Junk DNA can be vestigial. It had a purpose. It no longer does. If there's no selective pressure to get ride of it, it will remain, adrift. The belief that because it exists it must have a purpose could be a human bias
That they weren’t needed was another myth. They turned out to be helpful at stopping one of the main killers of early humanity: diarrhea. Still kills lots of people in the third world. Appendix helps prevent stomach problems, too. Quite a few people whose were removed figured that out on their own.
Biology is more complicated than maths/physics. Multiple extinction crises that shaped the world are still written into our genome and there can be very subtle adaptations at play.
People with certain patterns in their non-coding DNA are at much higher risk of ALS, a terrible disease [0] - it certainly looks that at least this part of DNA plays some role in our organisms.
I guess what I’m wondering how we can be sure that structure is function but non-coding structure has no function and exerts no selective pressure - isn’t the Golgi apparatus analogously “non-coding”?
I don't know about the spine, is it really? Because the whole system looks very optimized for running upright to me, pretty much a perfect running machine.