Isolated populations "drift" genetically, which is how species form in the first place. Discriminating against people based on those differences sucks, sure, but it's still the ground truth.
Pretty sure there are genetic clustering algorithms which show that perceived race groups approximately correspond to measured race clusters. For example, random East Asians are more closely related to each other than to random West Europeans.
[0] https://bioanth.org/about/aaba-statement-on-race-racism/