It seems the issue we are grappling with here finds resolution either in natural selection or natural purpose (functionality). (Or is it maybe both? -- i.e., are they complementarities in Niels Bohr's sense?)
We know that historically, Darwin's theory has had no truck with "teleology," or the theory that nature (and the universe) is purposeful in any way, shape, or form. That is, directed in such a way as to achieve goals, or fulfill ends.
Since I believe that nature, the living universe, expresses purpose at all levels, it has long seemed to me that there is no such thing as "junk DNA," now called by the currently fashionable moniker, "pseudogene." It seems to me such terms are "cop-outs," placemarkers denoting something that we do not (yet) know of or understand.
But really, I'm just taking it all in, and plan to be silent, leaving the issue to you and allmendream....
I'm grateful to you both for the opportunity to be an attentive, interested bystander!
Science itself is unable to ascribe motive or purpose to the universe because it it immeasurable, like beauty or music. That isn’t to say it is not without value. I too ascribe purpose to this miraculous universe and unlimited admiration of the rules by which it is governed; but I know it is philosophical or theological not scientific.
The concept of “junk” DNA has been exactly that, a place-marker awaiting further study. It is often spoken with the scare quotes. There are a lot of non-gene elements that have obvious function in transcription control and DNA packaging, still others are obviously mutated copies of other genes ‘psuedogenes’ or a mutated copy of a viral genome ‘ERV’s’ or staggered repeats. In all cases functionality is clearly tied to increased conservation between related species, and non-functionality is tied to decreased conservation and change is at the neutral mutation rate.
Indeed there was a recent study that called into question the assumption that a particular repeat element (a different type of “junk” DNA) had no function, however they did not show any function for this repeat, they just indicated that it ‘stood out from the crowd’ in regards to conservation between species. Most pseudogenes and ERV’s and repeat elements will change at the neutral mutation rate, but these repeat elements showed some conservation indicating that they might have a function (showing the predictive power of the theory). If it turns out that they do show a function for this particular repeat element (and I eagerly await the finding that would once again confirm the predictive power of the theory of neutral mutation and common descent), it will not show that all repeat elements have a function, only indicate that the ones that show conservation is a good place to look.