https://www.nature.com/articles/s41598-025-89818-z

"Genome or epigenome?"

"...epigenome."

I feel like I read of a similar study every few years, the first I can recall was 'Transgenerational response to nutrition, early life circumstances and longevity'[1], and it is always needlessly disappointing to thumb through past the headline and read that, inevitably, the media has decided to report this as a change to the genome when the actual research suggests otherwise.

Epigenetic changes are interesting in their own right! But they don't change human genes, at most they change gene expression.

[1] https://www.nature.com/articles/5201832

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.

Unfortunately, they are just choosing to misrepresent the research sometimes.

That's not a valid defense, otherwise they could write with a straight face that sun exposure causes genetic changes that make you darker, and how your descendants will inherit those changes too. It is dishonest writing, bordering on disinformation. Said article would attract clicks and attention like a cursed magnet, though.

Human systems are imperfect and messy. Understanding how they break down helps us make them better.

“…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.

The argument that "brains are rewired" or "generations of genetics are harmed" is popular in 'trauma informed' arguments for compensation or government help.

I don't think the activism/sociological angle here was supposed to be interpreted as being about targeted reconciliation toward existing victims of violence / their descendants. Even if those people are potentially "living life on hard mode" as a result of previous violence. (After all, finding and helping those people would require complex infrastructure and lots of money.)

Rather, I think the thrust of the implicit activist argument would be closer to:

1. Experiencing violence turns out to be even worse for you than we thought — and in non-recoverable ways! (You can't therapy your way out of epigenetic changes.)

2. And so more should be done to prevent/ameliorate violence and its impact on people, before it can cause durable epigenetic changes;

3. ...and some "low-hanging fruit" in reducing this impact for minimal cost, would be to supply more resources for escaping/coping with violence (e.g. shelters; crisis lines; social workers; restraining orders that actually work) specifically to groups who are demographically most likely to become victims of violence.

4. And perhaps we can even use this correlation we've found to also measure the effectiveness of interventions like these — sampling the trends in epigenomic changes in these vulnerable populations over time (i.e. a repeated cross-sectional study), to know if marginal increases in certain types of resources actually have measurable impacts on "cushioning" these populations from violence, enough to prevent these epigenetic changes.

That's a leap. After all, emotionally distressing experiences presumably caused the epigenetic changes to begin with, so why couldn't other mental experiences alleviate them? Not that we know how to do this at this point, I'm just stating that your claim is not a fact.

Crucially, because these "setup programs" silence themselves after running, these "setup programs" each only have one opportunity to run, at some genetically-defined point in an organism's lifecycle. The information is only collected once. Whatever this "setup program" observed at that point, that's what the epigenome records. There is no second chance to set it differently.

I don't know much about this violence finding, but one famous finding in epigenetics is that mammals whose mothers were often food-deprived during gestation, end up with a marker that correlates with the phenotype of eating more / being more food-motivated / tending more toward gathering more food than is necessary for their immediate satiation.

At least in the case of this food-deprivation finding, there is nothing you can do to/with the animal afterward, that reverses the impact of this epigenetic change. The animal's body doesn't go back and re-evaluate whether or not it "should" be more food-motivated, because the fact it's basing its food-motivation calculations off isn't about what's true now — it's about what was true then. The marker doesn't mean "the environment is currently food-poor", it means "the environment was food-poor when I was -6mo old."

(In fact, these early-natal-development epigenetic markers aren't even necessarily what you might call runtime flags — they're more like an #IFDEF statement in the DNA "codebase", their values first calculated during the long, continuous "build process" of development, and then macro-expanded later in that same build process to hard-code other things — e.g. how certain proteins/tissues and their chemical receptors get built. By the time a baby is born, that marker might actually have no further relevance, having done all its work and made its downstream impacts during gestation. If we had "epigenetic CRISPR" and turned that marker off in an adult person, doing so would only impact whatever that gene does after development — which might be "nothing.")

I just want to add the obvious addendum again: that we know of. We've tried a few obvious things and that didn't change the behaviour, but that doesn't mean much in something this complex.

Use this (faulty) explanation to make a statement about the impact of violence -> direct resources to one demographic or another based on that (faulty) explanation of why it's important.

Your fourth point is entirely valid, if we were performing these measurements & experiments at a large enough scale to have a valid baseline in the first place (which GP was arguing is not the case).

Incorrect. The parent comment was talking about using epigenetic measurements of specific people to decide if they get resources. The child comment was not talking about doing that, instead saying that this research can be used to argue for more resources in general.

The only mention of demographics in the child comment was about groups likely to experience violence. Those groups would have no markers. It would be purely about how we can most effectively reduce violence.

