the genetics of epigenetics

tschafer said: “I can see that ‘epigenetics’ is going to be this century’s excuse for socialism, just as ‘environmental determinism’ was last century’s excuse…. If enviornment predominates, well, we need to manipulate the environment to breed the New Socialist Man. If epigenitics is a factor, we must manipulate the environment in order to influence mutable genes.”

sho’nuff, the lefties seem to be lovin’ epigenetics: Why Your DNA Isn’t Your Destiny.

*facepalm*

epigenetics is cool, no doubt. along with other things, some epigenetic thingies [<< technical term] seem to be relatively short-term hacks of the genome in order to enable organisms to more quickly "adapt" to the environment. if there's a shortage of food, it might be useful that the next generation or two can metabolize food differently and, perhaps, extract more calories/nutrition than otherwise. (of course, if the environment doesn't remain so detrimental, the next generation or two might wind up obese and/or with high rates of diabetes.) this is a great adaptation to have — it means your lineage won't necessarily disappear immediately if the environment goes somewhat sour on you. gives the lineage a little time to adapt properly before being selected right out of the gene pool.

and that's the part that the happy leftists are missing from their thinking [sic] about epigenetics. epigenetics is obviously some sort of adaptation … so it must be coded for in our genes somewhere. that methylation happens to alter the expression of genes isn’t some miracle, however amazing it may be. it’s coded for:

“An N-ethyl-N-nitrosourea screen for genes involved in variegation in the mouse” [opens pdf]

“Despite the fact that the epigenetic state of the eukaryotic genome has profound effects on ultimate phenotype, little is known about the mechanisms by which these states are established. In mammals, genomewide epigenetic reprogramming occurs during both gametogenesis and early embryonic development (1). For technical reasons, mainly related to the challenges of manipulating such small starting material, it has been difficult to study these events. We have designed a screen to detect genes involved in establishing and maintaining the epigenetic state of the genome in the mouse by screening for mutations that affect variegated gene expression in the adult….

“Using a sensitized screen for modifiers of transgene variegation in the mouse, we have identified a number of mutations that affect epigenetic reprogramming during gametogenesis and early development….

“These mutant lines should provide a valuable resource for those working in the field of epigenetics. The study demonstrates the power of sensitized screens not only for the discovery of novel genes involved in a particular process but also for the elucidation of the biology of that process.”

in other words, there are genes behind epigenetics, and since all individuals are different, there are variations in these genes behind epigenetics. in fact, i’ll bet anyone $1.00 — no, $1.50! — that different frequencies of these genes will be found in different populations.

it might be epigenetics we’re talking about here, but it’s still biology.

see also: The case for transgenerational epigenetic inheritance in humans [pdf] and Transgenerational epigenetic inheritance: More questions than answers

(note: comments do not require an email. sugar and spice!)

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35 Comments

  1. if there’s a shortage of food, it might be useful that the next generation or two can metabolize food differently and, perhaps, extract more calories/nutrition than otherwise.

    I have similar ideas regarding the human diet.

    Think about what your diet would have been like 200 years ago (ten generations ago).
    Then think about what your diet would have been like just 100 years ago.

    Now look out your window.

    24/7 grocery stores and restaurants. Packaged foods of all varieties available whenever you want. “Fresh” out of season food stuffs available year round.

    Now go look in your kitchen. Which appliances in there could you have probably owned 100 years ago (five generations ago)?

    Now go down to your root cellar, the one right next to the shelves of the canned goods you just put up.

    This is why Americans are obese.

    Reply

  2. @rjp – “This is why Americans are obese.”

    what you said + the fact that americans just don’t move around enough.

    for many years i didn’t have a car and did a lot of walking. then i was pretty slim. then i got a car … and put on about 15 pounds (ok, 20!). got rid of the car again. (^_^)

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  3. I was unemployed in August 2009 and stepped on a scale …. 212.6 lbs.

