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Theory Suggests That All Genes Affect Every Complex Trait

quantamagazine.org

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Re: Theory Suggests That All Genes Affect Every Complex Trait

#71

Post by sriku »

There has been what I think is direct evidence of the possibility of this in the digital world. Adrian Thompson's work[1] in evolving an FPGA circuit to tell the difference between the spoken words "stop" and "go" (yes .. digital circuit design with an analogue task) threw many surprises. The evolved circuit was highly economical with gates and didn't use a clock. It had also started exploiting the specific physics of the FPGA chip and included transmitters and receivers. Digitally "useless" structures were critical to its performance.

If this is true of a simple evolved circuit - i.e. the connection between the circuit specification and the behaviour being complex, with the circuit specification already encoding physics beyond the digital gates - then I'm not sure what hope we should actually place in statistical attempts to connect genes with organism behaviour.

Pushing the link a bit more, just as the circuit representation went beyond the target domain of digital circuits, could what is encoded in our genes explicitly encode exploitations at quantum level? With this, the possibility of brain structures acquiring quantum error correction schemes doesn't seem too far fetched or crazy thought.

[1] https://www.damninteresting.com/on-the-origin-of-circuits/

Re: Theory Suggests That All Genes Affect Every Complex Trait

#72

Post by Osiris »

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…

Or perhaps it's like code where everything is in therl global scope. New code may add global variables and/or rely on existing ones, or even change existing ones. In code like, changing one line of code could have far reaching and unexpected consequences.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#73

Post by mrfusion »

jlg23 wrote: post #69
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.

I’m interested. Explain more?

Re: Theory Suggests That All Genes Affect Every Complex Trait

#74

Post by carapace »

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

Did you ever read "Mote in God's Eye"? It's like Motie engineering.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#76

Post by [deleted] »

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…

[deleted]

Re: Theory Suggests That All Genes Affect Every Complex Trait

#78

Post by chiefalchemist »

themodelplumber wrote: post #66

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…

> "It makes intuitive sense if I think of traits as one outcome of a system."

Put another way, if you were building something and you wanted it to survive, would you want a flexible multifaceted system, and not a dogma-esque checklist of X, Y and Z.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#79

Post by madhadron »

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

It's not a great example, and I'm sorry for it. Let me try another one. In the study of eukaryotic cell cycle, there's a notion of a checkpoint. For example, if you damage the DNA of a yeast cell severely, it will continue its cell cycle until some point and then arrest instead of arresting directly, and you can find mutants that don't arrest. There's a whole set of mutants that were used to figure out the checkpoints in the cell cycle.

Of course there's no little physical switch. This is a giant mass of molecules bouncing around. A fellow I know did some interesting work on replacing simple checkpoint models with entrained oscillators. But this makes the checkpoints look like an abstraction.

That's our view of it, though. It's not an abstraction. It's something that looks like one.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#80

Post by madhadron »

lisper wrote: post #58
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…

> Evolution doesn't abstract. That is a very profound observation. It suggests a way that one can distinguish between something that evolved vs something that was designed.

I've spent a little time considering what this class of things would be. It's like trying to turn a forgetful functor into a homotopy transformation and having some kind of universal measure of the distance from the end of the transformation.
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