7 ms·

Poverty leaves a mark on our genes

74 points by howrude 7y ago

conse_lad 7y ago
Same story shared one day ago. https://news.ycombinator.com/item?id=20190233 https://news.ycombinator.com/item?id=20190233
- Cynddl 7y ago
  And 2 months ago: https://news.ycombinator.com/item?id=19590567 https://news.ycombinator.com/item?id=19590567
- dang 7y ago
  Reposts are fine if a story hasn't had significant attention yet: https://news.ycombinator.com/newsfaq.html https://news.ycombinator.com/newsfaq.html. It's good to share links to previous threads, but only if there's actually a discussion there.
vipref 7y ago
> socioeconomic status (SES) is a powerful determinant of human health and disease, and social inequality is a ubiquitous stressor for human populations globally 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!
- rolltiide 7y ago
  My observations is that our society puts too much emphasis on having people prove they are self-reliant, instead of improving its population's productivity. In this dichotomy, the former is detrimental to the society, the latter would enhance it. 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.
  - ta1234567890 7y ago
    I agree with the sentiment of changing the narrative, but productivity seems to already be a big part of western society and it seems pretty soul-less. Why not focus on well-being of everyone?
    - rolltiide 7y ago
      > Why not focus on well-being of everyone? 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.
      - wallace_f 7y ago
        I'm not sure what fraction of paid jobs even contribute greater than their cost to society. The War on Poverty has spent trillions, and poverty has increased. A lot of industries obviously don't contribute (tax attorneys, lobbyists, bureaucrats, administrators (see the Rise of the Administrator in healthcare), even much of law enforcement, academia, or regulators). Actually even my first high-paid job working for a financial tech company, I'm convinced didn't contribute to society. Most of our work was mandated by regulatory laws, and most of our customers were capture by monopolistic competition or downright aggressive, questionable sales. 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.
        rolltiide 7y ago
        I don't agree on that being the immediate issue. 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.
- deleted 7y ago
  [deleted]
sci-hub 7y ago
Link to paper [PDF]: http://sci-hub.now.sh/go/10.1002/ajpa.23800 http://sci-hub.now.sh/go/10.1002/ajpa.23800
- dang 7y ago
  It's fine to provide the occasional link but please don't do special-purpose accounts on HN.
aluren 7y ago
>understandings of genes as immutable features of biology that are fixed at conception 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.
- johnchristopher 7y ago
  This understanding was still taught like that in the 90's, western continental Europe.
  - aluren 7y ago
    True. Most of what I've been taught after high school feels like "you've been lied to, everything you were taught in high school was wrong or grossly oversimplified and now you need to unlearn it all and relearn from scratch." Makes you wonder what the purpose of high school was in the first place.
    - davedx 7y ago
      I got the same impression from people who studied chemistry after high school too though. Some things are just simplified so our children can ramp up their understanding gradually instead of having the wild complexity of the universe thrown at them in one go.
      - thatcat 7y ago
        It makes no sense to leave things out of a description of a complex system to help someone to understand it better. 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.
apathy 7y ago
This paper is a PR gold mine but a methodological disaster, which is par for the course in "EWAS" (epigenome-wide association studies). At one point I had to remind a coauthor that pointing out structural problems in fashionable studies such as these is a quick way to lose (more) faith in modern peer review; for some reason she thought that EWAS enthusiasts gave a flying crap whether the "genes" they were studying were subject to structural variation (e.g. amplification and deletion). Ha! Ha! Ha! 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...
azeotropic 7y ago
Everyone who wrote and authorized this press release ought to be fired. The paper offers no evidence of relevance to epigenetic inheritance, and has nothing to do with nature vs. nurture. 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.
- KenanSulayman 7y ago
  > We did not find support for the hypothesis that low childhood SES would be associated with DNAm in young adulthood, independent of current SES. Prior research has reported sensitive periods of SES influence (Borghol et al., 2012; Lam et al., 2012), but our study is likely under-powered to test for this effect.

