this post was submitted on 07 Feb 2024
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See here for an overview of the current thinking on junk DNA: https://www.news-medical.net/life-sciences/Functions-of-Junk-DNA.aspx
Basically there are a variety of indicators that suggest A - Many "junk" regions are in some way evolutionarily important because many sections of "junk" are preserved across time, which, given the way DNA works, would almost certainly not be the case if they had no function, B - there is evidence non-coding regions actually do influence when and how other genes are expressed.
In essence, you could look at it as possibly metadata or maybe something very loosely along the lines of a Makefile for genetic code.
I think the assertion that it's not "junk" is more alluding to the fact that although it does not directly encode proteins, asserting that non-coding proteins are "junk" requires us to ignore that there is clear evidence that non-coding regions likely do serve other purposes, or rather, requires us to proactively assert they serve no purpose simply because they don't serve the very first purpose we hypothesized they should serve.
If a gene becomes disabled (a start triplicate pair gets changed to a nonsense triplicate), and it turns out that gene was no longer useful so there's no impact on survivability/reproduction, what happens to the rest of the pairs before the next start triplicate? That stop triplicate and everything before it is now useless. Except evolution doesn't understand useless, there's just as much chance of flipping that gene back on as there is of shortening all of that non readable DNA by just 1 codon length, DNA replicators are very good at not dropping codons. But not you have a gene that isn't being read (outside of replication) or transcribed, and it really isn't costing the individual any significant amount of extra resources to continue to produce that set of code in that strand, so it just hangs out.
There are dozens of other mechanisms to control the rate of protein synthesis, why would junk DNA be the controlling mechanism for it when there are epigenetics, gates, chemical limits, so many different ways rare limit down the path.
"It's there so it must have function" is spitting in the face of the theory of evolution. "It's still in the genetic code so it must've been selected for" is barely less offensive. Evolution does not select for efficiency, it's descent with modification, there is no pressure that says the genetic information must be as efficiently contained as possible. Example: https://en.m.wikipedia.org/wiki/Paris_japonica
Also I'm not at all arguing that proteins are junk (also not saying they're peak efficiency, but "junk" in a 'read' section of DNA is clearly not 'junk'), I'm arguing there are sections of DNA, especially repeating sections outside of start stop sections, that are without purpose.
This is a funny comment though, because "junk" DNA is involved with epigenetic regulation and cellular behavior.
"It's there so it must have function", "it's still in the genetic code so it must have been selected for" is the least nuanced take,
"It's there just randomly and therefore is junk", and "evolution does not select for efficiency" is an improvement,
But "it's there and it's doing something despite not having a bespoke, prescribed function" and "evolution is a cascade of emergent effects and random chance, none of our genome is non-functional even though it is random" is the most up to date take
You seem like a biologist, why not go read some of these papers? Like the one I linked by Dan Nichols? Most people don't have the background necessary to understand the language (no shade) but you seem to!
You can second-guess the current state of the literature on junk dna all you want but unless you have a research budget it's a bit meaningless.
Also, I never said, and no scientist said, it was THE SINGLE AND ONLY mechanism influencing gene expression. Nobody also ever said the fact the "junk" is preserved was the CONCLUSIVE AND DEFINITIVE PROOF that it does something. Just that it's a good indicator.
You're not really responding to what the current hypotheses are.