The only measurements suggested in the child comment would be for statistical purposes.

Isn't that exactly what the study purports to show? Why would psychological trauma (i.e. negative nurturing) effect epigenetics but not psychological healing (i.e. positive nurturing)? What we consider "trauma" by modern standards would have been experienced by a huge fraction of every prior generation, and over the course of generations the entire population countless times over via epigenetic inheritance. Either it works both ways, even if unevenly, or it's BS (the framing if not the science). Ideological motivations aside, it just happens to be much easier to identify and track discrete incidences of severe trauma.

Yes, you can cushion people from the effect of trauma as it's happening, by providing resources at or soon after the point of trauma.

But your epigenome is a record (almost exclusively) of stuff that was observed during your development — it's a log, not a state database.

A particular epigenome-affecting gene process would look like: "when I was -6 months old, a process kicked off that began expressing a gene. This gene caused the expression of a protein that acted to detect whether there was enough magnesium in my blood or not. It detected that there was enough — and so the protein recorded [by not methylating anything] that I shouldn't silence any of the copies of the magnesium-transporter in my intestinal-lining tissue cells. Then, the buildup of the protein caused the expression of another gene, which methylated [silenced] the first gene, permanently deactivating this magnesium detection step from happening again."

Which means that trauma during early development — if it is not cushioned at the time, such that its impact is felt fully* — will lead to some epigenome-affecting process that looks for "impact of trauma" observing said trauma as happening at the time it activates, and so recording it. That record, within the cell-line descending from the cell that made that observation, is now permanent; that tissue will now do whatever it does with that knowledge, from then on, for the rest of the organism's life.

Treating the trauma later, will help the organism psychologically, but will not change those markers (and whatever biological effects they have), because they are markers of "what was at a certain point", not "what is."

*edit

Anyone downvoting me should go read this study. The number of individuals exposed to the initial dose is in the single digits. There is no attempt to account for confounding variables. No mechanism is known that could account for the proposed effect. The preceding animal study they referenced has been HEAVILY criticized for methodological issues.

If you're speaking from an american perspective, this hand-wringing is unnecessary: we leave our own citizens exposed on the street. If we were capable of making decisions about who deserves xyz in the first place we wouldn't be living in such an obvious shithole to begin with. Maybe we should set our standards much lower if we aim for research to actually benefit humans.

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.

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...

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.)

A gene is a unit of heredity.

The genome is the sum total of all genetic information in an organism.

Both are extremely loose terms. Individual sub-fields of biology/biochemistry may use more specific variations in specific contexts, but the definitions above cover all of those meanings.

(I.e. per my sibling post, there were jargon terms with these names that had one particular definition under an early, black-box mental model of heritability that is no longer used/favored; and there are new replacement jargon terms with the same names, that have a different definition under the more-modern mental model of germline heritability.)

After all, there are entirely non-genetic mechanisms of heredity. You inherit some of your mother's immune histochemistry through developmental exposure, and more through consuming breastmilk. Yet there is nothing that "codes" for this histochemistry; it's just a stateful process (mother's immune system) interacting with another stateful process (foetal immune system) — working almost more like a "colonization" of commensal bacteria than like gene transfer.

In terms of "heritable traits" — "nature vs nurture" — such effects appear squarely on the "nature" side. But they're not germline heritable. Implant the fertilized egg into a surrogate mother, and you get different histochemistry. Have a wetnurse feed the baby, and you get different histochemistry.

If these things are "genetics" — if the information carried by the state of immune cells in response to observing natal antigens is "genes" — then the term "genetics" has no useful meaning / is useless to talk about the thing we want to talk about when we talk about genetics. Where "what we talk about when we talk about genetics", is how an organism's breeding/germline ancestry, predicts phenotypic outcomes.

And if you agree that that is the thing we want to talk about — then epigenetic information isn't "genes" (under the germline-heritability model) either. Your epigenetics is hereditary, but only in the same sense that your immunohistochemistry is hereditary — being passed via exposure in a natal environment, rather than being "written into" the fertilized egg.

(Also — at least AFAIK — we don't even consider our nuclear mitochondrial DNA to be a part of our genomes. Even though it is passed through the germline, and is intensely important in many congenital metabolic dysfunctions. Because our mitochondria are not technically "us" — we might call them organelles, but they're still more like commensal prokaryotes in how cells treat them: dividing on a separate timeline from our cells; not assortatively assigned to daughter cells by spindle fibers during mitosis; not observed + checkpointed to ensure sufficient numbers exist for daughter cells before telophase; etc.)

I am a biochemist. The term is absolutely used all the time, in the CS sense, in biology.