    Anyways, I started doing the math. Such and such burns 450 cals per hour. This burns 600 calories per hour …. I had a lot of time to think …

    I was like hell, I’ll never be able to lose this weight with exercise.

    Completely revamped how I eat. I snack and eat one meal a day usually (lunch). No longer does being late to eat turn me in to asshole that can’t concentrate on my work. I personally think almost everybody is addicted to sugar, I was.

    Since April 2010, my weight when I have weighed in, has been 148 to 153 lbs. Exercise is over-rated, it’s all diet. Plus I do walk 2.5 maybe 3 miles home from work everyday.

    I have other strange theories too about weight loss and diet.

    One is that any weight at which you stayed any significan level of time is a weight at which a level of toxins in the fat in your body was built up which is remarkablely more resistant to being broken down and metabolized by the body. At those weight levels you need to be extremely vigilant and committed to the weight loss in order to break through those points.

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  4. @rjp – “I personally think almost everybody is addicted to sugar, I was.”

    yeah, sugar is NO good. who the h*ck is adapted to eating sugar? not europeans (yet) — we’ve only been eating it for ca. 1000 years. for the most part, it still isn’t good for us (or our teeth!).

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  5. Heh! I noticed the leftists’ and the media’s fondness of epigenetics long ago. Here’s another thing they love: Neuroplasticity.

    I actually read an article about neuroplasticity in the newspaper this morning. Learning about neuroplasticity surely must have made that journalist’s day. And the conclusion, of course…………eeeeveryone can be a rocket scientist! Well, she didn’t actually write that, but you get the idea.

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  6. At one level, the enthusiasm for these pet concepts (epigenetics and neuroplacticity, among several others) may simply be a desire to bury “genetic determinism”, which is seen to be a highly pernicious doctrine to those on the left. I believe that hbd chick saw this in a recent exchange at Bloggingheads.tv.

    Besides the fact that the very phrase “genetic determinism” is a caricature of all but the most extreme viewpoints. I don’t know that I’ve met anyone who thinks that genetic factors are the sole explanation for one’s life trajectory, and even ignoring the possibility that variations in epigenetic factors or neuroplasticity in a population may themselves have genetic components (the former being the possibility raised by this post), it doesn’t seem to me that the existence of epigenetic factors in gene expression or the brain’s neuroplasticity neutralize genetic variation…they merely add nuance to the story, and these nuances don’t follow any set ideological pattern.

    In fact, it seems to me that epigenetics merely describes a set of mechanisms by which the environment interacts with our genes. In the past when nourishment wasn’t as abundant as it is today, most people didn’t grow as tall as is average today. I suspect that part of the mechanism for this was an epigenetic cascade that down regulated genes whose expression generally lengthened bones in appendages. This may have indeed masked some of the genetic differences present in the population at the time. However, as famine has become rare and our children are now well fed (perhaps too well fed), the full spectrum of possible heights becomes apparent. One possible message is that if the optimum environment is provided for this trait, inequality increases. I don’t see how that plays well into an ideology of the Left that was eager to leap on epigenetics as a confounding factor to stave off the specter of “genetic determinism”.

    Similarly, neuroplasticity is often embraced because the presence of a brain’s ability to change in response to a different set of conditions and this may allow explanations via solely environmental source. More than that, it is seen as a refutation of another conceptual bogeyman–the rigid “hardwired” brain, which though cartoonish and probably not really accepted by anyone, is seen as a horrid, horrid thought that must be expunged. The fact is that neuroplasticity may provide the mechanism for how the brain adapts to situations, but it doesn’t imply that there are no genetic differences in people’s ability to perform various tasks or skills. It’s really another mechanism taken as a refutation of a straw bogeyman that no one really believes in anyway, and in the end, it is merely another detail in the full picture, not a fundamental change to dynamics of human variation.

