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.

> 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.

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.

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

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"?

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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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.

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.

That was a good film. I always remembered del Toro’s recommendation about bulling more lighted fields for kids. Chinese society could learn a lot about how gaming is actually not that addictive when you look deeper into the problem.

War on drugs != War on drug users.

Shouldn't it be War on dug dealers?

I mean not to fan the flames of war on drugs - but its supposed to be targeting supply chain and large distributors

Sure but I think if an appeal to empathy was going to work we’d already have seen it work.

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

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.

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.

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.

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.

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.

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.

The real "uncomfortable truth" that the GP blithely glosses is the effect of multi-generational poverty. If a society has determined that some people are entirely expendable, then the misery of the latter over generations is easily dismissed as "biological destiny".

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