Nit: chromosomes mostly don't look like little X-shapes except during cell division, which was historically a useful time to image them (I think because the dye couldn't get through the cell-nucleus wall but during cell division it has dissolved?). But then you are seeing _two_ chromosomes that happen to be bound at a centromere before that centromere gets torn into two by the cytoskeleton dividing the cell in half.

It is not quite right to say: “a gene is … a heritable trait.” This definition equates gene with trait. Yes that is how Mendel thought about his results since he could only see and quantify traits. But there are still a depressingly large number of protein-coding genes without linkage to traits.

> It is not quite right to say: “a gene is … a heritable trait.”

This is a reality of communication you need to deal with: that's absolutely how people will interpret the term "gene".

> Yes that is how Mendel thought about his results since he could only see and quantify traits. But there are still a depressingly large number of protein-coding genes without linkage to traits.

From my perspective, from my exceedingly humble opinion, "heritable trait linked by reproduction and not culture" is absolutely how the public at large understands the term "gene". The fact that scientists cannot successfully link protein-coding to linguistically-bound traits is an issue that scientists will have to work around when communicating about the specifics of heritability, genetic determinism, and discretization of individuals. "Gene" is simply not a term you can reliably link to DNA in the popular consciousness and is likely not worth the effort or money to redefine.

No. There are two distinct ways in which humans communicate.

• Humans create and use words, whose usage stretches and spreads and grows and can only be defined descriptively.

• Humans (doing professional/technical/scientific work) also define-into-existence jargon terms — the meaning of which is set in stone at the moment of creation.

Jargon terms are verbal handles we use to grasp parts of particular, well-defined mental models — models that are taught and learned as coherent systems of such terms; models that exist to enable their users to think rigorously, and collaborate without corruption of meaning/loss of rigor, to "get things done" in those professional/technical/academic contexts.

Jargon terms, therefore, can always be said — definitively, objectively(!) — to have been employed correctly or incorrectly in any given text, per the mental model in which the jargon term is defined.

Sometimes, professionals/technical people/scientists are dumb and silly, and attempt to invent a jargon term made of words, where those words, put together in that order, have such an obvious, novel, and useful lay usage, that it is inevitable that anyone who hears the term will already think they know what it means, before ever being formally taught what it means.

"Begs the question" is an example of this — there is something so uniquely useful about the lay meaning of that phrase (essentially "a situation that demands that an unstated question be asked"), that whoever named (or more likely, translated from Latin into English) that logical fallacy, made a mistake by choosing to use those words to name it.

But that situation is rare.

Most of the time, professionals/technical people/scientists make up a word all on their own, to be jargon, entirely for their own use. (Often they use Latin for this, as an intentional way to dodge the aforementioned problem of the word "seeming like it has an intuitive meaning" in any living language. But they don't have to. They can also just make up a nonsense word, perhaps one inspired by a Latin prefix or something — a word like "gene.")

And then, through a pipeline of scientific discoveries, to science journalism, to pop-science, to regular people just talking about how their aunt has asthma due to "that bad gene she got from her father" — somewhere along the line, someone screws up in how they're using the jargon term; and that screwed-up understanding proliferates.

But jargon terms — at least the ones that are part of mental models anyone still employs any more — must still be used to do work. And they cannot function to do that work, if people can't use them with the implicit understanding that they are communicating an exact, precise, well-defined idea. Such words are not merely words; they are professional tools. The professionals that use these tools, cannot allow them to be corrupted, to have their meanings diffuse.

And so, at least the professionals themselves, will always be taught that any jargon term they learn has one specific meaning — that it acts as a handle for a particular concept in a particular mental model.

And those professionals will insist on this strictness when working with any technical writer or editor.

And this strictness diffuses from there, into any editorial context where editors consider themselves to be professionals, working for a publication that expects professionalism — whether that publication is technical or non-technical.

In professional editing, is always expected that if any term (word or phrase) is used which is known to be a (unique, non-colliding) jargon term rooted in some technical/academic mental model, then that term should only be permitted if it is being used with its original jargon meaning. Any other handling of such a term is considered a usage error, effectively a typo.

(For non-unique/colliding jargon terms where lay usage exceeds jargon usage, the lay-usage is given represented by plain printing, while the jargon usage is represented by italic printing. This only ever comes up with phrases — "begging the question" again — because even the most ivory-tower academics know that overloading the meanings of single extant lay words is a stupid way to invent jargon.)

In other words, it's about "those who know" being a role model for correct usage by "those who don't know."

(Why bother? Because then people are more likely to come into the profession with an understanding of the concept that's at least compatible with teaching them the model; rather than having an understanding of the model so debased that they need to actively unlearn it before they can learn the correct model.)

Who is the grand arbiter of whether or not use this use is "misuses" or, perahs "correct", whatever that means—the professionals, or the lay people?