    In sum, while such concepts are fashionable because they can possibly be integrated into a vision that minimizes the role of genetics in human variation, this is mainly just hand waving that necessarily ignores reality, where it is quite clear that genetics does play a major role in human variation and the only way to ensure that everyone performs at the same level is to take measures to crush the dreams of those with too much potential, a vision that I think most people, including most on the Left, would find horrifying if they took the time to fully consider it.

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  7. After typing my last comment here, I listened to an NPR podcast of a segment of the show Science Friday, where the host, Ira Flatow, was interviewing a Harvard neuroscientist, Jeff Lichtman, about his pursuit of fine-grained imaging of the connections in the brain. I like to the audio file is here.

    The part that I thought was amusing was 15 minutes in, after Lichtman explained that memories are likely distributed across main parts of the brain, Flatow came in to discuss what he thought was a related topic:

    Flatow: And one of the things you write about and we’ve talked about is how plastic your brain is, right?

    Lichtman: [reluctantly] Yeah.

    Flatow: It can be remolded, reshaped.

    Lichtman: Yeah, so I think the emphasis, especially as we get older is on how plastic our brains are, but of course there’s the other side of the coin, and I think this is often left unsaid, but I’d like to emphasize this, that the purpose of memory is to give you the opportunity, based on, often, one trial learning at some point in development, a lasting indelible impression of the way the world is, and that is a bit at odds with a constantly changing brain, and I think, if my own daughters’ comments to me are any reflection, as I’ve gotten older, I get the impression my children think that my brain has…hardened, calcified, I’m a little less open to new ideas that I was when I was younger, and I see this as wisdom, not really a bad thing, you know, that I’m left with a brain that’s consistent with the world, but of course the world’s changing very rapidly now, so this is a somewhat painful thing for people my age as new tools get invented.

    But I think memory’s main purpose is not to constantly change, but to hold on to, for example, how to ride a bicycle. If you learn as a child how to ride a bicycle, you can stop riding a bicycle for twenty, thirty years; you get on a bicycle as an adult and after a moment or two of unsteadyness, you’re riding pretty well. But look at an adult who’s never riden a bicycle as a child and its clear, there’s something about their brain, there’s some indelible trace about bicycle riding that’s missing and they have a hard time learning.

    Besides being a rather amusing example of a media personality leading the story to the topic he thought was poignant, rather than what the researcher thought was important, I think that that little segment helps highlight some of the issues with the media’s portrayal of neuroplasticity (as well as epigenetics).

    From what I understand, neuroplasticity plays an important role in learning and our brain is at its most plastic when we are youngest and grows less plastic over time. Lichtman thought it necessary not only to point that out, but also to highlight how that can be a good thing, while bringing the discussion back to the original topic of memory. The fact is that plasticity is a functional characteristic of the brain that fits into a broader strategy. By focusing on plasticity as a magic domain of inquiry, the media (and the broader cultural Left of which they are a part) loses focus of its place in the broader scheme of things, which is probably the most important element of covering the story in the first place.

    Tying back to epigenetics, I think it’s clear that epigenetic control is simply part of how the body works and reacts to the environment around it. While the narrative that it goes beyond genetics is enticing to a certain set of people, that narrative kind of misses the point. Epigenetics is another layer of complexity on top of simple gene expression, but it certainly doesn’t abolish the importance of genes and genetic variation; rather, it is another layer through which genes interact.

    The fact, as has been repeatedly advertised, that identical twins, for instance, have differences arising from stochastic events in the womb and develop different patterns of genome methylation over the course of their lifetimes, makes it all the more remarkable that identical twins show the levels of similarity that they do. Rather than serving as an argument against the power of genes, as it is often framed in these discussions, the similarity in patterns of looks and behavior shows how central to our lives the information within the nucleus of our cells is.

    Obviously the revelations of the paper are another example of how those who approach these subjects with an ideological agenda miss the forest for the trees when they fail to note that this miraculous area of study that promise to take us beyond genetics concerns a mechanism that is itself encoded in the genome.

