Epigenetics: Cultural differences do affect DNA, researchers say

_{Denyse O'Leary

January 24, 2017

Epigenetics, News}

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methylated DNA molecule/Christoph Bock/CeMM

The study examined DNA methylation — an “annotation” of DNA that alters gene expression without changing the genomic sequence itself — in a group of diverse Latino children. Methylation is one type of “epigenetic mark” that previous research has shown can be either inherited or altered by life experience. The researchers identified several hundred differences in methylation associated with either Mexican or Puerto Rican ethnicity, but discovered that only three-quarters of the epigenetic difference between the two ethnic subgroups could be accounted for by differences in the children’s genetic ancestry. The rest of the epigenetic differences, the authors suggest, may reflect a biological stamp made by the different experiences, practices, and environmental exposures distinct to the two ethnic subgroups.

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Researchers and clinicians have known for many years that different racial and ethnic populations get diseases at different rates, respond differently to medications, and show very different results on standard clinical tests: “For a whole range of medical tests, whether your physician is told that your lab result is normal or abnormal depends entirely on the race/ethnicity box that you tick on an intake form,” Zaitlen said.

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The researchers turned to epigenetics to search for answers to these questions because these molecular annotations of the genetic code have a unique position between genetic ancestry and environmental influence. Unlike the rest of the genome, which is only inherited from an individual’s parents (with random mutations here and there), methylation and other epigenetic annotations can be modified based on experience. These modifications influence when and where particular genes are expressed and appear to have significant impacts on disease risk, suggesting explanations for how environmental factors such as maternal smoking during pregnancy can influence a child’s risk of later health problems. Paper. (public access) – Joshua M Galanter et al., Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures. eLife, 2017; 6 DOI: 10.7554/eLife.20532 More.

With luck, epigenetics can thread the defile between “scientific” racism and unquantifiable claims about “environment.” From an epigenetic perspective, whether a person will be affected by a given problem may depend not so much on the genes inherited but on where their switches have been set in recent generations. And switches can be reset, after all.

See also: Epigenetics: How many methylation patterns can be attributed to ethnic ancestry?