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.

(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)

This also seems to be a semantic distinction largely irrelevant to understanding the article as presented.

I think neural nets show that, realistically, evolution requires backpropagation (epigenetics).

I read about DNA methylation (well, epigenetics in general) in one book for behavioral epigenetics.

  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

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.

Crucial difference, one is a mutation, the other an environmental adaptation.

It's in the title and it's clear throughout the text of the article.

So that's a totally moot point.

DNA methyl-groups, acetylated histones, etc — these are the config file generated by running `menuconfig`. They determine:

1. which components of the kernel the "compiler toolchain" (RNA polymerase) will actually "compile" (transcribe) into kernel-module objects (RNA sequences, proteins) — in turn determining which "features" (developmental or metabolic processes) each of the components (cell/tissue types) of the resulting system (organism) will have; and

2. which #IFDEFs (coding regions) within those modules will actually be macro-enabled (expressed) during compile-time (transcription) — in turn influencing / varying / tuning the strategies and logic (frequency of production / likelihood of expression, final shape / folding / binding affinities of proteins) used by any given component (cell/tissue type) to perform a given "feature" (developmental or metabolic process).

(And just a tweak to steer this intuition pump — your body doesn't have one kernel, compiled once at conception; rather, your body is more like a distributed system composed of machines running Gentoo — every cell has its own kernel, and each cell is "tweaking" and "recompiling" its kernel regularly. When cells undergo mitosis, both daughter cells inherit these tweaks — that's like setting up a new one of these machines by mirroring the hard drive from an existing machine, carrying over not just the kernel but also the at-snapshot version of the `menuconfig` configuration file.)

oh my god would you shut up already

The Information Theory of Aging

The Linux kernel is just a much closer analogy than your average piece of software would be, because the Linux kernel actually has this distinct step that generates a standalone build config file that later build steps read.

Most regular software build infrastructure (autoconf, cmake, etc) just directly "burns in" any passed-in build config as generated code, without any intermediary file storing the config itself — which is a very different and not-very-analogous process. (That'd be more like if our epigenome was an extra chromosome of DNA built up during development!)

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.

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.

As in after x generations the genes "go back to normal"

You seem to be disappointed in the headline because you're expecting narrower definitions.

I just think common sense should make us suspicious of anything having deep heritable effects like this. There are obvious potential confounds here, it’s not at all plausible that exposure to violence is random.

See also the excellent https://www.razibkhan.com/p/you-cant-take-it-with-you-straig...

I am a little confused by how there can be epigenetic genetic modifications. I'm not a biologist, but it seems to me that if it's epigenetic, it's not genetic and vice-versa.

Epigenetics is a recent discovery that the genes can be muted or not expressed).

The mechanism is that parts of the DNA strand often curl themselves up in a ball which prevents themselves from being replicated/expressed. Researchers are discovering there are many factors that influence this behavior.

It is indeed not a modification of the genetic code. And the transmission of epigenetic state from one generation to the next is much less straightforward.

  But there is another lasting effect of the attack, hidden deep in the genes of
  Syrian families. The grandchildren of women who were pregnant during the siege — 
  grandchildren who never experienced such violence themselves — nonetheless bear 
  marks of it in their genomes. Passed down through their mothers, this genetic
  imprint offers the first human evidence of a phenomenon previously documented
  only in animals: The genetic transmission of stress across multiple generations.

The article mentions Hama, where a massacre occurred, and 40 years later the inhabitants still show epigenetic changes caused by stress. Surely the environment still being stressful is more to blame than their ancestor's genetic memory.

There's great danger of misinterpreting this kind of research to bolster ideological agendas. I've seen this misused as "my grandpa was a victim of the holocaust, so I, born into and living a comfortable and peaceful life, am also a holocaust victim and deserve respect".

"The curse of every ancient civilization was that its men in the end became unable to fight. Materialism, luxury, safety, even sometimes an almost modern sentimentality, weakened the fibre of each civilized race in turn; each became in the end a nation of pacifists, and then each was trodden under foot by some ruder people that had kept that virile fighting power the lack of which makes all other virtues useless and sometimes even harmful."

[1] https://acoup.blog/2020/01/17/collections-the-fremen-mirage-...

The exception to this rule is when a society destroyed itself through civil war. The western Roman empire destroyed itself during the Crisis of the Third Century when one regional commander after another declared himself emperor. Even during Augustus' time, the elite had a habit of cutting off their sons thumbs to avoid being conscripted into the legions.

The steppe nomads who conquered China (Mongols), Persia (Mongols), Byzantines (Turks), and India (Moghuls) were able to rule for centuries thereafter even after becoming "civilized". I would also argue this "civilizing" process was also a myth. The ruling elite kept their own traditions and cultures and lived separately from the people they ruled.

