Poverty leaves a mark on our genes
eurekalert.org
eurekalert.org
Anyways. Their functional enrichment analysis is uncorrected for the known bias of the platform (something that has been repeatedly addressed by multiple authors since 2012), and no attempt appears to have been made to correct for cryptic stratification (i.e. structural polymorphisms, which are rampant in human populations, and particularly among so-called metabolic genes), though in the study population that may not be a major issue.
Quantile normalization is only appropriate if one can reasonably assert that the overall distribution of measurements is roughly the same between individuals and groups; this assumption has been shown to be invalid in the absence of positive and negative controls for gene expression, whence its original propagation, and more so for DNA methylation under various conditions. The batch correction approach used here is notorious for squashing real signal, although paradoxically that may have moderated some of the other methods choices.
Moreover, the paper demonstrates that a particular sample of high-SES vs. low-SES individuals in Cebu in the Philippines demonstrates some (fairly tiny) differences in DNA methylation at a relatively small number of CpGs (about 2000 out of 485000 or so measured and 110000 or so tested), without particular note as to whether the sites are clustered, functional, or otherwise of interest. The functional impact of these changes are difficult to interpret, partly because of the bias in the functional analysis (something that has been established for nearly a decade; the authors clearly went shopping for methods in a "confirmatory" style).
We shan't even bother to discuss the effect of [mal]nutrition on metabolism and thereby upon DNA methylation and cell composition (both intertwined, although an attempt was made to correct for the interaction), which further muddies the waters w/r/t SES as opposed to individual-level effects. The analysis is done with a fixed-effects model assuming unstructured shrinkage, which of course is a bit odd considering that the measurements have a relatively easily determined correlation structure (their sample size is sufficient to estimate this) and thus variance decomposition could have been highly informative. This is doubly odd for a population "epigenetics" study, given that variance components were literally invented in population genetics.
In conclusion, while it's a lovely piece for a PR department, the actual relevance of either the measurements or the phenomena to actual humans and public policy is quite difficult to interpret. Perhaps that was the point...
It is common to see why this could be a big problem for poor people as they have to worry about health, food, etc for day to day living while we take them as granted and can focus on other things like writing code, going to meetings, and the like without worrying about where the next meal is going to come from!
I think focusing on productivity would go further than the dichotomy's of "welfare or not", where people are mostly skeptical of whether a subsidized poor person is contributing to society with taxpayer's money.
Relegating the role of governance to productivity allows even prisoner rehabilitation to change. It allows jailable offenses to be viewed under the lens of whether this is useful to the productivity of society, instead of simply punishing someone.
Because that won't gain consensus.
But demonstrating how some parts of our culture undermine productivity can.
I think we could reach similar outcomes, if the lack of well-being can be proven to show that it undermines productivity.
I don't see anyone saying this, but I think fixing the bottom 10% of society requires fixing the top 90%. I see no way that happens. Nobody accepts blame for being wrong, and most people's cognitive capabilities are filled by an evening watching cable TV.
The bottom with disruptions to their income are detrimental to society’s health. Public sector monetary solutions are untolerated and private sector solutions of employment are often inaccessible or inadequate. We can address their productivity.
I don't believe the current system punishes offenders effectively or rehabilitates them. It's not great at segregating dangerous people either, as people are released when they've "paid their debt to society" rather than when they stop presenting a threat.
I'd prefer it if prisons were more like the prison farms in Scandinavia, especially for young non-violent criminals. They need to learn to produce things or render services that other prisoners will want. They should be able to build their own houses. They should have to learn how to work and freely trade with others BEFORE they are released.
Some criminals are a persistent threat to the population and must be tightly controlled. People who've murdered multiple people, for example. And some should never be released.
https://www.theatlantic.com/international/archive/2013/09/wh...
Anyway, a complicated topic for sure.
All that's going on here is that people in the Philipenes have differences in environmental exposures that affect gene expression in their immune system, and this, unsurprisingly, differs by SES. No evidence that any of these marks are more than temporary marks of current gene expression patterns let alone anything as shocking as passing through the germ line to the next generation.
This 'understanding' has been known to be wrong for 30+ years now. Rearrangements, microchimerism, epigenetics, chromosome organization etc. are all things that exist and modulate information transfer beyond the standard four letters or the 'environment' (whatever people think it means) and we're still only scratching the surface. I keep saying it and I'll say it again: DNA is not source code, your genes are not initial character stats in a video game. That's not how any of this works and it frustrates me whenever I read otherwise smart people making arguments that rely on premises originating from a high schooler's (or 1970's) understanding of genetics. It's even worse when the dreaded 'nature/nuture' gets mentioned.
Have you considered educators might not want 17 year olds to understand things that are "too dangerous"? Because that happens at a pretty basic level in chemistry.
Oh, I have an opinion about that:
Well. First and above all the first purpose of school and high school is to learn to follow authority (edit: authority in every other meanings. Tthe first authority to submit oneself to is the school). This is the first brick and if it's not assimilated in a way that suits the school the student will get thrown out of the system.
A century ago there's the industrial revolution mantra: produce workers who can read and understand semi-complex or complex instructions in written and oral forms and manipulate tools (typewriters, screwdrivers, hydraulics, mechanics, machines, etc.).
And now there's the "learn to learn" mantra because few things taught in the 'regular', 'normal' or 'general' school and high school cursus land jobs in the post-industrial and the information societies. Does not seem to apply to trade schools.
