Taxonomy, of books and mathematical objects as well as of organisms, is a process taken up in media res . We inherit a starting point, one which is given us by history, biological and cultural. Classifications are not so much constructed as iteratively refined on the basis of ongoing and sometimes changing interests. It may be that all humans are constrained to classify zoological phenomena in a particular manner because of our scale and biological structure, but as the interests of the science develop to include, for example, viruses and slime molds, our notions of individuality and kind develop too in order to deal with problematic cases, and even the biologically-given categories of human visual recognition can be radically altered in this way. In this regard, we are heirs to the historical process of which Linnaeus's System of Nature was a crucial step, but our criteria of naturalness is radically different.
All classification rests on some inherited functional properties of the classifiers.
When some organism is encountered, in the wild or in the laboratory, that does not fall within existing classifications, there arises a classification problem, whether to extend the intension of the class which an existing name properly denotes, or whether to create a new name with a new intension. The problem is not whether to recreate an entirely new nomenclature for all existing taxonomic categories. Those are the initiating conditions of this act of further classification. Those categories have their proper functional denotations, given to the systematist by the state of play. Classifications themselves evolve over time, and there is no sharp distinction between scientific and pre-scientific classifications, as the history of the subject would lead us to expect there would not be.