Maybe in the future even the drones will have ennui and want to become dancers.

I don't think that quote is about being brutish. The idea is that when times get easy, defence lowers (as why spend on defence?) and eventually someone else who is not living in luxury takes over, if they can reach you. I don't know if it's a valid theory, but I don't think it's about anyone's nature in particular.

My understanding is that coal, wood and iron ore were plentiful in England itself.

Why would you state this as if it were fact? It's not true.

Our own generals bombed the most important trade hub of the time, Atlanta, during the civil war.

Bombs are highly effective, and location matters little to their effectiveness or usefullness.

We dropped plenty of bombs in unreachable parts of Afghanistan. Were those effective? Yes, they were. Were those bombs as effective, in that region of uninhabitable tunnels and cliffs, as they would be in an urban setting? No, of course not.

Bombs are still the go-to attack and defense strategy. Bombs reduce the need for boots on the ground. Bombs reduce the enemy's ability to go to ground and hide.

If we faced a land invasion, in the USA, we would absolutely-certainly utilize modern weaponry, including bombs, to displace the enemy.

To say otherwise is to disregard history. To say otherwise is to place hope in pie-in-the-sky feelings and not the data we've accumulated over the last 200 years.

In the short term, yes. In the long term the US eventually gave up and left. Likewise, the US bombed Vietnam heavily, eventually gave up and left. You can't hold territory with bombs.

To say otherwise is to disregard history. To say otherwise is to place hope in pie-in-the-sky feelings and not the data we've accumulated over the last 200 years.

Every military historian will tell you the same thing I just did, and cite examples going back thousands of years - military arson serves the same function as bombing.

Why?

This sword of damocles shit that justifies the boot being on our face forever can fuck right off.

https://gizmodo.com/how-an-1836-famine-altered-the-genes-of-...

You’ve never once seen a university press release boiled down for the general public, without a link to underlying research?

It goes into more detail about how they established the genetic signatures and has a lot more images as well.

Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees

[0] - https://www.nature.com/articles/s41598-025-89818-z

Interesting that there is not just social pressure but also genetic pressure that may be perpetuating the trauma.

My grandfather drove a tank through Europe for the allies during WW2 and I know that is still impacting me and my kids. He self medicated his presumed PTSD with alcohol and died young before I was born. That impacted my father and the way he related to me. And I am sure it impacts how I relate to my kids too. I don't drink anymore because that history scares me. The rise in fascist and nationalist ideologies scares me too.

If we forget history we are doomed to repeat it. Both at an individual and societal level.

That's untrue. There was plenty of evidence for epigenetics before this study. The one that I remember is the Överkalix study in Sweden.

For example, is it ethical to create a company which automates the job of a large class of workers? Is it ethical to use such a product? I don’t even think the Golden Rule can account for it, frankly, because the “others” in “do unto others” can be multiple parties, some of whom are helped and some who are harmed.

Proverbs 26:4 (ESV) "Answer not a fool according to his folly, lest you be like him yourself." Proverbs 26:5 (ESV) "Answer a fool according to his folly, lest he be wise in his own eyes."

They are "contradictory" but yet right next to each other. It can rather be taken that these are both true in certain contexts and must be held in tension against one another and applied with wisdom.

There are multiple instances of this in the old and new testaments.

I'm not sure what's the point tho. If you start with abandoning logic - you cannot later return back to using it. Starting with 0==1 you can prove anything.

If Bible gets away with contradictions - you can't then accept the conclusions and use logic on them. The moment you abandoned logic you are left without it forever. Full-blown postmodernism. Nothing is true and everything is true.

Note: Exodus 20:5 and Similar Passages: The concept of "visiting the iniquity of the fathers on the children to the third and fourth generation" is often understood in the context of the collective nature of ancient Israelite society. It emphasizes the idea that the consequences of sin can affect subsequent generations, particularly in a communal and covenantal context. This does not necessarily mean direct punishment, but rather the natural repercussions and influence of one generation's behavior on the next.

So one interpretation is that: these people's descendants are not directly punished bust just less favorable by God given the jealous nature of God (i.e. the jealous nature to the degree that is expressed in Exodus 20:5 if we take Exodus 20:5 at face value as composed by Moses at the cultural-political time when he received the Commandments where God proclaimed that He is a jealous God)

On the other hand, regarding Ezekiel 18:20, it is a verse that is a part of a broader discussion in Ezekiel 18 that emphasizes individual responsibility when it was composed by the prophet Ezekiel ~6th century BCE, during the Babylonian exile. So once again, one good interpretation can be that due to the cultural-political background at that time, God's message to humanity (for the betterment of humanity) was in a tone where He emphasized less on His jealous aspect and more on the individualism of sins - which is interestingly very similar to the idea of karma formulated in Shakyamuni's Dharma, which was also around that time in human history.

