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There is a big long-running argument about what "functional" means in "non-coding" parts of the genome. The deeper I pushed into learning about the debate the less confident I became of my own understanding of genomics and evolution. See https://www.sciencedirect.com/science/article/pii/S096098221... for one perspective.

by wespiser_2018225 days ago|

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It's possible that the "functional" aspect of non-coding RNA exists on a time scale much larger that what we can assay in a lab. The sort of "junk DNA/RNA" hypothesis: the ncRNA part of the genome is material that increases fitness during relative rare events where it's repurposed into something else.

On a millions or billions of year time frame, the organisms with the flexibility of ncRNA would have an advantage, but this is extremely hard to figure out with a "single point in time" view point.

Anyway, that was the basic lesson I took from studying non-coding RNA 10 years ago. Projects like ENCODE definitely helped, but they really just exposed transcription of elements that are noisy, without providing the evidence that any of it is actually "functional". Therefore, I'm skeptical that more of the same approach will be helpful, but I'd be pleasantly surprised if wrong.

by cysteinechapel221 days ago|

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Such an advantage that is rare and across such long time scales would be so small on average that it would be effectively neutral. Natural selection can only really act on fitness advantages greater than on the order of the inverse of effective population size, which for large multicellular organisms such as animals, is low. Most of this is really just noisy transcription/binding/etc.

For example, we don't keep transposons in general because they're useful, which are almost half of our genomes, and are a major source of disruptive variation. They persist because we're just not very good at preventing them from spreading, we have some suppressive mechanisms but they don't work all the time, and there's a bit of an arms race between transposons and host. Nonetheless, they can occasionally provide variation that is beneficial.