Epigenetics becomes, increasingly, a normal study area in science

and

Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

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Comments

wd400: is it just your uninformed incredulity all the way down?
"Functional coherence" wd400, it is in need of an explanation ... Here is Douglas Axe:
What enables inventions to perform so seamlessly is a property we’ll call functional coherence. It is nothing more than complete alignment of low-level functions in support of the top-level function. … Alphabetic written languages, for example, use letters as the basic building blocks at the bottom level. These letters are arranged according to the conventions of spelling to form words one level up. To reach the next higher level, words are chosen for the purpose of expressing a thought and arranged according to grammatical conventions of sentence structure in order for that thought to be intelligibly conveyed. … If the point is to convey one simple thought, a sentence should suffice. If it’s to carry readers through an extended thought process, many sentences will be needed, each carefully crafted to make its own point in a way that coheres with the preceding points and paves the way for subsequent points. … All we’re doing in this chapter is unpacking this intuition to show why our firm sense that certain things can’t happen by accident is absolutely correct. What we’re seeing is that the amount of functional coherence routinely produced by human insight truly can’t be produced by accident. … Whether we speak of impossible coincidences or impossible searches, the hard fact is exactly the same: high-level functional coherence can’t be found by any blind search because this would amount to an impossible coincidence. Only insight can hit a target like that, which is no coincidence. … Although we encountered this hard fact by looking at coherence at the low level of letter combinations, the situation only gets worse as we move up the hierarchy. … Like letters, words must be arranged coherently, which involves choosing good words and putting these words in good order. It isn’t as easy to calculate the likelihood of this happening blindly as it was for forming words from letters. Still, we can easily see that vocabulary is tightly constrained by the writing objective. … Here, then, are eleven seven-letter words chosen randomly from the 93,000-word dictionary that came with my computing software: luffing, dickens, numbers, inbound, roofers, incisor, overlap, Brownie, genomes, avenged, and tallier. In these words I submit there is no hint of a coherent theme. We need go no further. Blind searching fails at all levels. As people who write, we know that the need for insight grows as we move up the hierarchy, and that only makes the coincidence of blind coherence greater and greater. Any process that can’t substitute for competence in either spelling or vocabulary certainly can’t substitute for competence in grammar or composition. Our design intuition has this one exactly right. We need knowledge to write useful instructions, and no accidental process can replace that knowledge. [Douglas Axe, 'Undeniable', ch.9]
Origenes_{January 25, 2017
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SA @ 25, Is that at serious argument? This is "tornado in a junkyard" (one of the worst arguments going) taken to describe development instead of evolution? I really think this might be the least coherent argument against evolution I've ever heard.wd400_{January 25, 2017
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SA, Your new story with the mussels is different than the old one (that they were maintaining a response that will one day be adaptive but has no purpose at present). Nevertheless... Nothing in the mussel paper demonstrates an inherited epigenetic state. Mussels in all populations in the US harden their shells in response to native crabs, in the region exposed to the new crab species they do the same to this new crab too. That requires only a mutation to the protein that acts as receptor to the chemical cues given by the crabs. Such an allele might already have existed and low frequency or have been created by mutation after contact. We could now test that hypothesis with genomic sequencing. But there is certainly no evidence that this is an inherited epigenetic trait.wd400_{January 25, 2017
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I could attempt to structure an argument for wd400: 1. Any number of organisms could either function as individual entities or as a unified whole. 2. As with chemical bonds, the exactness of the presence of similar chemical properties (hydrogen, oxygen & heat = H2O) yields a higher probability of a bond, and a more variable, dissimilar properties yield a lower probability of a bond. 3. The human body contains a large number of highly dissimilar elements (± 37 trillion cells that can differentiate in ± 200 different cell types). 4. Therefore the likelihood of them bonding together into one unified entity is virtually zero. 5. It follows then, that evolutionary theory, which claims it is highly likely that they will bond, fails.Silver Asiatic_{January 25, 2017
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Origines, I'm not very interested in the 20 questions routine. Do you have an actual argument, or is it just your uninformed incredulity all the way down? If you are interested in how cells pull together to make an organism then I suggest you learn about the molecular basis of cancer. Cancer is, more or less, what happens when cells stop working together. This is very nearly universally the result of mutations in the DNA of the affected cells....wd400_{January 25, 2017
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wd400
Again, I don’t think you are following what it being said. In that copy-paste the “future” state is part of the development of an organism, not an environment some descendant will face many generations hence…
It's a parallel idea. But back to the example given, where blue mussels adapted by thickening their shells when they encountered a new environment ...
Such rapid evolutionary response is a "nanosecond" compared with the thousands of years that it normally takes for a species to respond to a predator.