This is a rationalization. If you try to interpret it honestly you can find dozen different places where god punish random people for sins of their relatives (for example "unoborn kids" in cities genocided by Old Testament Israelites either through regular war crimes or direct God's magical intervention).

And then there's the fragment that says that God will not punish a city if there's even one honest man there.

The only way to make it consistent is to ignore contradictions. And I'd say it would be easier to ignore the few ones that are against collective responsibilty (because there's far fewer of them).

2. I'm not claiming to be genious. In fact I was pretty hardcore Catholic for like 22 years before I stopped lying to myself.

> You seem to forget that Egypt

Genociding Phillites' kids because some adult Egyptians were killing Jews is evil.

> The Canaanites, for example, practiced child sacrifice to Molek

Their infants did?

what a convenient all-purpose dismissal of any experiences that challenge your view

The side that takes pleasure in the misery of others does so because the negative effects can be -- just as this title states -- deleterious for generations.

We must evolve ourselves to, instead, sow the seeds of compassionate concern for all human beings to rid ourselves of the damaging effects of abuse of every kind, between any two people or groups of people.

Yes, accomplishing any progress in that direction is fundamentally difficult because it goes against our animal physiology and negative potential, not to mention the even more generations of institutional pack mentality that so permeates our cultures' seeking of power.

We could choose peace and compassion, if we chose to, but such a bold endeavor takes utter commitment and real work, for each and every one of us.

Compassion is always the solution to ALL our problems, because the lack of compassion is ALWAYS the fundamental cause of EACH and EVERY one.

It is both that simple, and that difficult, but it is also rewarding beyond normal comprension, for it is the most real kind of magic in this multiverse.

"Love, baby, love." --Louis Armstrong

I think the main problem is that something like "science proves generational trauma is real" is a nice headline, so people p-hack it into existence. "Science proves that generational trauma is not real" is just a null hypothesis being confirmed - not a publishable result and nobody cares, so you'll never hear about it. So be very skeptical of nice headlines, especially in university press releases!

Here’s the link to the study https://www.nature.com/articles/s41598-025-89818-z

Epigenetic changes are an important part of your genetic make-up. To give you an example, the only reason that your skin cells remain your skin cells when they divide, and your liver cells remain your liver cells when they divide, is due to the epigenetic make up. Their DNA is the same, but the cells are very different, and epigenetics pass that information along when the code is copied.

In the same way, these stress-related epigenetic changes are being copied down and inherited by the generation two under.

This is already known, I think it was first seen in the Swedish famine cohort. At that time it was not clear it was due to epigenetics, but there was a clear signal in the health of those descendants [1], published here in 2002.

[1] https://www.nature.com/articles/5200859

Alas, a new target for lasting, inter-generational psychological assault.

I mentioned this to her and she *adamantly* refused to accept the possibility.

I wish reporters were required to research their claims.

Apart from epigenetics, which influences offspring but confers no permanent genetic change, there is no inheritance of acquired traits. On this topic, for political reasons Joseph Stalin promoted Trofim Lysenko's incorrect views in this topic, which set Soviet genetics back decades. More here: "The destructive role of Trofim Lysenko in Russian Science" (https://pmc.ncbi.nlm.nih.gov/articles/PMC6777473/)

Articles like this should at least explain how and why their claims differ from established genetic principles.

Admittedly this was from a Dr Karl podcast.

Violence impacts virtually every aspect of human existence. Consider for one moment what life would be like in an alien world in which life existed in the total absence of violence. No wars. No violent crime. No child abuse. No sexual abuse. No police. No prisons. No weapons. No militaries.

Violence is a scourge. I have spent the past 20 years discussing the issue of violence with people in RL and online - and it is simply shocking how much males WANT violence. Enjoy violence. Consider it a part of their masculinity and that they would feel neutered in a world without violence. To me, that sense of pride in violence, is the scariest thing I have come across in my 72 year male life. And the saddest for what it portends for the future of our species.

This seems like a pretty charitable read on policymakers. We inflict violence all the time that has multigenerational downstream effects without a genetic component and we don’t really care about the human cost, why would adding a genetic component change anything?

We have no way of giving such an experience to those in power. The best we can do going forward is pick more well rounded people, and no, that doesn't mean great schools and great wealth. You must be experienced in life.

When first watching that movie, I really didn't like it right until the last scene, with Michael Douglas and his daughter in rehab, with the line "My name is Robert. And my wife, Barbara and I are here to support our daughter Caroline. And we're here to listen."

