical twin:-

    My mother was boisterous. She had a mercurial temper that rose fast and died suddenly, like a gust of wind in a tunnel. [...] Tulu was gregarious. She made friends easily. She was impervious to insults. Bulu was reserved, quieter, and more brittle.
     

     
    Twins struggle for place in the womb. One usually establishes itself as dominant.

    Well I got a bit mixed, because it seems the ants fighting to be queen are midway between fraternal and identical human siblings. But I still think superior robustness or canalisation may be the recipe for a champion ant.

    One of the ants leaped out of the Tupperware box onto my shirt. There was a momentary commotion—“They bite,” Yan said, matter-of-factly—and then we found the ant on my shoulder, making a desperate break for my ear.

    Aaargh! https://en.wikipedia.org/wiki/Harpegnathos_saltator

    Read More
  19. JAGILL says:

    I second the Razib’s take on the NYer article. It’s generally good with a few minor points that need criticizing. Jerry Coyne thinks the article is complete garbage, has dedicated two posts to it, but since he’s no expert on the subject has gathered other scientists to critique it for him. While this is a nice change of pace, those scientists he found (Mark Ptashne and John Greally) express opinions (nary a citation) in that post that are not consistent with the literature of our current understanding of epigenetics, especially in regard to histones. I suppose Ptashne can be excused since he’s a yeast geneticist.
    For instance, from way back in 2009 (200 citations)

    Histone modification levels are predictive for gene expression

    http://www.pnas.org/content/107/7/2926

    Read More
    • Replies: @Chad
    John Greally is an expert in the field and his "opinions" would reflect that of most who are also experts in the field. Part 1's of Why Evolution is True quotes many other leaders in the field. I especially recommend reading Steve Henikoff's, who has long been at the forefront. More importantly, I'd recommend the following to understand the history of the term and what sort of land mine Siddhartha stepped into: http://www.genetics.org/content/199/4/887.

    As for histones being predictive for gene expression. Sure, they can be....but one should not confuse a correlation with causation. Do histone modifications and DNA methylation drive gene expression differences or does gene expression differences cause changes in chromatin? I know of several cases where loss of a certain modification associated with certain gene expression states has absolutely no effect on gene expression, indicating that the association is non-causal, at least in the direction of the modification on gene expression. This is particularly true of gene-body methylation.
  20. Chad says:
    @JAGILL
    I second the Razib's take on the NYer article. It's generally good with a few minor points that need criticizing. Jerry Coyne thinks the article is complete garbage, has dedicated two posts to it, but since he's no expert on the subject has gathered other scientists to critique it for him. While this is a nice change of pace, those scientists he found (Mark Ptashne and John Greally) express opinions (nary a citation) in that post that are not consistent with the literature of our current understanding of epigenetics, especially in regard to histones. I suppose Ptashne can be excused since he's a yeast geneticist.
    For instance, from way back in 2009 (200 citations)

    Histone modification levels are predictive for gene expression
    http://www.pnas.org/content/107/7/2926

    John Greally is an expert in the field and his “opinions” would reflect that of most who are also experts in the field. Part 1′s of Why Evolution is True quotes many other leaders in the field. I especially recommend reading Steve Henikoff’s, who has long been at the forefront. More importantly, I’d recommend the following to understand the history of the term and what sort of land mine Siddhartha stepped into: http://www.genetics.org/content/199/4/887.

    As for histones being predictive for gene expression. Sure, they can be….but one should not confuse a correlation with causation. Do histone modifications and DNA methylation drive gene expression differences or does gene expression differences cause changes in chromatin? I know of several cases where loss of a certain modification associated with certain gene expression states has absolutely no effect on gene expression, indicating that the association is non-causal, at least in the direction of the modification on gene expression. This is particularly true of gene-body methylation.

    Read More
    • Replies: @JAGILL
    "As for histones being predictive for gene expression. Sure, they can be….but one should not confuse a correlation with causation."

    It's a cheap trick when you want to criticize something to insist on an unrealistic standard, as John Greally and you are doing here. Innumerable ChIP seq assays demonstrate that H3K9ac is highly correlated with active promoters. As is H3K14ac and H3k4me3.

    And that one time you read a paper showing something different is irrelevant as someone of high standards would understand.

    Here's what Greally said about histones: "And there is no evidence that coiling and uncoiling of DNA has a causal effect on gene activity."

    in response to this:

    "We finally found a protein that makes a specific chemical change in the histone, possibly forcing the DNA coil to open. And when we studied the properties of this protein it became quite clear that it was also changing the activity of genes.”

    To say Mukherjee was being somewhat provocative is one thing; to call what he said "harmful" and "terrible" is actually further from the truth than the original piece.
  21. JAGILL says:
    @Chad
    John Greally is an expert in the field and his "opinions" would reflect that of most who are also experts in the field. Part 1's of Why Evolution is True quotes many other leaders in the field. I especially recommend reading Steve Henikoff's, who has long been at the forefront. More importantly, I'd recommend the following to understand the history of the term and what sort of land mine Siddhartha stepped into: http://www.genetics.org/content/199/4/887.

    As for histones being predictive for gene expression. Sure, they can be....but one should not confuse a correlation with causation. Do histone modifications and DNA methylation drive gene expression differences or does gene expression differences cause changes in chromatin? I know of several cases where loss of a certain modification associated with certain gene expression states has absolutely no effect on gene expression, indicating that the association is non-causal, at least in the direction of the modification on gene expression. This is particularly true of gene-body methylation.

    “As for histones being predictive for gene expression. Sure, they can be….but one should not confuse a correlation with causation.”

    It’s a cheap trick when you want to criticize something to insist on an unrealistic standard, as John Greally and you are doing here. Innumerable ChIP seq assays demonstrate that H3K9ac is highly correlated with active promoters. As is H3K14ac and H3k4me3.

    And that one time you read a paper showing something different is irrelevant as someone of high standards would understand.

    Here’s what Greally said about histones: “And there is no evidence that coiling and uncoiling of DNA has a causal effect on gene activity.”

    in response to this:

    “We finally found a protein that makes a specific chemical change in the histone, possibly forcing the DNA coil to open. And when we studied the properties of this protein it became quite clear that it was also changing the activity of genes.”

    To say Mukherjee was being somewhat provocative is one thing; to call what he said “harmful” and “terrible” is actually further from the truth than the original piece.

    Read More

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