Genetics

As pretty and modularized and extendable as my species taxonomy code was, it was all backwards.
I was wrong in assigning taxonomy willy nilly. Taxonomy is not given to an organism in nature. It should instead be deterministically interpreted based on the organisms' genetics.
Given a set of genetics, an organism should inherently be classified as a given species.
An organism's species is not assigned somewhere in a natural database, it is deduced, based on something else. Species, and the full taxonomy of an organism, is not given to it at birth. It is simply a way of grouping organisms based on a shared, but extremely varied, chemical setup - genetics.
There is no notion of different species in nature. To nature, all organisms are simply organisms with different genetics. Different chemical compositions.
Although no two organisms will ever have an identical chemical composition, groups of organisms have a similar composition. Similar enough for them to look alike, and behave alike. For them to be able to produce viable offspring. For them to even be attracted to each other to be able to attempt reproduction in the first place.