Either it's a consequence of not teaching critical thinking or a reason we don't teach it is up to debate but the results remain.
I think that depends which person at the school you ask. I am married to a low-income neighborhood high school English teacher and we talk curriculum often. Seems to me that it's about striking a balance: One side is what you said, the other side is teaching students to unite against that authority in productive ways.
Too far in one direction, and you wind up with a society where none of the competent people you know have enough faith in the system to run for office. Too far in the other direction and the dominant class sees the everyone else as a threat and puts walls up.
It's a difficult balance to strike, but I know a lot of teachers that work very hard at finding it.
I want to make it clear that my thought is that the first authority to submit oneself to or to follow is actually the school. Even if the school puts emphasis on critical thinking you won't have a place in it if you don't submit to its authority.
But seriously, in my understanding it's taught that way to try to rid people of mystical pre-evolutionary notions. Once they have firmly grasped the basics they can move on to super-interesting corners where stranger things may happen, and about which people are still arguing.
The physics analogy is people arriving with mistaken intuition about "when does the dead body roll out of the truck" level problems. The fact that Newton isn't the end of the story doesn't spare you from having to un-learn Hollywood/Aristotle first. Nor will your earlier confusion be any help in wrapping your head around post-Newton concepts.
Chapter 9, pg 161 covers epigenetics, p 162 gene linkages, Ch11 covers gene methylation.
I’d find additional specific examples, but that’s all that’s laid out explicitly in the table of contents.
[1] https://www.pearson.ch/HigherEducation/BenjaminCummings/EAN/...
https://www.pearsonhighered.com/assets/preface/0/1/3/4/01348...
It's important to note that heritability is not some kind of magic bullet that explains everything with "genes". If you want to convince a biologist that "genes" are the cause for a given phenotype, you've got to show an actual genetic causal mechanism or you've got nothing. This is, again, due to the myriad of interfering mechanisms that make "genes" very, very removed from the actual phenotype. And again, I'm not talking about the environment.
One of which is roughly DNA that codes for a protein, or controls such, and indeed the causal mechanisms from there to phenotype can be extremely complicated and hard to figure out.
In the context of "variation between people" there's another meaning, of just whatever it is that causes inheritance. We could say many things about this (e.g. from twin studies) even before we'd discovered DNA, and non-DNA routes (like if most babies get some microbes from their mothers) would still count.
Your second point is not true for complex polygenic traits like height. Height is strongly influenced by genetics but we will likely never understand the exact mechanisms that do this.
It is source code, it's just that source code is self-modifying.
Aren’t we somehow simulating how life works? Higher abstractions/constructs improve the way the lower constructs work :). Of course, just an oversimplification.
I am no expert, but I have read a couple of good books on the topic and my understanding is that while it is true that your DNA can modify itself to some extent in response to stimulus, the extent to which this happens is very limited in scope, and limited to ancient genetic pathways, which means these get activated only in times of severe biological stress, like through starvation or famine.
Take physics as an example, quantum physics has "a lot" more than classical physics, but no physicists will discard classical physics as being no longer valid, or no longer useful for explaining everyday physical world, or you should always use quantum physics in engineering, etc.
My, admittedly weak, understanding is that the analogy is (much) more apt than not. Sure, the means by which that code is 'compiled' and 'executed' is much different than in the computers we've built, but, for one, DNA, genes, chromosomes, and all of the other various levels of organization of those units of information seem to be remarkably, amazingly stable, for many (most? almost all?) organisms, which seems to strongly imply that 'DNA is source code' is about as true as 'Earth is a sphere'. Sure, they're both only approximately true, but how approximately they're true (or not) is very important. Asimov explained this extremely well:
- [Asimov - The Relativity of Wrong](http://chem.tufts.edu/answersinscience/relativityofwrong.htm)
'Epigenetics' itself seems like it might not be a particular thing among different people:
- [The misunderstanding of epigenetics – Insitome](https://blog.insito.me/the-misunderstanding-of-epigenetics-a...)
What epigenetics is not is anything like Lamarckian inheritance, at least not at all to the same degree.
> Rearrangements, microchimerism, epigenetics, chromosome organization etc. are all things that exist and modulate information transfer beyond the standard four letters or the 'environment' (whatever people think it means) and we're still only scratching the surface.
Sure, but that doesn't mean that the central dogma of biology is entirely wrong, just that it's not always and everywhere true exactly. The current best understanding of epigenetics (quoted from my second link above) is that, whatever it is, it is such that:
> very little of [genetic] inheritance is perturbed by epigenetic effects
To be clear, @aeorgnoieang's response is basically correct. The central dogma holds, the epigenetic program's role is well-characterized to be relevant to development/differentiation only under normal circumstances, epigenetic imprinting effects are weak, etc. As @aeorgnoieang correctly points out, the other things you cited (microchimerism, rearrangements, chromosomal organization/spatial effects) don't actually conflict with the "DNA as source code" metaphor in any way.
This is not to say that the popular understanding of these things is perfect - there are lots of misconceptions - but the way to fix that is by finding better ways to describe what we know and put it in context. A big issue is that as we learn more, media events around new discoveries make it hard to put the relative effects (of things like chimerism/mosaicism, polygenic risk factors, horizontal gene transfer, etc.) into context if you're not already an expert.
It's good to share links to previous threads, but only if there's actually a discussion there.