    Reply

  8. @r.a. – Obviously the revelations of the paper are another example of how those who approach these subjects with an ideological agenda miss the forest for the trees when they fail to note that this miraculous area of study that promise to take us beyond genetics concerns a mechanism that is itself encoded in the genome.

    well that’s the thing, isn’t it? they don’t want to see the forest. they barely see the trees, either, with their lack of understanding of anything biological. to “believe” in science and evolution is, for most people nowadays, just a trendy thing — they haven’t given a moment’s thought to any of it.

    epigenetics and neural plasticity and any other plasticity that you can think of all make sense when you give half a thought to natural selection and how things work out there in Mother Nature. an organism that had no flexibility in any of its systems would inevitably become extinct unless it had an eternally unchanging environment and no competition from any other organisms. it makes sense to have a few hacks (like the methylation things that seem to happen during famines) in order to be able to respond to changing circumstances. it makes sense to have some neural plasticity, again, to be able to respond to changing life circumstances. but if our brains were 100% plastic, we’d barely be able to walk or talk. (~_^) (the bicycle example was great — i’m gonna reference that a LOT going forward.)

    @r.a. – “In fact, it seems to me that epigenetics merely describes a set of mechanisms by which the environment interacts with our genes…. I think it’s clear that epigenetic control is simply part of how the body works and reacts to the environment around it.”

    exactly!

    thnx for those thoughtful comments, btw. lot of food for thought there! (^_^)

    Reply

  9. @r.a. – “At one level, the enthusiasm for these pet concepts (epigenetics and neuroplacticity, among several others) may simply be a desire to bury ‘genetic determinism’, which is seen to be a highly pernicious doctrine to those on the left. I believe that hbd chick saw this in a recent exchange at Bloggingheads.tv.”

    the funny thing is, that little exchange at bloggingheads had the reverse on me than what, i suppose, many of the commenters there intended: the intensity of their hostility and the obvious fact that they were arguing from pure emotion just worked to convince me that i am right. (~_^) or, at least, on the right track.

    after all, the majority is always wrong.

    Reply

  10. “may simply be a desire to bury “genetic determinism”, which is seen to be a highly pernicious doctrine to those on the left.”

    Blahblahblah, LEFTIES are out to get us with a soshulist nightmare!

    Seriously, how can conservatives blab about Teh Left’s misappropriations of science? Because some jerk wrote an article titled “Why DNA isn’t destiny”? That’s your representative sample of Teh Hated Left?

    Pathetic. And from the ideological corner whence Creationism — er, Intelligent Design — sprang. I seriously think y’all lack a workable theory of mind — no ability to fathom the motives of others.

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  11. “Seriously, how can conservatives blab about Teh Left’s misappropriations of science?”

    Easily. There’s Boas, Gould, Lewontin and hundreds more as examples. The blank slate idealogy is and was a deliberate lie.

    .
    “Pathetic. And from the ideological corner whence Creationism — er, Intelligent Design”

    The blank slate is leftist creationism.

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  12. So let me be sure I understand this weighty retort: Since Gould et. al were lefties back in the day who propounded the silly blank-slate idea, then some fool writing “Why DNA isn’t destiny” is therefore a representative sample of Teh Insidious Left-Liberal-Lefties-Far-Left-Leftisms. And as a result, Teh Commie-Libs are clearly doing their nefarious best to use epigenetics to put factories under worker control.

    That about right? Great premise.

    Of course, that’s not to go into the details, such as the fact that rock-ribbed conservatives like Noam Chomsky and E.O. Wilson loudly opposed the ridiculous blank slate idea, and it died an ignominious death, poor, alone, and unknown sometime last century.

    But let us take seriously for a moment the premise that Teh Far-Left-Liberal-Left is scheming to take our freedom fries with soshalist control. How deep does this effort go? Is this what our president and vice propound, as well as the Dem presidential nominees of 2008? How ’bout Dem congressmen?