74 points by howrude 7y ago

Same story shared one day ago. https://news.ycombinator.com/item?id=20190233 https://news.ycombinator.com/item?id=20190233

Cynddl 7y ago
And 2 months ago: https://news.ycombinator.com/item?id=19590567 https://news.ycombinator.com/item?id=19590567
dang 7y ago
Reposts are fine if a story hasn't had significant attention yet: https://news.ycombinator.com/newsfaq.html https://news.ycombinator.com/newsfaq.html. It's good to share links to previous threads, but only if there's actually a discussion there.

vipref 7y ago

> socioeconomic status (SES) is a powerful determinant of human health and disease, and social inequality is a ubiquitous stressor for human populations globally 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!

rolltiide 7y ago
My observations is that our society puts too much emphasis on having people prove they are self-reliant, instead of improving its population's productivity. In this dichotomy, the former is detrimental to the society, the latter would enhance it. 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.
- ta1234567890 7y ago
  I agree with the sentiment of changing the narrative, but productivity seems to already be a big part of western society and it seems pretty soul-less. Why not focus on well-being of everyone?
  - rolltiide 7y ago
    > Why not focus on well-being of everyone? 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.
    - wallace_f 7y ago
      I'm not sure what fraction of paid jobs even contribute greater than their cost to society. The War on Poverty has spent trillions, and poverty has increased. A lot of industries obviously don't contribute (tax attorneys, lobbyists, bureaucrats, administrators (see the Rise of the Administrator in healthcare), even much of law enforcement, academia, or regulators). Actually even my first high-paid job working for a financial tech company, I'm convinced didn't contribute to society. Most of our work was mandated by regulatory laws, and most of our customers were capture by monopolistic competition or downright aggressive, questionable sales. 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.
      - rolltiide 7y ago
        I don't agree on that being the immediate issue. 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.
deleted 7y ago
[deleted]

sci-hub 7y ago

Link to paper [PDF]: http://sci-hub.now.sh/go/10.1002/ajpa.23800 http://sci-hub.now.sh/go/10.1002/ajpa.23800

dang 7y ago
It's fine to provide the occasional link but please don't do special-purpose accounts on HN.

aluren 7y ago

>understandings of genes as immutable features of biology that are fixed at conception 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.

johnchristopher 7y ago
This understanding was still taught like that in the 90's, western continental Europe.
- aluren 7y ago
  True. Most of what I've been taught after high school feels like "you've been lied to, everything you were taught in high school was wrong or grossly oversimplified and now you need to unlearn it all and relearn from scratch." Makes you wonder what the purpose of high school was in the first place.
  - davedx 7y ago
    I got the same impression from people who studied chemistry after high school too though. Some things are just simplified so our children can ramp up their understanding gradually instead of having the wild complexity of the universe thrown at them in one go.
    - thatcat 7y ago
      It makes no sense to leave things out of a description of a complex system to help someone to understand it better. 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.

apathy 7y ago

This paper is a PR gold mine but a methodological disaster, which is par for the course in "EWAS" (epigenome-wide association studies). At one point I had to remind a coauthor that pointing out structural problems in fashionable studies such as these is a quick way to lose (more) faith in modern peer review; for some reason she thought that EWAS enthusiasts gave a flying crap whether the "genes" they were studying were subject to structural variation (e.g. amplification and deletion). Ha! Ha! Ha! 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...

azeotropic 7y ago

Everyone who wrote and authorized this press release ought to be fired. The paper offers no evidence of relevance to epigenetic inheritance, and has nothing to do with nature vs. nurture. 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.

KenanSulayman 7y ago
> We did not find support for the hypothesis that low childhood SES would be associated with DNAm in young adulthood, independent of current SES. Prior research has reported sensitive periods of SES influence (Borghol et al., 2012; Lam et al., 2012), but our study is likely under-powered to test for this effect.