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Comment by moralestapia | Hacker News Reader

>But it remains true that there are large amounts of non-coding junk DNA which is under no selection pressure.

Nope, you cannot ever assert that.

Did you understand the article? What was once thought to be junk turned out not to be. Extrapolate from that.

Selection pressure can be measured. If a big chunk of DNA is missing from a third of a population with no apparent ill effects, the onus is on you to show that it was somehow important. Of course there is plenty of non-coding DNA which is under selection pressure and therefore does something important, but everyone has known this for decades.

The single most common sin in all of science is to misrepresent the null hypothesis because it makes getting positive results easy. In article form, this translates to when you see a title "Everyone thought X but actually Y," 99% of the time nobody thought X and Y is otherwise unremarkable. They wanted to remark on Y, though, so they cooked up "Everyone Thought X" to facilitate the presentation.

>the onus is on you to show that it was somehow important

What? Like ... not at all? Onus does not get assigned "by default" due the nature of things, lol. The onus falls on whoever comes up to propose an hypothesis.

In this case that hypothesis is "all other DNA/RNA is junk", well, then "prove that thing is true", which is unfeasible and hence why one could not assert such thing.

>In this case that hypothesis is "all other DNA/RNA is junk",

Strawman.

It is not as black and white as you think it is. Some non-coding DNA/RNA is functional. Some is not. Selection/conservation is often used as quick way to tell whether something is functional or not.

Nobody actually in the field of genetics would say "all other DNA/RNA is junk". You'd get laughed out of the room, kind of in the same way if you said "all non-coding DNA is functional because 'epigenetics' ".

It's like this: now that full-genome sequencing is getting pretty cheap and common, you can tell how string the selection pressure is on a chunk of DNA just by looking at frequencies of variants. If it turns out there are very few variants, you can be confident the chunk is doing something, even if you don't know what. If the variation looks like random drift, you can be pretty confident it is.

No, you seem to only have a casual/superficial understanding of the field.

There's an abysmal number of post-transcriptional effects that are functional. Start with something like [1].

There's also plenty of evidence (like TFA and [2]) of "junk" DNA turning out to be functional through some contrived and completely unexpected mechanisms.

Every time someone says something like "this is how Biology works" one can lmao all the way to the lab.

1: https://en.wikipedia.org/wiki/Epigenetics

2: https://pubmed.ncbi.nlm.nih.gov/36484387/

As others and I have mentioned above, there are absolutely parts of the genome that are functional despite being non-coding. There is no debate about this. You have shared links and arguments emphasizing that there is function in these parts. However, you have not addressed the fact that there are large stretches of DNA that are not conserved across species, show no differential selection pressure compared to what would be expected from random genetic drift, and that there are hugely varying sizes of genome between species.

From my reference below: "If most eukaryotic DNA is functional at the organism level, be it for gene regulation, protection against mutations, maintenance of chromosome structure, or any other such role, then why does an onion require five times more of it than a human?"

Of course, one can always say, "How arrogant to think we know everything." But given our current understanding of evolution and genetic function, the specific identity of a genetic sequence correlates with its function. If that function is important, the sequence should be preserved to a degree better than random chance.

To deny this is to suggest that any random sequence of genetic material can serve a vital purpose while being subject to endless mutation without consequence. This raises the question: What do we mean by a "specific sequence" if it isn’t conserved and is constantly mutating?

I assume you are familiar with the information I’ve just shared. I’m curious where we are diverging in our views because it feels like we are not discussing the same thing.

This artcle fairly represents my understanding of what I mean when I say "junk DNA": https://journals.plos.org/plosgenetics/article?id=10.1371/jo...

You're refuting a strawman. The junk DNA claim is not, and as far as I can see never had been, that all non-coding DNA is junk. It's that most of our genome -- around 90% -- is junk[1][2]. But since the genome is over 98% non-coding, that implies that something like 8% is functional non-coding DNA, which is several times the amount of coding DNA. Finding small amounts of additional functional non-coding DNA does not significantly challenge this[3].

[1] https://sandwalk.blogspot.com/2022/08/junk-dna-vs-noncoding-...

[2] https://en.wikipedia.org/wiki/Junk_DNA#History

[3] https://judgestarling.tumblr.com/post/154553548091/long-nonc...

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