What is your explanation for that? This was not a case where a beneficial mutation occurred in an individual and then spread through inheritance and selection for generations. This, instead, is called an example of epigenetic change.Silver Asiatic_{January 25, 2017
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wd400:
Origenes: Do you seriously hold that differentiation of our cells is driven by DNA?
Pretty much, yes.
The human body consists of ± 37 trillion cells that can differentiate in ± 200 different cell types. Do you agree that a coherent result is inconceivable without some higher level coordinative power? If not, why not?
wd400: ... the developmental program that let to creation of each cell is certainly in the DNA of every cell ...
How do you explain that 37 trillion separate programs function as one organism?Origenes_{January 25, 2017
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Do you seriously hold that differentiation of our cells is driven by DNA
Pretty much, yes.
Do you hold that DNA in ± 37 trillion cells have organism-wide control?
I don't think any cell has "organism-wide control". But the developmental program that let to creation of each cell is certainly in the DNA of every cell (with exceptions for mature red blood cells and a few somatic mutations etc)wd400_{January 24, 2017
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wd400: ... genetics is driving epigenetic states ...
Simple question for wd400: what controls the differentiation of cell types, and how are they all coordinated so as to function as one organism? Do you seriously hold that differentiation of our cells is driven by DNA? Do you hold that DNA in ± 37 trillion cells have organism-wide control? If so, why is it that this makes sense to you? Frankly, I cannot even consider that possibility without making a grimace.Origenes_{January 24, 2017
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Again, I don't think you are following what it being said. In that copy-paste the "future" state is part of the development of an organism, not an environment some descendant will face many generations hence...wd400_{January 24, 2017
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Thanks to Origenes for the Stephen Talbott excerpt.
The genes are kept, so to speak, in a finely poised state of “suspended readiness”, so that when the decision to specialize is finally taken, the repressive modifications can be quickly lifted, leading to rapid gene expression
That's what I said, wd400. The genes are "ready" for a future state. You said you don't know of any examples of this. Perhaps you could ask Mr. Talbott for a better one than I gave you? I'll add, this is not change by mutation and selection. Agreed?Silver Asiatic_{January 24, 2017
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For me this article by Stephen Talbott has been real eye-opener wrt DNA and epigenetics. Excerpt:
If you arranged the DNA in a human cell linearly, it would extend for nearly two meters. How do you pack all that DNA into a cell nucleus just five or ten millionths of a meter in diameter? According to the usual comparison it’s as if you had to pack 24 miles (40 km) of extremely thin thread into a tennis ball. Moreover, this thread is divided into 46 pieces (individual chromosomes) averaging, in our tennis-ball analogy, over half a mile long. Can it be at all possible not only to pack the chromosomes into the nucleus, but also to keep them from becoming hopelessly entangled? … Histone proteins, several of which can bind together in the form of an extremely complex histone core particle, are the single most prominent constituent of this chromatin. Every cell contains numerous such core particles — there are some 30 million in a typical human cell — and the DNA double helix, after wrapping a couple of times around one of them, typically extends for a short stretch and then wraps around another one. ... Histones can even be removed from a spool altogether, leaving it “incomplete.” And certain proteins can slide spools along the DNA, changing their position. As we have seen already, a shift of position by as little as two or three base pairs can make the difference between gene activation or repression, as can changes in the rotational orientation of the DNA on the face of the histone spool. … Further, not only the exact position of a nucleosome along the double helix, but also the precise rotation of the helix is important. “Rotation” refers to which part of the DNA faces toward a histone surface and which part faces outward. … The canonical nucleosome core particle is a complex of histone proteins, each of which has a flexible, filamentary "tail". This tail can be modified through the addition of several different chemical groups — acetyl, methyl, phosphate, ubiquitin, and so on — at any of various locations along its length. A great variety of enzymes can apply and remove these chemical groups, and the groups themselves play a role in attracting a stunning array of gene regulatory proteins that restructure chromatin or otherwise help choreograph the drama of gene expression. … Nucleosomes will sometimes move — or be moved (the distinction between actor and acted upon is forever obscured in the living cell) — rhythmically back and forth along the DNA, shifting between alternative positions in order to enable multiple transcription passes over a gene. In stem cells a process some have called “histone modification pulsing” results in the continual application and removal of both gene-repressive and gene-activating modifications of nucleosomes. In this way a delicate balance is maintained around genes involved in development and cell differentiation. The genes are kept, so to speak, in a finely poised state of “suspended readiness”, so that when the decision to specialize is finally taken, the repressive modifications can be quickly lifted, leading to rapid gene expression
It’s more than clear that something incredibly complex/mysterious is controlling gene expressionOrigenes_{January 24, 2017