    Not a one. Well, maybe Kucinich woulda. You never know.

    And the creationists? The Republican field is freaking packed with them. Only Romney stands out as unsupportive of Creationism, and he’s too afraid of the rest of the Repub electorate to publicly oppose the idea. Oh, and Paul. But I could sit here all day counting the Bachmanns and the Santorums and O’Donnells.

    That’s not to mention the vast field of conservative pundits and think tanks arrayed to destroy basic biological science concepts. I’m having a hard time believing that people knowledgeable in biosciences would consider these people as ideological brethren. Y’all are undergrads, right?

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  13. @chris – “I seriously think y’all lack a workable theory of mind — no ability to fathom the motives of others.”

    “Y’all are undergrads, right?”

    quit it with the personal insuts or i’ll ban your ass.

    Reply

  14. chris

    “So let me be sure I understand this weighty retort…blah…Y’all are undergrads, right?”

    Straw man nonsense loaded with passive-aggressive ad hominems avoiding the issue.

    Blank-slate idealogy is and was Marxist creationism. It’s a pack of lies designed, created and enforced by people like Boas and Gould to aid a specific political agenda.

    Marxists and their fellow travellers have no right to criticize creationists while the earth-circling lies of blank slate idealogy are still rigidly enforced by an academic inquisition.

    .
    “That’s not to mention the vast field of conservative pundits and think tanks arrayed to destroy basic biological science concepts.”

    ditto the left and their blank slate idealogy except multiply the array by 100.

    .
    Since Tim Wise’s little genocidal rant i take “y’all” to be a thinly disguised anti-white slur.

    Reply

  15. and that’s the part that the happy leftists are missing from their thinking [sic] about epigenetics. epigenetics is obviously some sort of adaptation … so it must be coded for in our genes somewhere. that methylation happens to alter the expression of genes isn’t some miracle, however amazing it may be. it’s coded for:

    Uh, the Time article you quote in no way missed that point.

    At its most basic, epigenetics is the study of changes in gene activity that do not involve alterations to the genetic code but still get passed down to at least one successive generation.

    and

    it’s important to remember that epigenetics isn’t evolution. It doesn’t change DNA. Epigenetic changes represent a biological response to an environmental stressor. That response can be inherited through many generations via epigenetic marks, but if you remove the environmental pressure, the epigenetic marks will eventually fade, and the DNA code will — over time — begin to revert to its original programming.

    You seem to be arguing with a strawman here.

    Reply

  16. I guess my point is, can you show me the passage in the Time article where the guy shows he is unaware that that epigenetic changes are a type of adaptation and that they must be coded for in our genes? Because from the parts I just excerpted and the rest of the article I read, the author seems pretty aware of that.

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  17. @ricky raw – “I guess my point is, can you show me the passage in the Time article where the guy shows he is unaware that that epigenetic changes are a type of adaptation and that they must be coded for in our genes?”

    just to be clear: the epigenetic changes themselves — for instance, the methylation of dna — are NOT “coded for in our genes.” that is the whole point. the epigenetic changes happen in the epigenome.

    what must be coded for in our genes, though, is the process by which methylation (and other epigenetic processes) happen. it must be. how do epigenetic changes happen otherwise? where do they come from? the ether? no. it is a biological process, that’s all. the researchers in the article that i quoted in my post looked into just this: which genes regulate epigenetic processes.

    the journalist from the time article misses this completely. he discusses at some length that methylation happens, and even some of the mechanics of it, but he doesn’t explain what regulates it.

    it’s been my impression that this is a major point that most politically correct proponents of epigenetics miss. they are delighted to hear that our gene expression can be “overcome” by epigenetics — by “nurture” — but they don’t seem at all to think about the biological foundations of the process. (not that i know what they are! but i have grasped the fact that epigenetics is not magic.)

    my prediction is that teh scientists will find that different populations have different genes (alleles) related to epigentic processes. i betcha methylation, for instance, happens at different rates and in different ways under different circumstances in different populations. not that there’s anything wrong with that! that’d just be a result of evolution by natural selection.

