Obviously, because it isn't junk; it is of value to the organism. Even if it's not of any use right now, even if it's completely biologically inactive at present. Because it is still extremely high entropy information. They're remnants of solutions other living systems once used, at some point, to solve the problem of staying alive.
If I were going to try and exploit genetic mutation to produce novel solutions to biological problems, I would start from an existing genome. In fact, I'd start with as much data, from as many organisms, as I could get my hands on and store. Perhaps we carry junk DNA because mutations in existing coded sequences, even mutated, currently useless ones, are far more likely to be functional, and so potentially a useful adaptation, than literal randomness. It's life's portfolio of solutions, badly photocopied little snippets accumulated over the years, and we all carry it around for future generations that might live in an environment where it's useful.
Can maladaptive mutations really be caused by copying DNA that's not used much (as far as we can tell, like the DNA for endogenous retroviruses in our genome)?
The fact that we can tap junk at some future point is probbly just an accidental side-effect... though there is another theory that claims having lots of junk provides some protection against environmentally-induced damage because most of the time it is a junk section that gets damaged. Hows that for the next error protection algorithm: pad the message with mostly zeros so occasional bit corruption doesn't matter. Take that Shannon!
If you want a specific example of this mechanism working: primate 3-color vision. In our two color blue-yellow seeing ancestors the yellow pigment sequence got duplicated, then eventually slightly mutated. That's why the red and green receptors overlap so much yet blue is standing way off by itself. It is high likely this started as a useless duplication and was carried around for a long time before one of the duplicates got mutated.
In other cases, there are just lots and lots of duplicates of the same genes over and over. Other parts appear to be forges of gene creation- either through gene duplication and divergent evolution, or through some other mysterious mechanism we don't know yet.
Certainly, we've had parts that looked like they were nothing at all and ended up being very important, and other parts that looked like they were incredibly important, but were really just the side effect of some effective parasite.
It's sort of not even an interesting debate any more, as most of the initial positions everybody held were changed when we interrogated more, and better data.
I’m thinking by analogy of executable programs that have runs of zeros. The zeros don’t necessarily do anything, but remove them and everything else is out of alignment.
We already know that enhancers "work at a distance" and it's not clear what "distance" exactly means, and it gets into complicated 3D structure of the genome inside a cell; see https://en.wikipedia.org/wiki/Enhancer_(genetics)
Personally I think that the best way to think about the genome is to unlearn most of the preconceptions you learned in genetics and instead think about it in terms of biophysics and development and machine learning: you'll never realyl be able to understand the true function of every little bit, but you cvan probably create an approximate model that explains the vast majority of biology with relatively few variables, and some deep models that contain all the necessary statistics to model these systems accurately.
ALU elements: Know the SINEs [short interspersed elements]
Alu elements are primate-specific repeats and comprise 11% of the human genome. They have wide-ranging influences on gene expression. Their contribution to genome evolution, gene regulation and disease is reviewed.
https://genomebiology.biomedcentral.com/articles/10.1186/gb-...
[1] https://utorontopress.com/9781487508593/whats-in-your-genome...
- Is extremely difficult to remove, at a worthwhile scale, from the genome of any large & long-lived organism
- Can be thought of as a huge pile of tickets for the Extremely Favorable Random Mutation lottery
Science is fantastic to dig into areas it can already see, and terrible at seeing new areas from the greater unknown.
ISBN-13: 978-1442634992, ISBN-10: 1442634995
If the primary goal is survival based primarily on efficient use of energy. A lot of evolution is about organisms becoming more efficient by adapting to their environment. So then keeping unnecessary junk around is inefficient and we would expect orgasms that lose to would benefit and out breed the others.