And the related problems of Elvish aging. Certain characters have to be born in certain places and married in certain places, and if the Elvish aging rate is inappropriate for that then things fall apart.
There's a lot of ink spent answering this problem.
Middle earth is confirmed to have atoms and isotopes.
The Valar told the elves about them, but didn't explain what they are for, so elvish nuclear engineering is canon-compatible, but not implied by canon.
Middle Earth does not have a single tree of common descent, but multiple acts of special creation, each of which then speciates further.
Souls are directly created by Eru for all sentient races (elves, men, dwarves, ents) and sent directly from outside creation.