Pushing Phylocode

What if we decide to rename every living thing on Earth?

By Joshua FoerApr 28, 2005 12:00 AM


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Last summer on a warm Paris morning, a few dozen members of the International Society for Phylogenetic Nomenclature gathered at the National Museum of Natural History. The occasion was a talk by Jason Anderson, a professor of veterinary medicine at Western University of Health Sciences in Pomona, California. Anderson’s talk—the fifth of the day—was about Lepospondyli, an extinct group of small four-limbed creatures that may be the ancestors of modern amphibians. To the uninitiated, it would have seemed deeply pedantic: The title of the talk was “Phylogenetic Taxonomy of Lepospondyli: Top-Down Versus Bottom-Up Approaches to Nomenclature in Uncertain Topologies.” Yet Anderson’s real subject was a revolution that could shake the foundations of how we describe life on Earth.

The 60 taxonomists from 11 countries who came to Paris for the society’s inaugural meeting had a radical agenda: to overthrow the system of classifying species that has reigned for a quarter of a millennium and replace it with a new one called the PhyloCode. Proponents of the PhyloCode say the old system, originally developed by Swedish botanist Carolus Linnaeus before Darwin discovered natural selection, is so archaic that every taxonomic grouping needs to be redefined. It’s a plan as ambitious as it is controversial. Science is supposed to shed its old habits when better ways of doing things come along. But who decides when one way of doing things is better than another? And what happens when not everyone agrees? “Science the process is objective,” says Yale paleontologist Jacques Gauthier, one of the leaders of the PhyloCode movement. “But scientists are people, and they aren’t objective.”

At the conference l’esprit révolutionnaire was in the air, and it was infectious. A pair of French graduate students were greeting conferencegoers at the door, wearing T-shirts that read “Join the Rebellion!” and “PhyloCode, May the Force Be With Us!” During coffee breaks, scientists chatted about “winning over hearts and minds.” Depending on how you look at it, their efforts are either heroic or quixotic. A century from now, Gauthier says, “People will look at this as history being made—or they’ll have a big laugh at our expense.” Either way, this revolution will not be televised.

Kingdom, phylum, class, order, family, genus, species: Every organism belongs to a species, every species to a genus, and every genus to a family, right on up the chain. When Linnaeus developed this system in the middle of the 18th century, evolution was still an exotic hypothesis, and fossils were thought to be the remains of animals that hadn’t made it onto Noah’s ark. Linnaeus himself freely mixed biology and theology: He believed his classification scheme was a window into the divine order of the universe. “God created, Linnaeus arranged,” he noted.

Since Darwin, however, most scientists have agreed that life on Earth is linked in a giant evolutionary tree, with single-celled organisms at the root and modern species at the tips. Between that root and those tips lie millions of branching points, representing historical moments of evolutionary divergence. The Linnaean system predated this theory by a century, but it worked because its nested hierarchy was much like Darwin’s tree of life. Linnaeus cataloged the natural world by grouping things that looked alike; Darwin showed that things that look alike tend to be closely related. As evolutionary theory evolved, however, the system had to be jury-rigged. In the 1960s, the German entomologist Willi Hennig invented cladistics, a method of determining which branches go where on the tree of life. Since then, taxonomists have tried to group organisms according to common ancestry rather than mere similarity.

The PhyloCoders don’t think that they’ve done a very good job. Regrouping species according to cladistics has only complicated an already confusing and outdated system, they say. Better to start from scratch, with taxonomic groups defined solely by their position on the tree of life rather than by common traits. In Gauthier’s words: “The feathers don’t make the bird; the bird makes the feathers.” Under the traditional system, for example, mammals might be defined as warm-blooded animals with hair and mammary glands (in fact, there’s no single definition, and at least 10 have been used over the years). Under the PhyloCode, they might be defined as all creatures descended from the most recent common ancestor of Homo sapiens and the platypus. The new definition is the equivalent of pointing to the tips of two twigs on the tree of life, tracing the branches back to where they meet, and describing the taxonomic group as everything in between.