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The challenge is to explain how this genetic response mechanism arose, which is sensitive enough to respond to novel characteristics in the environment. Features in the organism, with no apparent, immediate fitness benefit, have to be preserved for the time when a new environmental trigger arises.
Your example is not like this at all though? I'm not sure which bit of that study you are misunderstanding, so not sure how to correct you...wd400_{January 24, 2017
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wd400 You stated:
No doubt some of the marks are in fact such a plastic response to an environmental cue.
The challenge is to explain how this genetic response mechanism arose, which is sensitive enough to respond to novel characteristics in the environment. Features in the organism, with no apparent, immediate fitness benefit, have to be preserved for the time when a new environmental trigger arises. An example:
Mussels Evolve in an Evolutionary Heartbeat http://www.livescience.com/954-mussels-evolve-evolutionary-heartbeat.html "The mussel's inducible response to H. sanguineus reflects natural selection favoring the recognition of this novel predator through rapid evolution of cue specificity or thresholds," the researchers write in the Aug. 11 issue of the journal Science The mussels most likely evolved quickly because they are used to being prey to many species in these waters. "When Hemigrapsus came along the mussels' wheels were well-greased to respond," said co-author James Byers, associate professor of zoology at the university. "That's our best guess."
As above, Prof. Byers uses the term "well-greased" meaning there is a function already in place, anticipating a future state which may or may not occur.Silver Asiatic_{January 24, 2017
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SA,
As above, he doesn’t understand the debate. It’s not a matter of how it affects evolution, which he admits he doesn’t understand anyway — but how that response mechanism arose through random mutations and selection over a long period of time.
That might be your question, but I don't think many anti-evolutionists are saying this. For the most part they conflate every epigenetic result with transgenerational epigenetics and say "Lamark was right, Darwin was wrong" and end about there.
It’s the preservation of features for a future, unknown benefit – and evolution is not supposed to do that.
Do have an example of this to cite? I don't know now of any..wd400_{January 24, 2017
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I've said this before, but a good question for someone trying to make a lot out of an epigenetic result to ask is "how is this different than the lac operon?"wd400_{January 24, 2017
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This illustrates a lot of what's wrong with the way News and others report epigenetics. For the record. There is no reason to think any of these marks can be inherited over generations, the study itself shows most of the measured variation in methylation is the result of genetic variation (i.e. genetics is driving epigenetic states), there is no evidence that other marks are an adaptive response to the shared environment of the socially-constructed ethnicity (rather than passive consequence of shared exposure). No doubt some of the marks are in fact such a plastic response to an environmental cue. But it's absolutely bizarre to imagine that regulation of gene expression and gene-environment interactions are not part of evoluioanry biology. Evolutionary biologists had to invent quantative genetics (in the 1920s!) to deal with these topics, and they've been a major focus ever since.wd400_{January 24, 2017
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For some reason today I took a look at our competitor (they think they are) site The Skeptical Zone. From there I started reading VJ Torley's comments on Early embryonic mutations, responding to Meyer & Axe's top 5 problems with evolution. Within that, I noted Prof. Torley dismissing epigenetics as a problem stating "Professor Larry Moran has addressed it more than adequately in his recent post, What the Heck is Epigenetics?" and concluding "So much for epigenetics, then." That struck my interest - certainly. So, off to Prof. Moran's blog. And now my head still hurts - more from Prof. Torley than Moran. I'd expect some hand-waving from a committed evolutionist, but to cite that article as "so much for epigenetics?" He can't be serious. No, you're not supposed to just claim epigenetics as part of the theory - you have to explain the origin of this process. The Cornelius Hunter article is devastating in comparison. Moran, like wd400, doesn't even want to admit that the term epigenetics has legitimacy. But then in the comments to the very same article that supposedly refutes the problem of epigenetics, Moran states:
The debate is centered on INDUCED changes in methylation and/or histone modifications. The argument is that these changes can be affected by the environment and then passed on to subsequent generations. That's how epigenetics is supposed to affect evolution.
As above, he doesn't understand the debate. It's not a matter of how it affects evolution, which he admits he doesn't understand anyway -- but how that response mechanism arose through random mutations and selection over a long period of time. It's the preservation of features for a future, unknown benefit - and evolution is not supposed to do that. Moran continues ...
But those kinds of change are associated with the regulation of gene expression. That's why you can make the Lamarckian argument. (It's not clear whether they are cause or effect.) By definition, those kinds of change are reversible—that's how they arose in the first place.
That was good enough for Professor Torley to have no further concern?Silver Asiatic_{January 24, 2017
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Thanks, Silver Asiatic, I'll take a closer look when I get a little free time.daveS_{January 24, 2017
