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Poverty leaves a mark on our genes

eurekalert.org

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Re: Poverty leaves a mark on our genes

#41

Post by aluren »

mannykannot wrote: post #28
aluren wrote: post #21

Earlier quoted context omitted.

Also the compiler is self-modifying. And the compiler flags as well. And the OS. And the chip architecture sometimes. Like, at what point do we decide that pushing the analogy further is just silly and just drop it altogether?

And yet something guides the human zygote in developing as a human. At what point do we stop focusing on refuting simplistic ideas and turn our attention to what is now known?

That 'something' you mention is called developmental biology and it's yet another level of abstraction removed from the basic cell machinery that operates around DNA. It also has nothing to do with compilers or anything computer related. At some point the analogy is just more harmful than anything else.

Re: Poverty leaves a mark on our genes

#42

Post by raz32dust »

aluren wrote: post #21
heavenlyblue wrote: post #19

Earlier quoted context omitted.

>> DNA is not source code It is source code, it's just that source code is self-modifying.

Also the compiler is self-modifying. And the compiler flags as well. And the OS. And the chip architecture sometimes. Like, at what point do we decide that pushing the analogy further is just silly and just drop it altogether?

At the end of the day, if the gene is self-modifying, the meta-code that modifies the gene also lies somewhere within the gene. Or are you talking about externally modifying a gene by inducing certain mutations?

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.

Re: Poverty leaves a mark on our genes

#43

Post by ak217 »

amelius wrote: post #36
aeorgnoieang wrote: post #34

Earlier quoted context omitted.

> DNA is not source code 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?) org…

To test how much this corresponds to reality, has someone cloned an organism yet with entirely synthetic DNA material?

I'm not sure what exactly you're looking for, but yes, Craig Venter's team at JCVI and later Synthetic Genomics has been building synthetic organisms starting with Mycoplasma laboratorium in 2006. Most recently, an E. coli analog was built using DNA synthesis (https://www.nature.com/articles/s41586-019-1192-5).

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.

Re: Poverty leaves a mark on our genes

#44

Post by KenanSulayman »

azeotropic wrote: post #30

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…

> 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.

Re: Poverty leaves a mark on our genes

#45

Post by aluren »

reasonaway wrote: post #16
aluren wrote: post #6

>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.…

Genes do explain much of the variation between people for many characteristics. You can think of them as initial character stats that are then modified by environmental factors and random noise.

Again, that's not how our modern understanding of genomics works, and hasn't been since the 1980's. There's much, much more to it than genes+environment. See all the mechanisms I've mentioned in GP. Also, you brought up 'variation between people', which can be aditionnally confounded by things that have nothing to do with DNA at all, such as the various microbiomes.

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.

Re: Poverty leaves a mark on our genes

#46

Post by mehrdadn »

arkades wrote: post #10
BearsAreCool wrote: post #9

Earlier quoted context omitted.

This is new knowledge to me, where do I read about this?

Every biology, molecular biology, and genetics textbook made for freshmen and sophomore bio majors. You can't pick a wrong one - this has been core material for at least two decades.

Really? So like, say, Campbell Biology? That's what I've seen used in high school and colleges, and I don't recall any mention of epigenetics in it. (At least in the 7th edition one, published 2004... not sure how much it's changed since.)

Re: Poverty leaves a mark on our genes

#47

Post by educationdata »

aluren wrote: post #32
educationdata wrote: post #26

Earlier quoted context omitted.

I still don't buy the "There is no nature vs. nurture" statement. Maybe there's more than nature vs. nurture, or more complicated than nature vs. nurture. But totally no nature vs. nurture? Overstatement.

Nature vs. nurture hasn't been a thing since the 2000's when second generation sequencing dramatically expanded the breadth of information we had about species' genomes and (along with other discoveries made at the time) made us realize there was indeed a lot more to it than this dichotomy. It's about as relevant in our modern understanding of genomics as the debate between GOTOs vs. structured programming is to our…

No. It's not about whether there was "a lot" more. It's about how much it can add on top of "nature vs. nurture" to explain common social phenomena. It is very possible the new knowledge can be 100 times more complicated, but it only adds 1% more explanation power to everyday phenomena.

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.

Re: Poverty leaves a mark on our genes

#48

Post by arkades »

mehrdadn wrote: post #46
arkades wrote: post #10

Earlier quoted context omitted.

Every biology, molecular biology, and genetics textbook made for freshmen and sophomore bio majors. You can't pick a wrong one - this has been core material for at least two decades.

Really? So like, say, Campbell Biology? That's what I've seen used in high school and colleges, and I don't recall any mention of epigenetics in it. (At least in the 7th edition one, published 2004... not sure how much it's changed since.)

So I don’t have a copy of Campbell’s underhand, but a quick google search for its table of contents brought up the ToC for 7e.

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.

Re: Poverty leaves a mark on our genes

#49

Post by johnchristopher »

__MatrixMan__ wrote: post #37
johnchristopher wrote: post #25

Earlier quoted context omitted.

> Makes you wonder what the purpose of high school was in the first place. 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 throw…

> The first purpose of school and high school is to learn to follow authority. 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 direct…

I added an edit in parenthesis.

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.

Re: Poverty leaves a mark on our genes

#50

Post by iguy »

aluren wrote: post #45
reasonaway wrote: post #16

Earlier quoted context omitted.

Genes do explain much of the variation between people for many characteristics. You can think of them as initial character stats that are then modified by environmental factors and random noise.

Again, that's not how our modern understanding of genomics works, and hasn't been since the 1980's. There's much, much more to it than genes+environment. See all the mechanisms I've mentioned in GP. Also, you brought up 'variation between people', which can be aditionnally confounded by things that have nothing to do with DNA at all, such as the various microbiomes. It's important to note that heritability is not som…

It's worth noting that there are two uses of gene here, or at least of "genetic".

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.

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