What about all those hierarchical ranks in the Linnaean system, like phylum and family? Because they are just artificial constructs that reflect nothing inherent in the natural world, they become unnecessary under the PhyloCode. Homo sapiens would still belong to a taxonomic group called Mammalia, but Mammalia would no longer be a class. Thus every taxonomic grouping would get a new definition and in some cases even a new name. Gauthier says, “Everything else has changed since Darwin, but not this.”

Gauthier grew up in central California, on the leeward side of the Sierras in what he calls cowboy country. He wears string ties and speaks with deep, elongated vowels, gesticulates like a traveling preacher, and has a fondness for phrases like “that’s the way the weenie wiggles.” Gauthier also happens to be one of the most important vertebrate paleontologists of the past 50 years. He was responsible for much of the landmark work that affirmed the theory that birds are living dinosaurs.

Gauthier’s coconspirator in the PhyloCode movement, Kevin de Queiroz, couldn’t be more dissimilar. De Queiroz is a curator of amphibians and reptiles at the Smithsonian’s National Museum of Natural History. He has the earnest, well-groomed look of a retired Air Force pilot, with a runner’s build, cropped hair, and a voice that makes far fewer trips across the tonal register than Gauthier’s. While Gauthier is happy to invent his own folk taxonomies—dividing Homo sapiens into those who treat garlic like a spice and those who treat it like a vegetable, for instance—de Queiroz tends to preface every answer with a pause for deliberation. One colleague calls them “the odd couple.”

They met in graduate school, first at San Diego State University, where they both received master’s degrees, and then in the Ph.D. program at the University of California at Berkeley in the early 1980s. They shared the same adviser there, Richard Estes, and wrote papers together on the phylogeny of lizards. As part of their work, they created a lizard family tree, but when they began to assign names to the important branching points on the tree, they realized there were more groups to name than there were ranks in the traditional system. “I started using these exotic ranks like parvorder, cohort, and microorder, and all that kind of crap,” Gauthier says. “Then we’d learn more about the tree, and all the names would have to change. I thought, ‘That sucks. All these ranks, they’re a problem.’ ”

Dan Winters

Order in the court

The traditional Linnaean system for classifying organisms and the upstart PhyloCode look very similar at first glance. Species are organized in a branching hierarchy, and their names bear more than a passing resemblance. But a closer look reveals some fundamental differences. In the Linnaean system, groups of organisms are nested within each other based on their physical similarity. The hierarchy is organized in neat rows so that every species belongs to a family, every family to an order, and so on. The PhyloCode does away with these strict rankings. Instead, it classifies species in a true family tree, with each organism connected to others by common ancestry. Biologists now know, for instance, that crocodiles and birds are descended from the same early reptiles. The PhyloCode reflects this by grouping Crocodilia and Aves on adjacent branches that lead back to the group Reptilia. Taxonomists have tried to reshuffle the Linnaean system in recent years to take common ancestry into account, but vestiges of the old thinking remain. For example, in the Linnaean scheme above (one of several configurations), Reptilia and Aves are both major classes of equal rank in the hierarchy.

Proponents of the PhyloCode have yet to settle on a convention for naming individual species. In the version above, proposed last year by Benoit Dayrat, a postdoctoral fellow at the California Academy of Sciences, species names would keep their original Linnaean epithet but would also include the name of the scientist who first described them and the year in which he or she did so. Humans, for instance, would no longer be Homo sapiens but rather sapiens Linnaeus 1758.