It was such a simple yet clever way to end the movie and highlight a central theme in the movie, which is that the way to solve our problems isn't to demonize the people that caused them, but instead to listen to them.

It was weird, because it sort of retroactively made me really like the rest of the movie.

I feel like I'm willing to put up with a lot of the more slow-paced stuff if I know it's going somewhere. If I know that this is building up to an interesting theme, then I don't get bored.

It's now become one of my favorite films.

Shouldn't it be War on dug dealers?

And you don’t need armored vehicles and SWAT teams to get to a better place.

What does this mean?

But, making things illegal that (clearly) people will buy anyway just pours billions into criminal enterprises. The vast majority of crime is funded by drug money in one way or another. The same thing happened during US prohibition: people did not stop drinking alcohol, but all the money from alcohol suddenly poured into the criminal economy. This is a well-trodden path and we should know better by now.

Has "the war" worked out? We're several decades in with no win in sight.

The "War on Drugs" is just a massive subsidy for the cartels via US markets. A sane approach to actually reduce drug use and fentanyl deaths would be to mirror the policies that have brought American tobacco use to a historic low and invest the tax revenue from legal narcotic sales into addiction treatment centers.

1: https://en.wikipedia.org/wiki/Heroin#History

Perhaps there's some weight to the idea that demonization of distributors harms consumers—but this doesn't seem to be an ideological barrier between being aware of the harms to users and the obvious economic boon of taking advantage of regulation to exploit the market advantage.

Besides, on a practical note, the war on drugs is what created large distributors. There weren't any when it started.

Instead, we'll get another 100 years of half-assed decriminalization, where it's still illegal to sell, dealers are still motivated to kill cops, deadbeats, and rivals, where 100,000 people die because it's laced with fentanyl and even decriminalized illegal street drugs can't be regulated. I eagerly await all the downvotes this opinion will get.

One more change I would like to see: get rid of advertising this stuff. Giant billboards pushing alcohol, tobacco, and cannabis, are bad for all of us.

I don't find exact numbers for 1990-2010 but the number from 1996-2015 was over 32 million according to drugpolicyfacts.org [1]

https://www.drugpolicyfacts.org/table/total_arrests

Anyway, Menendez has gotten off extremely lightly and everyone can see this.

[1] https://en.wikipedia.org/wiki/List_of_American_federal_polit...

Humanity risks a global return to a state of gleeful cruelty. "Lupus est homo homini". [1]

The well-being of people is a characteristic of successful society. And labour is fundamentally valuable. For those who seek economic pre-eminence, it makes perfect sense to invest in the people doing the work.

However, there are narrow-minded groups and individuals who see another equation: put workers in an exploitable condition and keep them in such condition over generations. Wars have been fought to preserve the investment in maintaining such conditions.

Labour is valuable, but the individual cost in human life is usually dismissed through demagogy and populism. We had broken the historical cycle of misery, but we now risk the achievements of our civilisation.

[1] _ https://en.wikipedia.org/wiki/Homo_homini_lupus

>Not everyone will respond to an appeal to empathy

I don't even think we use the word "empathy" correctly. It makes sense to me when we're talking about a non-general empathy, where you see a particular person close to you (physically, if not emotionally) and you feel for them. You can't have empathy with some abstract hypothetical. You can't even have empathy for some large loosely defined group of people of the non-hypothetical sort. And, most of all, it's largely spontaneous. If you go into it having already decided you feel empathy for them "just on principle", then what you're feeling isn't empathy. It's performative. It's virtue signaling. Pretending that is empathy does empathy no favors, and it does no favors to the people who are supposedly being empathized with. Because it is performative, it's always just this thin veneer of compassion over an inadequately hidden contempt. Worse still may be those who lie to themselves so successfully that they believe that it's real empathy, the hatred is buried deeper but festers all the more for it.

Appeal to pragmatism instead of empathy. You can make rational arguments if you're trying to be pragmatic. Appeal to justice. Appeal to anything but empathy. When I hear the word "empathy", I know that I'm about to have a load of horseshit dumped on me. You all know it too, even if you're worried that other people will shun you if you admit it out loud.

To get a better understanding, let's use something very analogous - Cringe. When we watch someone do something cringe, we feel it. The same is true for empathy you see, that's what it is. We feel someone else's pain. Psychologists say those that don't feel it are sociopaths.

"Worse still may be those who lie to themselves so successfully that they believe that it's real empathy"

Again, you have difficulty identifying real or not real empathy. This is not a problem for people that were raised without confusion. You can just say I'm from environments where I couldn't figure out if anyone cared about me or not (common). Is there a universe where you can accept this diagnosis or are you pure? We are all a constant work in progress.

