10 ms·

"There's new evidence that historical trauma is passed down through changes to the genome!" "Genome or epigenome?" "...epigenome." I feel like I read of a si

• svara 2y ago
  DNA methylation is epigenetic, and that's a direct chemical alteration of DNA. The title isn't wrong, and your example sentence isn't wrong either.
  • red75prime 2y ago
    Epigenetic changes are scrubbed from germ cells. It's unclear whether observed persistence is explained by the changes escaping scrubbing process or by reintroduction due to other mechanism (being raised by a single mother, refugee hardships and the like).
• ForTheKidz 2y ago
  > But they don't change human genes, at most they change gene expression. It's not clear in this case what the difference is between gene, gene expression, and gene encoding. What does gene mean if it does not imply either encoding or expression? If this is a disagreement about the semantics of encoding, surely it'd be easiest to express this in terms of encoding. If this is about gene expression, surely it'd be easiest to express this in terms of expression. "gene" largely has no meaning outside of encoding/expression. It seems clear to me the article is indicating a distinction of encoding. I'm not sure where the ambiguity is.
  • JumpCrisscross 2y ago
    > What does gene mean if it does not imply either encoding or expression? The less mutable part. The strongly heritable stuff. Genes are part of your body, as is your brain, that doesn’t mean your every thought is equivalent to DNA.
    • ForTheKidz 2y ago
      So, you're referring to encoding via DNA? Why not just say that explicitly rather than refer to some occluded understanding of the word "gene"? This also seems to be a semantic distinction largely irrelevant to understanding the article as presented.
    • tpoacher 2y ago
      Having said that, there's some very recent research to suggest that memories / neuronal weights are actually encoded directly in neuronal DNA. (this does not mean that this DNA is directly heritable, since it does not necessarily end up in the gametes, but it is still interesting that, yes, in fact, it involves DNA change)
  • sdwr 2y ago
    Yeah, people are holding on to the rigid, simplistic, outdated notion that DNA is the "genetic code" that defines everything. I think neural nets show that, realistically, evolution requires backpropagation (epigenetics).
    • rightbyte 2y ago
      I don't think it requires it but it would certainly be an edge with "backpropagation"?
  • derefr 2y ago
    First, a point of clarification: coding and encoding are two different things. "Encoding" is a CS term that doesn't come up much in biology. (You could say that DNA is an encoding of a base-4 number sequence.) "Coding" is a bioinformatics term — DNA base-pairs code for particular RNA sequences; and then, only if they're in a coding region. (Analogy: flux patterns on a floppy disk code for particular bytes, but only if they're in a sector.) Second: what are genes? A "gene" is an abstraction. Let's first define a "genome". A genome is the complete dump of raw data of "what the DNA base-pair sequence string says" — before any coding or expression occurs. Whenever we sequence DNA, it's [parts of] this raw base-pair string that we get back — not the codons, not the expressed RNA sequences. And this is why we care — sequencing is the tool we have, so it's the lens by which we look at DNA. And that lens shows us the raw data. When we talk about "genes" (or "SNPs" / other bioinformatics terms), we're basically talking about the ways in which that raw data we can extract through sequencing, relates to observed phenotypic changes. A "gene" is a particular part of a "genome" (DNA base-pair sequence) that can be uniquely identified as being the cause of interesting phenotypic consequences when changes are made to it. (Which in turn is how we figure out what genes are "responsible for" doing what.) Note how these concepts, "genome" and "gene", both completely ignore epigenetics / gene expression. That's because these terms were invented before epigenetics was invented, and these terms are part of a model that uses a lens (DNA sequencing) that itself ignores epigenetics. Gene sequencing shows you the world of DNA as if epigenetics didn't exist. Now let's talk about DNA. If you think that epigenetics is about changing how DNA encodes information, then you might be thinking of "DNA" via the lie-to-children model, of it just being a long sequence of nucleotides. But consider: why do chromosomes look the way they do — little X shapes? A long string of base pairs, on its own, has no reason to assemble into that macroscopic shape. This is because "DNA" — which is really a shorthand for "the DNA complex" (i.e. a complex of multiple weakly-bound molecules that together form the chromatin of a chromosome) — is not just