Violence alters human genes for generations, researchers discover

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.

If the editor is only editing for style and readability while adding factual mistakes along the way, they could be entirely replaced with ChatGPT in a tight loop with the science writer. Write article -> make style changes -> writer reviews again for correctness.

It’s inexcusable that the quality of science communication is so low.

> 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

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.

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These arguments sometimes reach juries, who are asked to award damages based on "physical harms," in a separate category from "mental anguish."

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

> 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.

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.

Yeah this study is pretty bad and I expect to unfortunately be hearing about it in corporate trainings in 10 years.

*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.

A lot of sociology research is activist in nature and not rigorous. Is the study similar?

I've seen literal 7 year olds make the same mistakes when doing school projects on butterflies. Can professionals not do better than literal children?

> 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”?

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.

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...

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.)

> 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.

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).

But since many of them misunderstand the role of gene sequences, that may be less meaningful than you imply.

Should it not be "affects" or "influences"?

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).

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.

Personally, I think of DNA as being like the Linux kernel codebase. There's a lot of raw "code" there — but not all of it ends up in every running kernel!

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.)

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.

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.

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.

One is heritable, the other mostly not.

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I think it’s better to describe methylation as up or down regulation.

The article says this.

  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.

So why do we discuss genes if we actually mean heritable traits? Scientists should probably take the lead in abandoning "gene" as a generally useful concept outside of their field.

Of course, then we have groups like 'The United States of America', which has been at war basically every single hour in the last 100 years, and seems to be doing just right. At some point, you become powerful enough so that infrastructure does not help against you anymore (and may even become a liability: The conflicts the US does the worst in is wherever guerrilla warfare is waged, not where there are highways and telecommunication networks).

Civilization makes a society successful in war because of the destructive power of the weaponry available. But it absolutely seems reasonable that individual people could be less fit for physical combat as the above aspects of civilization (materialism, luxury, etc.)

> The Industrial Revolution is why England could conquer half the planet, not the brutish nature of the English

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.

Furthermore the Industrial Revolution stimulated the need for a trading empire to supply its materials. Nowadays we have global free trade (enforced by the US Navy - yet more technology) so trading empires are unnecessary.

Technology may be more predictive of conflict abroad than at home. If we faced a land invasion, for example, we would not be able to bomb our way out of it.

Honestly it's one of those ideas that make less sense the more you think about it. That quote and wikipedia link is drawing a connection between history as it was understood in the 19th century (e.g. unilineal evolutionism) and the behaviour of dodos.

To give you a better understanding of how this works, if my university didn’t include a link to my research in the press release about my publication, I’d contact them to issue a correction. That’s how fundamental it is to link to the research article.

Yes, it is. Top universities do.

Bronze age morality was rather different than what most readers here will have in mind when seeing you use that word.

Using any of these passages as a prooftext for a particular position about the effects of God's wrath and drawing a singular conclusion from them is indeed incorrect, but it does not mean that there is a real contradiction. For example take these two passages.

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.

The Bible is a small library of different books written by different people at different times. I don't think it's all that surprising that there are contradictions. In fact, I would say that pretty much every faith tradition with a long literary history suffers from this problem. I don't think that undermines that idea we can glean meaningful wisdom from sacred texts.

I think the interesting thing here though is the notion of `am a jealous God`.

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.