    (in any case, epigenetic effects are really quite rare, so they probably don’t matter much in terms of evolution and changes to populations.)

    Reply

  18. i guess i’ll have to just agree to disagree with you then. you seem to just be reaching for a reason to critique the article. i don’t see him ignoring what you say he’s ignoring at all just because he’s not explicitly harping on it. nothing he says is actually contrary to what you’re saying, and your point doesn’t really change his ultimate point either.

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  19. it’s been my impression that this is a major point that most politically correct proponents of epigenetics miss. they are delighted to hear that our gene expression can be “overcome” by epigenetics — by “nurture” — but they don’t seem at all to think about the biological foundations of the process.

    i have never read these types of articles you mention. this one from time definitely doesn’t fall into this category, so i imagine that these other articles you mention don’t either. the Time article seems to think about the biological foundations of the process pretty clearly. he clearly says that epigenetics doesn’t actually change the genes, and that genes will return to expressing previous traits if the environment was ever to return to previous states as well. he’s not ignoring the biological foundations of anything.

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  20. @ricky raw – ” the Time article seems to think about the biological foundations of the process pretty clearly. he clearly says that epigenetics doesn’t actually change the genes….”

    yes. but he doesn’t explain where epigenetic processes come from. that is my point.

    nor have i seen any pop sci article anywhere attempt to explain that … although i haven’t read many pop sci articles on epigenetics in a while.

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  21. @T. AKA Ricky Raw:

    Look, you and I have argued about this before. As the above link indicates, it’s unclear that Lamarckian epigenetic changes – the kind that can get passed down from parent to offspring – even take place. The entire subject (which is worthy of investigation, as are most things) is, thus far, largely built on an enormous pile of BS.

    That might change at some time in the future, but we’re not there yet. I’m content with dismissing epigenetic claims whenever they’re brought up (99.9% of the time done to dismiss genetic inheritance) unless they’ve got some good evidence.

    Indeed, I’ve been mulling around the idea of of compiling a page of “HBD-denial Tells”, which would include arguments which – when invoked – generally signal that the person who invoked them has no idea what the h*ll they’re talking about. “Epigenetics” would be near the top of that list.

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  22. @jayman – “Wiring the Brain: The Trouble with Epigenetics (Part 1)

    Wiring the Brain: The Trouble with Epigenetics (Part 2)”

    yes! good ones. thanks! (^_^)

    Reply

  23. @ricky raw – “…your point doesn’t really change his ultimate point either.”

    well, i’m not sure what the time journalist’s ultimate point is, but i think that the ultimate point of most of the very vocal proponents of epigenetics in the popular press is that — hallelujah! — epigenetics will somehow free us from the influence of our genes.

    however, my point is that epigenetic processes are, in fact, rooted in our genes. the way that epigenetics works is coded for in our genes — so we’re back to square one again.

    Reply

  24. […] *) Aktuell höre ich immer mal wieder was von “Epigenetik”, nach der irgendwie Lamarck doch Recht in Sachen Vererbung gehabt haben könnte. Vor allem Linke scheinen diese Epigenetik zu stützen. Dass sie jedoch nicht als Beweis taugt, die Erblichkeit der Intelligenz zu widerlegen, liest man sehr nett geschrieben hier. […]

    Reply

  25. Excuse me but, epigenetics can cause mutation non randomly too, so finding out a mutation can have an affect on eg: methylation does not actually mean the cause is genetic.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4622673/
    http://www.ncbi.nlm.nih.gov/pubmed/23281708

    Your beloved additive genetic model, everything right down to the core of “HBD” is totally contested now thanks to epigenetic research.

    http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080

    Its funny because you guys have no idea of the beat down thats coming. The final beat down.

    Reply

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