nucleotide base-pairs. The nucleotide base-pairs form one molecule (the deoxyribonucleic acid string itself); but then you've got other stuff. You've got histones — little tape-spools the DNA string is wrapped onto. You've got methyl groups — little markers hanging off particular places on the DNA string. You've got other stuff I don't personally understand/know about. When lay-people talk about "DNA", they're really referring to the whole complex of molecules that makes up each one of your chromosomes. "Genes" are just the bioinformatic data representation of the deoxyribonucleic-acid-base-pair-string part of that complex of molecules. But gene coding, and gene expression, are both a result of what the other molecules in that complex are doing. (Think about it: if gene coding + expression were encoded in-band by the DNA itself, then that information would be appear in DNA sequencing — and so we'd be unable to differentiate that information from changes to the DNA itself — and so we wouldn't even have a concept of "epigenetics", because it would all just look like "genetics"!) Here's a picture: https://www.genome.gov/sites/default/files/media/images/2022-05/Histone.jpg https://www.genome.gov/sites/default/files/media/images/2022... Histones — those little tape spools — attract or repel each-other due to chemical modifications to the histones themselves. Two histones that "snap together", prevent the region of DNA "tape" between them from being physically accessed by the RNA polymerase enzymes that "read the tape" to produce RNA. Methylation markers hang off of the initial "landing sites" for RNA polymerase enzymes (CpG dinucleotides — think "floppy-disk sector header"), and repel them. When you sequence DNA, you ignore these transcription-silencing signals. You can picture DNA sequencing as "unrolling" the deoxyribonucleic acid off of its histone carriers, rendering them irrelevant; and then using molecular tools to read the sequence — tools that, unlike RNA polymerase, are not repelled by methyl-groups. If you use more-modern techniques to capture this additional information about where these silenced regions are, and by what mechanism they've been silenced, then you get what we call an "epigenome" — which isn't a post-translated version of DNA, but rather sort of a "metadata track" that runs parallel to the DNA "data track." (And you can, in theory, combine the two to calculate an "expressed genome." I don't think we've ever done that yet — partly because "whole-epigenome sequencing" doesn't yet exist in the way that "whole-genome sequencing" does; and partly because epigenetic metadata is probabilistic — with some modifications decreasing the probability of a region coding for something, rather than turning it off altogether — and so current approaches, that derive the epigenome "by reaction", would observe something like "weak bits" on a floppy disk — regions that read differently each time, requiring many passes to calculate a "flux strength" for each region and to find each silenced region's true borders.)
• sensanaty 2y ago
  I'm a complete layman here, but what is the difference exactly?
  • bigbacaloa 2y ago
    [dead]
  • arrosenberg 2y ago
    DNA is source code, and there is a bunch of RNA processes that read it and do stuff to make you live. Parts of DNA can be turned on and off, that’s called expression. Epigenetics is the study of how genes are expressed. Gene expression can change without the genome itself changing depending on external conditions, which is a key part of adaptability.
    • deleted 2y ago
      [deleted]
  • derektank 2y ago
    The gene itself determines the shape and character of a protein; Gene expression refers to the quantity of a protein produced. Changes to the genome are long lasting and somewhat rare inside a living person, while changes to the epigenome happen fairly regularly. A good way to think of this is cell differentiation. Every cell in your body, except eggs and sperm, contains a copy of your entire genome but what differentiates a nerve cell from a liver cell from a skin cell is gene expression. All it takes is some changes to the epigenome of a stem cell during mitosis for one the resulting cells to become a new, differentiated cell.
  • rcthompson 2y ago
    Imagine you have the text of a book in a word processor. You can change the text by typing new words or deleting ones that are there. You can also change the font, size, alignment, etc. The latter category of changes does not alter the words in the text, but it can affect how that text is interpreted, which parts of the text a reader focuses on, etc. The difference between a genetic alteration and an epigenetic alteration is conceptually similar. Genetics is changing the "text" of the genome while epigenetics is changing aspects of the genome that affect how that "text" is interpreted and used.