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The article about Michael Skinner that BA77 posted is very good. As with the paper here in the OP, evolutionists will now talk about epigenetics as if there is no problem at all with evolutionary theory. It's just called "epigenetic evolution". Once you assume that evolutionary theory is true, there is never any need to prove the origin of anything found in biology. Even though such things like this contradict the theory. Some sort of mutational path has to be show for how an organism's DNA can change when introduced to a new environment. In evolutionary theory, the organism should either die, or just get lucky with a mutation that enables survival for some. Eventually that should lead to a new species. Instead, the organism responds immediately and the changes occur in order to preserve itself, not to cause it to change into a new species.Silver Asiatic_{January 24, 2017
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Thank you SA and BA77. I will look at the links this evening.Truth Will Set You Free_{January 24, 2017
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daveS & TWSYF BA77's links are very good, as always. It's complicated because when we say "contradicts evolution" we have to mean strictly that it "contradicts the theory of evolution as claimed by mainstream science today". What eventually happens is that term "evolution" will be used to cover the topic of epigenetic change also since organisms are seen to change. But that's wrong because there is no theory that explains epigenetic change and nothing that explains its origin. wd400 for example, avoids this problem and just says something like "we've known about so-called [he doesn't even like the term] 'epigenetics' for decades and it's all fully a part of evolutionary theory." But epigenetics is radically different from neo-Darwinian evolution. In epigenetic changes, the genome is responsive to environmental changes and DNA will adjust itself with built in markers that anticipate environmental stimulus. So, there's a non-random relationship between the genetics of a population of organisms and the environment. Explaining the origin of this would require an explanation of the fitness benefit of a relationship that anticipates future changes - as well as the rapid modification of cell functions in response. In evolutionary theory, mutations occur randomly in individuals, and then by "selection" (the dying off of those that don't have the beneficial mutation) the population gradually changes. There's no response to the environment, although we mistakenly think it appears that there is. It's really just an accidental mutation that enables an organism to survive better. The mutation doesn't know or care about the environment - nor does the DNA itself. But with epigenetic changes, the organism is able to make genetic changes in response to the environment and it occurs within the population, not in an individual getting a random mutation and then waiting centuries for it to spread.Silver Asiatic_{January 24, 2017
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TWSYF:
The Mysterious Epigenome. What lies beyond DNA - video http://www.youtube.com/watch?v=RpXs8uShFMo "The Mysterious Epigenome: What Lies Beyond DNA" - May 2012 - podcast http://intelligentdesign.podomatic.com/entry/2012-05-30T12_57_28-07_00 Chuan He: Evolution Created Epigenetics - Cornelius Hunter - PhD in Biophysics - May 3, 2015 Excerpt: They never predicted it, then they denied it could be heritable, and then they denied it could cause lasting change. “It” in this case is epigenetics and in spite of being wrong, wrong and wrong again, and in spite of the fact that there is no scientific explanation for how epigenetics could have evolved, evolutionists nonetheless insist that it, in fact, must have evolved. Evolution loses every battle but claims to win the war. http://darwins-god.blogspot.com/2015/05/chuan-he-evolution-created-epigenetics.html Michael Skinner on Epigenetics: Stage Three Alert - Cornelius Hunter - December 4, 2016 Excerpt: What Skinner and the evolutionists don't tell you is that in light of their theory, none of this makes sense. With epigenetics the biological variation evolution needs is not natural. It is not the mere consequence of biophysics -- radiation, toxins, or other mishaps causing DNA mutations. Rather, it is a biological control system. It is not simple mistakes, but complex mechanisms. It is not random, but directed. It is not slow, but rapid. It is not a single mutation that is selected, but simultaneous changes across the population. This is not evolution. As Skinner inconveniently realizes, such epigenetics are found across a wide range of species. They are widely conserved and, for evolution, this is yet more bad news. http://www.evolutionnews.org/2016/12/michael_skinner103338.html The Science Contradicts The Theory - Cornelius Hunter - video - 42:00 minute mark https://youtu.be/HTIlHEn9hXs?t=2501
bornagain77_{January 24, 2017
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Silver Asiatic,
I will reluctantly agree with wd400 … none of these papers ever say that such findings are a problem for evolution. Even though it really is! But we end up as the only ones drawing that conclusion.
I don't know anything about epigenetics, but could you explain how it is a problem for evolution? If I understand correctly, it concerns physical changes that can be inherited (for a few generations, at least). Does it contradict evolutionary theory?daveS_{January 24, 2017
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Forgive my ignorance, but I don't really understand epigenetics. What is it in a nutshell and why is it a problem for evolution?Truth Will Set You Free_{January 24, 2017
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I will reluctantly agree with wd400 ... none of these papers ever say that such findings are a problem for evolution. Even though it really is! But we end up as the only ones drawing that conclusion.Silver Asiatic_{January 24, 2017
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Of semi-related note: Jonathan M has the Jonathan Wells video up:
Design Beyond DNA: A Conversation with Dr. Jonathan Wells - video https://www.youtube.com/watch?v=ASAaANVBoiE
bornagain77_{January 24, 2017
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Very interesting.Dionisio_{January 24, 2017
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