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Comment by kingkawn | Hacker News Reader

The concept of junk DNA was mostly taken apart a few years ago. Those sections often serve regulatory functions and other purposes related to controlling how genes are used and at what rates.

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You're referring to regulatory regions which really represent a tiny component of the genome (in terms of base fraction)... but nobody has really constructed a strong argument (that can be tested) that long stretches of Alu (which comprise most of the junk DNA) actually have a regulatory or other function.

It's speculated those regions are gene foundries, but it's mostly speculation with limited evidence.

I think there's a 'balancing game' between "I need my DNA to be as compact as possible" (no waste of energy, faster to duplicate, less chance for errors) and "I need space in my DNA to allow new things to evolve".

In zebrafish and mouse, the more "developmental" a gene is, the more SPACE it seems to have around it. More space means more regulation and more potential for new regulation.

That's a fine hypothesis, but proving it is near impossible.

I thought they were part of the structural mechanisms of the regulatory regions, ie they need long stretches of dna to facilitate it looping regulators back onto the allele

That's a hypothesis, but not one with enough support to be considered true.

No, it really hasn't been. Projects like ENCODE which claimed that 80% of the human genome was functional were done in ignorance of genomes of other organisms. There are animals like the pufferfish that have almost no junk DNA. And there are amoebas with more junk DNA than do humans. If junk DNA was in general functional, this would not be the case.

I mean, 'junk' DNA is just the noncoding regions. It contains everything that would look like a conditional jump to us CS folks, or a gate to EE folks. The coding regions are closer to .rodata; literally tables of the protein chains.

The relative lack of non coding DNA in other, simpler cells doesn't tell us that we don't need ours. It's equally possible that our DNA is just making significantly more dynamic decisions.

But the fact that some have more non-coding DNA doesn't really fit that idea. Unless you think amoebas are secret masters of the world. The simplest explanation is still that it is neutral baggage of neither benefit nor hindrance and organisms can gain or lose it by chance.

Or their strategy is to generate proteins with less of a concern for how their environment is dynamically changing. Which more aligns with single celled and very simple animals.

And it's not necessarily that they have more coding regions. It's that they have a greater percentage vs noncoding. It's a proportional thing.

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