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-...
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.