• derefr 2y ago
  I work as an editor sometimes. I've worked in technical writing, though not specifically science journalism. My guess for why this keeps happening, is that it's a two-step process, fueled by a failure of communication: 1. The science writer themselves does understand epigenetics — but doesn't think it's important to the point the article is making for the reader to understand epigenetics. The writer wants to remove the requirement/assumption of "understanding epigenetics" from their writing, while still being technically correct in everything they say. So they choose to gloss an epigenetic change as "causing changes to the DNA." (Which it certainly does! Either chemically — to the DNA molecules themselves, through methylation; or structurally/topologically — through modifications to the histones around which the DNA is wrapped.) 2. The science writer's not-so-scientific editor comes along, doing a stylistic editing pass; sees the word "DNA"; and says "hey, that's jargon, and we're aiming for accessibility here — we need to replace this." And they (incorrectly) decide that a valid 1:1 replacement for "DNA" is "genes" or "genome." This invalidating change could be caught... if the publication had a formal workflow step / requirement for the editor to perform a back-check with the original writer after copyediting + stylistic editing, to ensure that validity has not been compromised. I believe that big-name science journals and science magazines do tend to have these back-check steps. But smaller publications — like the PR departments of universities — don't.
  • rcthompson 2y ago
    I can't speak for every institution, but our PR department does as many back and forth passes as it takes for the scientists who did the work to sign off that any edits made still preserve scientific accuracy.
    • bluGill 2y ago
      I've never been in a science position, but if there are too many back and forths I assume it is a who has more willingness to put up with process before they just give up and sign off on anything.
      • nitwit005 2y ago
• robwwilliams 2y ago
  These studies are at the interface of genetics, sociology, and political action. They are underwhelming in all three domains. The genetics are based in puny sample sizes, and this has been true going back to the Yehuda study (2015, PMID: 26410355) and remains true of this broader followup (42 controls and only 18 in the germline exposure group). I do not understand designing experiments like this and taking the results seriously, unless we move on to sociology and political action; in which case the motivation is clear: “…may encourage policymakers and humanitarian agencies to provide targeted resources to vulnerable populations…” Hard to argue with that, but do we now use a handful of epigenetic markers generated using a cheek swab sample to decide who gets “healthcare access, special lodging, sanitation, and nutrition”? No, never. One could get a lot further a lot faster doing well controlled experiments in animal models. But even here the sociological context intrudes. Mike Meaney’s original work in the early 2000s is still open to questions.
  • blackeyeblitzar 2y ago
    A lot of sociology research is activist in nature and not rigorous. Is the study similar?
    • robwwilliams 2y ago
      Alas, even the rodent studies are not rigorous.
    • TeMPOraL 2y ago
      Activist "science" is how you turn "hard to argue with" cases into "there's plenty to argue with" ones.
      • TwoPhonesOneKid 2y ago
        I would say it's even better: if flushes out the engineers who never bother to grasp what "science" actually referred to. you'd think empirical observation and iteration would be an easy to grasp concept, but there are individuals that people get tripped up by something unidentifiable. you can spot a mile away. You can see it here, too. Not sure what causes the mental block but it seems to form serious social impediments.
• rcthompson 2y ago
  Describing a change to DNA methylation "alters" a gene is technically correct in the sense that it is an change to the molecular structure of the DNA that makes up the gene, but is indeed misleading, because without further clarification a majority of people would assume it refers to a change in the gene sequence.
  • johnisgood 2y ago
    Should it not be "affects" or "influences"?
    • rcthompson 2y ago
      DNA methylation means adding one or more methyl groups to the DNA, so technically it is an alteration. But most people would assume that altering a gene specifically means changing the "letters" of the gene sequence that encode the protein, and that's not what DNA methylation does.
      • johnisgood 2y ago
        Oh, yeah, I suppose I read "influences behavior" a bit too much. I read about DNA methylation (well, epigenetics in general) in one book for behavioral epigenetics.
  • adamc 2y ago
    But since many of them misunderstand the role of gene sequences, that may be less meaningful than you imply.
• jyounker 2y ago
  Gene and geneome are expansive terms. The genome refers to the sum total of all genetic material in an organism. Epigenenetic markers such as methylations are part of the genetic material, and are therefore part of the genome. You seem to be disappointed in the headline because you're expecting narrower definitions.
• epgui 2y ago
  > they don't change human genes, at most they change gene expression. This is an extremely pedantic distinction, especially since the article as a whole is pretty clear. In nearly all cases, what matters is whether we're talking about information that is encoded and passed down. That's the case here, even if the encoding and persistance characteristics are different.