The gene expression of apathy needs to be studied as well.

I don't bake cakes, so I of course can't recognize a cake. Everyone knows this. Magical thinking demands that it be true. You have an immaterial soul that connects you to the universe, Jeebus, and the ghost of Elvis Presley.

>watching someone cry over current events would be unrecognizable to a sociopathic person. They may even accuse the person of lying or putting on a performance.

Sure, they might do that if they were lying. Which in many cases they are. So much of the real world around you is inexplicable, isn't it? There are these secret sociopaths all around you, they look just like anyone else and they're all serial killers waiting to Hannibal Lecter you!

Or maybe, everyone's like this, but some large fraction of the population is engaged in this weird cultural phenomenon where you all compete to appear more virtuous to each other than you really are. But admitting it would just ruin the fun, eh? And what if you admit it, and then everyone else doubles down and insists it was real for them, outting you as the serial killer? Can't have that.

Empathy is only possible for people within your Dunbar number. Everyone beyond that only requires and only gets whatever civility is merited for diplomatic purposes. In your way of thinking, these so-called sociopaths... every single human is one. At least to the other 8 billion people who don't happen to be in their Dunbar circle. This explains how the cops can be so callous to the wrongly accused and to the victims alike. How soldiers are so quick to run off and commit war crimes (with or without sanctioning by superiors). Why those schoolteachers abuse the little kindergarten kids. And on and on and on. To you it's mysterious. Invisible monsters out there ready to pounce and eat you. It's why you can't fix any of this, why all those problems seem to grow out of control. Too busy trying to get everyone to pretend they have empathy which they don't.

>We feel someone else's pain.

You pretend you feel it. You don't. This isn't Star Trek, you don't have telepathy. This isn't Harry Potter, you don't have magic. But again, people will look at you weird if you admit you can't.

>Again, you have difficulty identifying real or not real empathy.

I don't at all. I have a superior talent for recognizing it. As in, you have no ability to recognize it, no potential to develop such a skill, and can't even think about it rationally enough to appreciate your shortcomings.

>You can just say I'm from environments where I couldn't figure out if anyone cared about me

"Please humiliate yourself so I can go back to competing in the Virtue Signaling World Championships! Your mama didn't love you nyah nyah nyah!"

Except she did. And I've had a few people in my life over the years who did care about me. I'd say instead it's people like yourself who have the confusion. Constantly complaining about narcissists that you somehow don't see coming a mile away. Constantly begging for updoots on reddit, your entire generation, for whining about how you might have to go no contact with your parents because they won't acknowledge your new puppy as just as important as their actual grandchildren. Hell, the most extreme of your sort have invented entire new crackpot pseudo-religions where you're not allowed to eat food because you're supposed to have empathy for it.

>Is there a universe where you can accept this diagnosis or are you pure?

Are you a licensed psychiatrist? Please private message me about the state you are licensed in, and which business name you practice under. I will accept your diagnosis if I have these details.

Plenty of research out there that investigates and shows nervous system/heart beat co-/dys-regulation amongst strangers. Not that I need any of that to know how I am feeling with others, totally random strangers. I cannot turn it off. Oh boy, I often wish I could. You can choose not to believe me, sure, I'm just inventing this to lie to your face for the kick of it. Or you can choose to look at the research. Or actually experience it for yourself, e.g. in a NVC practice course.

Okay, I understand you. You are wrong, but that is the nature of expression when it comes to agitation and anger. It’s not necessarily your entire being, but such forces can co-opt a person for quite some time. Some people get addicted to indulging in righteous indignation (which somewhat corroborates your point about performance, but I’ll amend the point to include that it’s happening to extremes on both sides. You yourself have wholesale invalidated the emotions of the other side, possibly reciprocally).

Sometimes just acting like something becomes you. So there is your mindfuck. You ever had to fake it a bit until you caught your rhythm? It’s in us to truly feel, just try.

Experiment:

https://youtube.com/shorts/j4TVuoicPrY

Watch that after taking a deep breath and calmly try to tell yourself that “this is a woman who is probably more emotional than me, and I have seen women cry before over a lot of things. She is also of Hispanic origin and may have additional emotions here. She is also American and is a beneficiary of the labor of these people. I have to try to believe these are real emotions, even though even though my entire being is telling me she is a liar”.

You have to fucking try.

If you walk out with “I still think it’s performative”, then FINE. At least you tried, we’re all still here talking to you right?

I will say one thing though, you sound batshit enough for the two of us to become friends.

To make it real when there's no compassion, loving kindness, or the golden rule:

War reparations: https://en.wikipedia.org/wiki/War_reparations