The tree or anything cannot be just atoms and empty space.
Everything is atoms and empty space + SOMETHING ELSE WE CANNOT FIND WORDS IN A HUMAN LANGUAGE.
This SOMETHING is the most important thing, and it ALWAYS drastically changes ALL your conclusions and interpretations.
So, actually we cannot make any conclusions per se. Or if it's just for having fun, then yes . But not for the sake of the truth or something like the truth.