Theory Suggests That All Genes Affect Every Complex Trait • Hacker News Board

Re: Theory Suggests That All Genes Affect Every Complex Trait

#11

Post by onychomys » Wed, Jun 20, 2018, 8:41 PM UTC

fizx wrote: post #7

api wrote: post #4

Having studied biology and genetics this is common sense to me. Genetic systems are probabilistic chemical systems where everything influences everything to varying degrees in parallel. They are nothing like the linear assemblies of modules that humans prefer to engineer.

Common sense from the machine learning side too! (that said, the ex-physicist in me would like to remind everyone that science and reality are not required to match your common sense) If true, this means that evolution could look more like stochastic gradient descent, and less like brute force luck plus survival of the fittest.

From an evolution point of view, it actually just means that selection happens at the organismal level, not the gene level.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#12

Post by fizx » Wed, Jun 20, 2018, 8:50 PM UTC

onychomys wrote: post #11

fizx wrote: post #7

Earlier quoted context omitted.

Common sense from the machine learning side too! (that said, the ex-physicist in me would like to remind everyone that science and reality are not required to match your common sense) If true, this means that evolution could look more like stochastic gradient descent, and less like brute force luck plus survival of the fittest.

From an evolution point of view, it actually just means that selection happens at the organismal level, not the gene level.

You misunderstand my point... larger ratio of base pairs to behavior means that the behavior is likely more robust to noise, and the original evolution of the behavior would have been smoother (i.e. proceeded in less of a step-wise manner, because each step would be a much smaller fraction of the required change than previously thought).

Re: Theory Suggests That All Genes Affect Every Complex Trait

#13

Post by aphextron » Wed, Jun 20, 2018, 8:52 PM UTC

api wrote: post #4

Having studied biology and genetics this is common sense to me. Genetic systems are probabilistic chemical systems where everything influences everything to varying degrees in parallel. They are nothing like the linear assemblies of modules that humans prefer to engineer.

>Having studied biology and genetics this is common sense to me. Genetic systems are probabilistic chemical systems where everything influences everything to varying degrees in parallel. They are nothing like the linear assemblies of modules that humans prefer to engineer.

I'm really glad that this mental model I've built up seems to reflect reality. The idea of neatly editing specific genes to produce a desired result always sat with me as the pinnacle of human hubris. The more I learn about Biology the more I just throw up my hands and say "magic".

Re: Theory Suggests That All Genes Affect Every Complex Trait

#14

Post by [deleted] » Wed, Jun 20, 2018, 8:53 PM UTC

spruciefic399 wrote: post #8

This is a paper that I'm glad was published (maybe not Cell, but somewhere), because it presents an interesting and pretty clear theory. At the same time, it seems like it's fairly clearly falsifiable almost on its face, because there are many genetic disorders involving clear, substantial mutations (in a chromosomal topography sense) that are circumscribed in their effects, at least to one extent or another. I think…

[deleted]

Re: Theory Suggests That All Genes Affect Every Complex Trait

#15

Post by toasterlovin » Wed, Jun 20, 2018, 8:57 PM UTC

gwern wrote: post #5

R.A. Fisher was right, as usual.

Off topic: I see you on here commenting on discussions related to evolution pretty frequently, so I figured I'd ask you:

Are there any communities like HN, but focused on evolution, population genetics, etc. that you would recommend?

Re: Theory Suggests That All Genes Affect Every Complex Trait

#16

Post by frgtpsswrdlame » Wed, Jun 20, 2018, 8:58 PM UTC

These kinds of strange findings are going to keep occurring because these researchers are too far invested into a mode of research (genetics) that won't actually find the determinism they desire. It's the environment not the genes.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#17

Post by jds375 » Wed, Jun 20, 2018, 9:00 PM UTC

madhadron wrote: post #10

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…

Very interesting comment, thanks!

Could you elaborate on what you mean by ‘evolution doesn’t abstract’? I did not totally understand what the example given had to do with abstraction

Re: Theory Suggests That All Genes Affect Every Complex Trait

#18

Post by bookofjoe » Wed, Jun 20, 2018, 9:01 PM UTC

aphextron wrote: post #13

api wrote: post #4

Having studied biology and genetics this is common sense to me. Genetic systems are probabilistic chemical systems where everything influences everything to varying degrees in parallel. They are nothing like the linear assemblies of modules that humans prefer to engineer.

>Having studied biology and genetics this is common sense to me. Genetic systems are probabilistic chemical systems where everything influences everything to varying degrees in parallel. They are nothing like the linear assemblies of modules that humans prefer to engineer. I'm really glad that this mental model I've built up seems to reflect reality. The idea of neatly editing specific genes to produce a desired resu…

>The idea of neatly editing specific genes to produce a desired result always sat with me as the pinnacle of human hubris.

See, for example: Gene Therapy in a Patient with Sickle Cell Disease https://www.nejm.org/doi/full/10.1056/NEJMoa1609677

Re: Theory Suggests That All Genes Affect Every Complex Trait

#19

Post by aphextron » Wed, Jun 20, 2018, 9:04 PM UTC

bookofjoe wrote: post #18

aphextron wrote: post #13

Earlier quoted context omitted.

>Having studied biology and genetics this is common sense to me. Genetic systems are probabilistic chemical systems where everything influences everything to varying degrees in parallel. They are nothing like the linear assemblies of modules that humans prefer to engineer. I'm really glad that this mental model I've built up seems to reflect reality. The idea of neatly editing specific genes to produce a desired resu…

>The idea of neatly editing specific genes to produce a desired result always sat with me as the pinnacle of human hubris. See, for example: Gene Therapy in a Patient with Sickle Cell Disease https://www.nejm.org/doi/full/10.1056/NEJMoa1609677

I literally can't understand a single word on that page. Care to explain?

Re: Theory Suggests That All Genes Affect Every Complex Trait

#20

Post by pishpash » Wed, Jun 20, 2018, 9:04 PM UTC

madhadron wrote: post #10

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…

To add to that, evolution does generate compositions, and some of the abstractions that do occur come from those.