Taxonomies are hard

Responding to my earlier comments about science being easier at a distance, both Nude Cybot and Justin Mason have offered up substantial and useful comments on the subjects of biological taxonomies. (Justin’s have moved to email.)
“Classification in Biology, or phylogenetics, is fraught with issues that we typically do not face when creating our own systems of classification such as organization of content content on a website.” Is actually the exact opposite of my starting position as I learn about these. I thought that the ‘underlying realities’ of biology, that this descended from that, or in chemistry, there are this many electrons in a shell, lead to ‘natural taxnomies.’ Boy, was I ever wrong. (The periodic table can be read as a taxonomy, and the position of atoms in it predicts certain characteristics of those atoms. For example, the ‘noble gasses’ are off to the far right, and their electron shells are filled.)
It turns out that even with such natural divisions, there are many good ways to classify the kingdoms of nature. Ironically, Nudecybot points to Six Degrees: The Science of a Connected Age as a possible answer. Six degrees is, of course, a reference to a classic Milgram study that I wrote about a few days ago, saying that Milgram was better at the experiments than at the theories around them.
So, there’s no perfect taxonomy, only the question of is a taxonomy useful for the purpose at hand. And the purpose at hand needs a tighter definition than it has today.