Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

Theory Suggests That All Genes Affect Every Complex Trait

quantamagazine.org

Post reply on HN
Print view View original

61–70 of 125 posts

Re: Theory Suggests That All Genes Affect Every Complex Trait

#61

Post by kristianov »

jds375 wrote: post #17
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

DNA is spaghetti code where modularization happens by accident.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#62

Post by foobarian »

kristianov wrote: post #61
jds375 wrote: post #17

Earlier quoted context omitted.

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

DNA is spaghetti code where modularization happens by accident.

Reminds me of our corporate codebase after 10 years of A/B testing

Re: Theory Suggests That All Genes Affect Every Complex Trait

#63

Post by felipemnoa »

civilitty wrote: post #42
jds375 wrote: post #17

Earlier quoted context omitted.

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

I think it's easier to understand if you rephrase it as "evolution doesn't encapsulate." Just because a bunch of smaller proteins fold into a bigger quaternary protein structure doesn't mean that those smaller proteins become "private" members of the new protein "class". Any chemical binding sites that are still exposed on the surface of the complex protein will still be chemically active and affected by evolutionary…

>>evolution doesn't encapsulate.

I'm not a biologist or geneticists but from everything that I've read about cellular biology and genetics I get the strong feeling that there is a lot of encapsulation going on. Sure, it isn't 100% percent perfect but there is still encapsulation going on. Evolution would probably be way harder without it.

One hint is the human body, there are lots of encapsulations: eyes, heart, kidneys, digestive system, etc.

Evolution can repurpose an existing system for a completely different use with just some tweaking.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#64

Post by inventtheday »

jds375 wrote: post #17
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

Isn't abstraction just the emergence of simpler, lower fidelity, and higher density structures of information? Are we not a part of nature?

Re: Theory Suggests That All Genes Affect Every Complex Trait

#65

Post by dkural »

ancorevard wrote: post #26

Two things: 1. The theory of "junk DNA" of which the authors received Nobel Price is increasingly looking like...well...junk. 2. The recent discovery of Epigenetics adds a whole other dimension for understanding traits and genetics. Lots of biological science needs to be rewritten/updated in the years to come.

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 back when, for different use cases. It also has "injected code" ie ancient viral DNA, and other weird artifacts that's not relevant to the functioning code base of today. Sure, it is useful from a meta-evolutionary perspective, those parts can be refashioned for another use... but so can real-world "junk" :)

Re: Theory Suggests That All Genes Affect Every Complex Trait

#66

Post by themodelplumber »

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 though additional systems, like social group, atmosphere/environment, etc.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#67

Post by resource0x »

dkural wrote: post #65
ancorevard wrote: post #26

Two things: 1. The theory of "junk DNA" of which the authors received Nobel Price is increasingly looking like...well...junk. 2. The recent discovery of Epigenetics adds a whole other dimension for understanding traits and genetics. Lots of biological science needs to be rewritten/updated in the years to come.

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

Re: Theory Suggests That All Genes Affect Every Complex Trait

#68

Post by telchar »

felipemnoa wrote: post #63
civilitty wrote: post #42

Earlier quoted context omitted.

I think it's easier to understand if you rephrase it as "evolution doesn't encapsulate." Just because a bunch of smaller proteins fold into a bigger quaternary protein structure doesn't mean that those smaller proteins become "private" members of the new protein "class". Any chemical binding sites that are still exposed on the surface of the complex protein will still be chemically active and affected by evolutionary…

>>evolution doesn't encapsulate. I'm not a biologist or geneticists but from everything that I've read about cellular biology and genetics I get the strong feeling that there is a lot of encapsulation going on. Sure, it isn't 100% percent perfect but there is still encapsulation going on. Evolution would probably be way harder without it. One hint is the human body, there are lots of encapsulations: eyes, heart, kidn…

I think that's a misleading observation though. It is squinting at the macro structure of the body and saying "ah ha, encapsulation!". When you look closer the apparent encapsulation seems less and less like an accurate notion. For example the newer research showing how the gut affects cognition. [0]

This is a bit off-topic but I think paleo-ontologists fall into a similar trap, at least based on popular writing about e.g. sharks. Claims that they haven't evolved in 100M years because they're the same shape as they used to be completely ignore all the other aspects of the shark that could change without affecting the overall shape.

0. https://www.ncbi.nlm.nih.gov/pubmed/24997042

Re: Theory Suggests That All Genes Affect Every Complex Trait

#69

Post by jlg23 »

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…

4. Few biologists have dived into automata theory. The divide in background theoretic knowledge and thus language is too great for biology to directly profit from advances in automata theory.
Post reply on HN