  • ASalazarMX 2y ago
    It's a crucial difference. Encoding and persistence in your genome means permanent changes, not for a few generations, PERMANENT. Epigenetic encoding and persistence is temporary, even if it expresses for more than one generation. Crucial difference, one is a mutation, the other an environmental adaptation.
    • epgui 2y ago
      Essentially yes, and the article makes pretty clear that the changes last for generations. It's in the title and it's clear throughout the text of the article. So that's a totally moot point.
• blackeyeblitzar 2y ago
  If this headline’s claim were true, why would it apply just to violence and not all experiences? Wouldn’t it imply that all kinds of activities alter genes? For example if you play sports, you might get one type of change and if you were a lawyer, you might get another kind of change and so on.
  • krapp 2y ago
    You should read the actual article, which provides necessary context and nuance, and not just the headline. The article is specifically discussing the effect of stressors caused by trauma (violence) on the transmission of genes from mother to child. The effect discussed does not generalize to all experiences.
• adolph 2y ago
  Although the article text doesn't claim genomic changes, the untitled graphic mentions "germline" in the "1980 Group" column. Not certain how to interpret that. I don't see the graphic in any publication of Mulligan, Panter and Dajani altogether. Mulligan CJ, Clukay CJ, Matarazzo A, Hadfield K, Nevell L, Dajani R, Panter-Brick C. Novel GxE effects and resilience: A case:control longitudinal study of psychosocial stress with war-affected youth. PLoS One. 2022 Apr 4;17(4):e0266509. doi: 10.1371/journal.pone.0266509. PMID: 35377919; PMCID: PMC8979449. Clukay CJ, Dajani R, Hadfield K, Quinlan J, Panter-Brick C, Mulligan CJ. Association of MAOA genetic variants and resilience with psychosocial stress: A longitudinal study of Syrian refugees. PLoS One. 2019 Jul 17;14(7):e0219385. doi: 10.1371/journal.pone.0219385. PMID: 31314763; PMCID: PMC6636744. Panter-Brick C, Eggerman M, Ager A, Hadfield K, Dajani R. Measuring the psychosocial, biological, and cognitive signatures of profound stress in humanitarian settings: impacts, challenges, and strategies in the field. Confl Health. 2020 Jun 23;14:40. doi: 10.1186/s13031-020-00286-w. PMID: 32582366; PMCID: PMC7310257. FAAH, SLC6A4, and BDNF variants are not associated with psychosocial stress and mental health outcomes in a population of Syrian refugee youth Christopher J. Clukay, Anthony Matarazzo, Rana Dajani, Kristin Hadfield, Catherine Panter-Brick, Connie J. Mulligan bioRxiv 685636; doi: https://doi.org/10.1101/685636
• ilyagr 2y ago
  I'm my mind, gene expression is at least as important as the coding genome. AFAIU, the later mostly encodes the structure of proteins, which naively are the factory machines of or cells (enzymes, that is) and some of its building blocks. The gene expression tells the factory what to produce (a tail or an ear, say), when to produce it, and how much. More relevant to the topic of this article, the gene expression would determine which structures and pathways of the brains (or adrenal glands, or any other organs) to suppress, and which to reinforce and build up in a new generation of humans. The building blocks are important, but once they are good enough, it matters more what you choose to build with them.
  • ilyagr 2y ago
    Perhaps what the grandparent meant is that we have little clue to how exactly any particular change in non-coding DNA actually affects the functioning of our minds and bodies, we have few tools to study that beyond the seemingly obvious fact that it does have to encode the structure of all the organs of our body and the fundamental structure of our brains somehow.
• TwoPhonesOneKid 2y ago
  Surely any distinction bewtween ledgers is just as dumb at this point. Who gives a damn how the traits are passed down if that these traits are passed down is still a true statement of fact?
• lukas099 2y ago
  'Course the epigenome affects the genome to via natural selection at the population level.
• rowanG077 2y ago
  It's also fun to see this marketed as generational trauma. Just because gene expression has changed does not mean that is equivalent as trauma.
• casey2 2y ago
  This is implied to me at least by "for generations" As in after x generations the genes "go back to normal"