“ we wouldn't have appendices that need removal”

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.

Could, but it also could be an indicator of "we don't really understand biology yet".

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.

[0] https://pubmed.ncbi.nlm.nih.gov/38802183/

Any reading on the topic you could point me to? Whenever I head about vestigial DNA, I’m reminded of the preserved wetlands which forced the roads to arc the long way around it. And in so doing, structurally affected traffic despite no cars ever going inside its bounds.

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”?

It's just that very often when we judge like that, it later turns out we might have been mistaken. The appendix is a perfect example.

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.