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Theory Suggests That All Genes Affect Every Complex Trait

quantamagazine.org

101–110 of 125 posts

Re: Theory Suggests That All Genes Affect Every Complex Trait

#101
post #25

Earlier quoted context omitted.

Presumably they mean that material evolution doesn't involve ideas, which is what abstractions are. This is a physicalist line to take which implies that the universe is entirely material, and abstraction is just something human minds perceive.

> ...abstraction is just something human minds perceive. This itself is a physical phenomenon :)

For physicalists, yes.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#102

This reminds me of systems theory; anyone else? It makes intuitive sense if I think of traits as one outcome of a system. Rather than converging to a single particle-like "cause," such as a gene, it seems that the wider system is the basis for the trait--the objective appearance of the trait is an expression of the system. It seems it should follow that you can continue tracing the trait from the individual level up…

This is basically what it is : basic systems theory applied to basic genetic knowledge. Having worked in this field during my studies, I can say that most of the leading figures were not impressed by the Omnigenics paper. It was simply the right claim at the right time, it made a splash, but it will probably not change at all how research is conducted.

Some say that the view it is pushing (core vs peripheral genes) is simply wrong as evidence of it cannot be found in the data (and there is a lot of data), see the end of the article about Naomi Wray's article. Also see the many mentions of the paper's critics! I like the phrase "provocatively phrased extension of earlier ideas".

There are bigger issues that need addressing but all of them are much much harder to get right and they would probably not make it to Quanta magazine ;) For example, phenotype heterogeneity and patient stratification are two big thorns in precision medicine's side.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#105
post #104

Old news. Pleiotropy is an example for it. https://en.wikipedia.org/wiki/Pleiotropy What is a bigger problem: Even an average idiot must now realize, that GM food may be riskier than you think.

> Even an average idiot must now realize, that GM food may be riskier than you think.

Yes and no. It may lead to dangerous expressions, but plain chemical testing and analysis prior to commercial release should ensure nothing toxic makes it into people's food.

If your apples suddenly start producing magnitudes more cyanide after modifying something, just don't sell them.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#106
post #104

Old news. Pleiotropy is an example for it. https://en.wikipedia.org/wiki/Pleiotropy What is a bigger problem: Even an average idiot must now realize, that GM food may be riskier than you think.

> Even an average idiot must now realize, that GM food may be riskier than you think. Yes and no. It may lead to dangerous expressions, but plain chemical testing and analysis prior to commercial release should ensure nothing toxic makes it into people's food. If your apples suddenly start producing magnitudes more cyanide after modifying something, just don't sell them.

Yes. Since you know especially what toxins to look for. Not.

And you know exactly under what conditions the toxins are expressed. Not.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#107

There's a couple of things that are slowly changing in the thinking of biologists related to this: 1. Genes are not loci. The "one gene = one protein" dogma of molecular biology (expanded: "one trait selectable in breeding experiments = one compact locus of the chromosome") was a priori wrong, but it's taken us decades to undo the damage. We were led astray because there are traits that do map to a single locus, or s…

> Evolution doesn't abstract

What does this mean? Are cells, for example, not abstractions?

Re: Theory Suggests That All Genes Affect Every Complex Trait

#108

There's a couple of things that are slowly changing in the thinking of biologists related to this: 1. Genes are not loci. The "one gene = one protein" dogma of molecular biology (expanded: "one trait selectable in breeding experiments = one compact locus of the chromosome") was a priori wrong, but it's taken us decades to undo the damage. We were led astray because there are traits that do map to a single locus, or s…

>If a human engineered it, we'd call it a leaky abstraction, but please don't get caught up on that. Evolution doesn't abstract.

Why not? Humans are products of evolution too, and they abstract.

I mean, what we consider conscious (e.g. human activity) and what we consider accidental (e.g. the result of evolutionary forces clashing) are not very well defined. Heck, we haven't even solved the determinism vs free will issue yet.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#109
post #107

There's a couple of things that are slowly changing in the thinking of biologists related to this: 1. Genes are not loci. The "one gene = one protein" dogma of molecular biology (expanded: "one trait selectable in breeding experiments = one compact locus of the chromosome") was a priori wrong, but it's taken us decades to undo the damage. We were led astray because there are traits that do map to a single locus, or s…

> Evolution doesn't abstract What does this mean? Are cells, for example, not abstractions?

Parent means it doesn't consciously abstract -- not that abstractions cannot result from it.

In the same way the banana skin is a great packaging solution, but it wasn't created to serve as packaging for our consumption.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#110
post #65

Earlier quoted context omitted.

The article above has nothing to do with Junk DNA. "All genes" is still about 1.5% of the genome. I think Junk DNA is a bad term for the parts of the genome that describe it. In human-engineered physical systems, we are used to all or most of the parts having a purpose of some kind, even if it is an aesthetic purpose. The genome is more like source code that evolved over millions of commits, and has code from way bac…

Quote: Male mice grow ovaries instead of testes if they are missing a small region of DNA that doesn't contain any genes, finds a new paper published in Science. Source: https://www.crick.ac.uk/news/science-news/2018/06/14/non-cod... EDIT: I think the finding is significant enough to warrant a separate discussion. Submitted a link: https://news.ycombinator.com/item?id=17361545

The press release is misleading - no one is claiming 98% of the DNA is "junk", contrary to what the press release claims with no evidence. Regulatory regions around genes are understood be crucial to gene function and taught in undergraduate education. Usually people claim that mobile elements + repetitive regions constitute the "junk" region, which is about 40% of the genome. Also, there are dozens of studies showing you can survive with large chunks of it missing. Each human in fact has thousands of such structural variations.
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