Recently, I read this post by artist James Prosek on the failure of scientific names to capture the beauty and diversity he saw in his subjects, fish and birds. And while I generally agree with assessment that past authorities should not be taken at face value, I'm struck by the same sort of discontent at changing taxonomy as I read in Naming Nature. In both there is a tendency to dismiss biological nomenclature as unnecessary or not based in reality, an appeal to emotional response similar to the story Richard Feynman told about his artist friend. The name only adds to the beauty of the organism, because the name, really, all names in biology, act as a general reference system for information about organisms and their relationships.
A general reference system is the ultimate purpose of taxonomy as a science, as proposed by Willi Hennig in Biological Systematics (1966). And it has unfortunately been limited in advancement recently by many molecular studies that do not even attempt to put names on their hypothetical taxa. Often these are done for some particular purpose, to assist some particular investigation, but as Quentin D Wheeler points out, taxonomy is at its best when done for it's own sake, in investigation of the diversity of life as the distribution of that diversity (characters), and ultimating in a general reference system for all biology.
So what is a 'general reference system', and what makes a good one? David Allen of the famous (or infamous, depending on your inclination) Getting Things Done productivity method suggests building a reference filing system that is both simple and dynamic, so that any one piece of information could be filed in only a few places. Limiting the complexity means that files can be quickly and easily removed and rearranged as needed. Though more complicated than Allen's system, the International Codes of Nomenclature attempt a stable yet dynamic system for holding information about biodiversity by assigning unique identifiers (scientific names) and rules on how to apply them. But the complete, best reference system goes deeper than just assigning unique names; we don't, for example, organize our names alphabetically. For a higher reason, we put the names in a branching hierarchy of groups. The reason for this, of course, is evolution.
As Hennig explained, the general reference system should map the known lineages of life, and therefore hold information not only in the nodes (the names of species or higher taxa) but also in the pattern of the hierarchy. This fulfills Darwin's hope that 'descent with modification' would be integrated into all fields of study in natural history sciences, and that "[o]ur classifications will come to be, as far as they can be so made, genealogies" (Chapter 14, On the Origin of Species).
In the light of Evolution, the best general reference system will have three qualities: it will be descriptive, it will predict, and it will explain. It describes, through the pattern of the hierarchy, what we know so far of the phylogeny: which species are most closely related, which groups all share close common ancestors, which lineages have which characters, both molecular and morphological. It predicts the distribution of characters in organisms that are yet not fully know to us; since all mammals feed their young with milk secreting glands post-natally, we would hypothesize any newly discovered mammal would do the same. Likewise, we would hypothesize that any newly discovered insect would have 6 legs and three major body segments. Or that a new grasshopper would be plant feeding. We can predict that a new species of Wolffia is a flowering plant, despite the flowers being rare and nearly impossible to find. And finally, it explains the distribution of characters and diversity of life, and provides hypotheses towards explaining the routes of evolution of those characters. This is why monophyletic groupings are so important; whenever a paraphyletic or polyphyletic group is coined, the system looses predictive and explanatory power.
The general reference system is a tool, THE tool, the ULTIMATE tool of the biologist. It's the filing system that makes everything work. And the names that disturb the umwelt and bother molecular systematists are what keep track of all this information, all the information ever written about every group and relationship. Through the biological species concept we know the reality of species and through systematics we know the reality of their relationships. The general reference system of biological nomenclature ties these together and only adds to the beauty of every organism.