Taxonomy twitches

There has been a very interesting thread on the Taxacom list recently. Entitled "Do rogue taxonomists need rogue publishers?," it is an attempt to address what is seen as poor, or even malicious, taxonomy. The initial complaint was that one of these rogue taxonomists has published an inappropriate description in an inappropriate forum. A lengthy discussion ensued.

Everyone agreed that providing names for organisms is inherently very important. Most believe the Codes (the ICZN, here) can, or at least are intended to, provide "standards, sense and stability for animal names in science." Some propose that taxon names should only be validly published by some predefined "whitelist." Others propose that we should just all get along, and described some heroic transcontinental fish-naming event of grand proportion. Some think anyone should be able to publish anything, and if it fits with variously selected parts of The Code (there were no guidelines for selecting one's own subset of the Code to follow), the rest of us are just stuck with it. Others think it's up to the rest of us to ignore "bad" names, or to publish revisions. Someone tries to divert attention to Apple's latest press conference. Someone suggests a complicated computerized registration process, followed by electronic censorship. All studiously ignore the 800-pound gorilla lurking in the center of the room.

Let's briefly pretend that we're scientists of another discipline - chemists, perhaps. Say you've set some mist nets in your back yard (I confess to not being a chemist, but I assume this is how new chemicals are collected), and something you don't recognize has shown up. You collect it, do some tests, describe it's chemical properties, and a species is named. This name is self-evident; another chemist might have acquired a member of the same species anywhere on the planet any time in history and, upon comparison, you would both instantly and unambiguously recognize that you're talking about the same species. The compound's own makeup would have dictated what you both call it, universally and regardless of local names or minor variations. There exists a taxonomy based upon the physical properties of the compound that allows this to happen. Nifty, eh?

That, boys and girls, is science. A chemist might not know what "chumvi" or "salt" is, but you can bet they'll know NaCl. Salt is always and unambiguously salt - no chemist will ever try to convince you that it's properly a subspecies of table sugar, or that kosher salt deserves a promotion while table salt and sea salt are indistinguishable. Any such claims would be testable, and all competent testers would reach the same conclusions. That isn't to say that EVERYONE would reach the same conclusions. Speakers of Swahili will continue to ask you to pass the chumvi, and cooks will continue to promote their favorite brand of sea salt. Individual variation is expected, and people who can appreciate it have ways to deal with it. However, all of these people, with proper training, are capable of recognizing and naming the basic substance as NaCl, regardless of contaminants or structural variants.

At least one effort has attempted to bring this level of quantification to biology, and was met with considerable scorn and resistance. The arguments are endless (and mostly self-centered) as to why this is a fatal mistake, but I now firmly believe it to be the only plausible future for taxonomy, should that discipline wish to provide something truly useful to managers and conservationists. The locals will always talk about "deer mice," and biologists may continue to talk about variations within individuals, populations, and species, but if we are to elevate naming to the level of science we must find testable ways to pigeonhole individuals. The most obvious involve genetic sequencing, which may determined from any individual and compared to a standard. There are problems to overcome, and the final solution may not be simple, but I do not believe simplicity is a consideration. Perhaps several dependent genetic tests are required - Test 1 tells you this is an animal and dictates Test 2a, which tells you this is a mammal and dictates Test 3m, which tells you this is a deer mouse. I am not suggesting any particular test or set of tests, nor am I advocating any categorical breaks in applying the results. I am merely advocating a quantifiable method by which we can measure similarity and differences between individuals.

Applying these measurements to wild populations, specimens in museums, or collected individuals is another matter entirely. However that happens, it should have a quantifiable basis. Saying "I consider this is a member of that population because the X sequence varies by less than y%" is a very different matter than saying "I consider this is a member of that population because I've arbitrarily chosen to accept one long-dead author's opinion over another" or "some Code requires me to use this arbitrary string, even though nobody else knows what I'm talking about," or "this thing just looks like it's a member of the arbitrary group that I consider, for deeply personal reasons, to be that species."

What shall it be, taxonomists? Continuation of an obviously flawed system (which happens to pay your salary whilst keeping you firmly in your comfort zone), or a serious discussion about progressing the art of naming organisms to a quantitative science?