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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

#81

Post by simonh »

raincom wrote: post #54

A similar debate goes on in Cognitive Neuroscience and/or neuropsychology/neurophysiology: can cognitive phenomena--like emotion, learning, memory, affect, etc--be localized in the brain? can fMRI solve this localization-distribution issue? Whatever we have known so far, early phases of the input system (sensory) and later phases of the output system (motor) can be localized. Even there is an overlap between the inpu…

Then there’s the problem that fMRI is hardly providing us with a complete view of everything going on in the brain. The same goes for the other instruments we have. Who knows what parts of the puzzle we’re not yet even seeing?

Re: Theory Suggests That All Genes Affect Every Complex Trait

#82

Post by jccooper »

dboreham wrote: post #77

There's an encoding scheme used (probably several) and we don't understand it. This is like showing someone the hex dump of an mpeg file and expecting them to know it makes a picture of a kitten.

...and a picture of the Grand Canyon, and a recording of Beethoven, and also somehow a couple of sonnets, depending on what the temperature is.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#83

Post by skosuri »

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…

Re: 1: It wasn’t wrong. There are Mendelian traits and complex traits. We shouldn’t forget we’ve basically tracked down most Mendelian diseases since the human genome was published. Still some to go but we will hopefully have all soon. This is a huge accomplishment.

Complex/quantitative traits on the other hand have been known for quite some time. I don’t think it’s anything new, but the landscape is becoming increasingly clear thanks to large scale GWAS and analyses from many groups including Pritchard’s.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#84

Post by polski-g »

nonbel wrote: post #75

Of course, to me this is obvious: "everything correlates with everything else". Wait until we start seeing the results of the hyped up "gene editing" studies where they follow up for a few years and look at more than one/few outcomes at a time...

Don't even need that. Later this year BGI will allow you to submit zygotes and they'll provide a 23andme compatible report. And you can plug that in to dnaland and find out which zygote you should select for the most intelligent offspring.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#85

Post by polski-g »

jcims wrote: post #22

I was hoping CRISPR/Cas9 (or some similar system) was going to answer many prayers. Maybe this means it's less likely?

No it just means more than one gene would be needed to be modified. Don't know who was ever thinking that traits weren't polygenic. If they were monogenic then there would be no variance in traits.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#86

Post by fragsworth »

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.

But we don't actually know if evolution doesn't abstract. It's possible that our genome has been around long enough to develop tendencies to cause mutations that change us in certain ways that might be considered "abstract". For instance, we might be able to mutate longer or shorter arms or legs.

This notion should be supported by the fact that we don't mutate in completely random ways, and the fact that most mutations don't kill us.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#87

Post by ravinizme »

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…

The coding part of the genes are 1.5% of the genomes.it is called the Exome.(32 millions) But when looking at all genes (including UTR, pseudogenes) from a basepair prespective It's closer to 40% of the genome.(1.2 billion bases)

Re: Theory Suggests That All Genes Affect Every Complex Trait

#88

Post by themodelplumber »

chiefalchemist wrote: post #78
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.

That's a great way to put it. You'd want a system that would instinctively re-implement patterns as a way of protecting itself, as well. I've noticed lately that if you take business process development, personal productivity, value-creation philosophy, socio-political framework-building (e.g. development of democracy) and combine that sort of thing with the traditional "software OR firmware OR hardware" definition of technology, the human system is always building "technology" toward what might be called survival+. In this human systems/outside-systems interaction there is a periodicity aspect where at times (e.g. giant meteor approaching) human "survival" is definitely the question, and other times we surge way past just putting meat on the table, so to speak.

Also, a trait, e.g. a psychological trait, or a group of them ("values-centered, empathetic, philosophical" vs. "productivity-centered, logical, process-oriented") could be seen as a technology orientation that helps the system build technology of a specific kind.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#89

Post by adrianN »

sriku wrote: post #71

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 o…

What do you mean with "quantum level"? All of biochemistry is best described by quantum mechanics. Do you mean large scale entanglement and coherence as would be required for quantum computation? That seems a bit unlikely in a warm soup like our bodies. We haven't been able to achieve it on a useful scale even in the controlled environments of physics labs.

Re: Theory Suggests That All Genes Affect Every Complex Trait

#90

Post by adrianN »

xyhopguy wrote: post #41
speby wrote: post #38

Earlier quoted context omitted.

#2 is perhaps one of the most confounding recent areas of research that really starts complicating the study of DNA and how changes to it map to an organism's outcome in the real world over time and in different environments. As new studies emerge on identical twins/triplets/etc., it has become clear that even identical DNA does not at all have 100% clone of the person, even if they do in fact share the same DNA. Ran…

Eh I disagree. It's been known for a while that you need something other than just DNA to get the heterogeneity of cellular phenotypes. Remember that your Iris and toenails have the same DNA, yet wildly different gene expression profiles. Without cellular memory that would be impossible and we would all still be single celled organisms :)

I think the interesting discovery has been that epigenetic traits can be inherited to some degree.
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