The Linnaean system requires a standardized ending for the names of all the taxa at a given rank (at least at the level of family and below). In the zoological code, family names must end with the four letters idae, for example, and subfamily names must end with inae. If taxonomists decide that a group once considered a family should instead be ranked as a subfamily, the group must, under the rules of the current system, get a new name. This frustrates the PhyloCoders to no end. “It’s still the same tree,” Gauthier says. “Nothing has changed, except how we spell the names. In a day when all this information is going onto the Internet, this is a bad idea. It’s a constant change of PIN numbers.” Some taxa have gone through a number of different names over the course of just a decade. Several years ago, for instance, it was decided that the great-ape family Pongidae couldn’t exist at the same rank as the human family Hominidae because humans are a subset of the great apes. To fix the problem, researchers proposed that humans and their great-ape relatives be combined into a single family, Hominidae, and members of the family Pongidae become the subfamily Ponginae. This can make literature searches a real pain, Gauthier says: “To a computer, there’s a world of difference between iguanidae and iguaninae.”

Beginning in 1983, Gauthier and de Queiroz worked every Friday—“from whenever Jacques woke up until midnight,” de Queiroz says—trying to figure out a better scheme. Finally, in 1992, they published a rabble-rousing paper in Annual Review of Ecology and Systematics. The paper condemned the Linnaean system as “a body of conventions based on a pre-Darwinian worldview” and broadly outlined an alternate phylogenetic system of taxonomy. “My idea was that we’d let the traditional codes take up these ideas,” de Queiroz says. “But a lot of us figured we’d be waiting for decades.” He was reluctant to draft a new code on his own, knowing it would be a legalistic and intensely pedantic exercise. But eventually Philip Cantino, a botanist at Ohio University and an early adopter of the PhyloCode, agreed to help.

In 1998 a group of 27 scientists from five countries gathered for a workshop at Harvard University to discuss the new system. Two years later, a draft version of the PhyloCode—a preamble, 21 articles, and two appendixes—was posted on the Internet. That’s when things started to get ugly.

In Paris last summer, in the back left corner of the auditorium where the conference was held, a bespectacled and goateed 31-year-old Kurt Pickett studiously took notes. Pickett is a postdoctoral fellow at the American Museum of Natural History. He’s also a counterrevolutionary. Two weeks after the conference, he delivered a caustic, unscripted critique of the PhyloCode to the Willi Hennig Society, a group of taxonomists passionately opposed to it. His talk was titled, “A Brief Report From a PhyloCode Mole.”

Opponents of the PhyloCode have dismissed its advocates as spinmeisters, arrogant usurpers, and practitioners of “Orwellian antilogic.” They’ve compared them to communists one minute and fascists the next. James Carpenter, an entomologist at the American Museum of Natural History and director of the laboratory where Pickett works, has spearheaded the opposition. One of his colleagues says that at age 49, Carpenter is “not afflicted by the need to be politic.” PhyloCoders prefer to call him a human pit bull. On a recent afternoon at the museum, he was wearing a flower-print shirt, with his white hair pulled back in a ponytail. “I ignored the PhyloCode stuff for the better part of a decade, just assuming that because it was so obviously silly it would disappear,” he said. “Years later I was persuaded, against my will, to take it seriously and do something about it.”

 Carpenter has written several papers condemning the PhyloCode. One critique appeared in a special issue of the journal The Botanical Review, with a cover illustration of Linnaeus flanked by the Swedish exhortation “Säg bara NEJ till fylokoden!” (Just say NO to the PhyloCode!) Nothing rankles him more than the PhyloCoders’ contention that the Linnaean system is nonevolutionary. “They want to present themselves as the new revolutionaries,” he says. “But that’s all just spin. The Linnaean hierarchy is—duh—a hierarchy. One hierarchy can be translated into another hierarchy. That’s all there is to it.” When the Linnaean names don’t map onto the evolutionary tree, they can be changed.

These changes may create some momentary confusion, Carpenter says, but it will be nothing compared with the chaos the PhyloCode will cause: “We’ve got 2 million or so taxa named under this 250-year-old Linnaean system, and they want us to go to something new. Their sophomoric philosophy misses the real point—that nomenclature is a communication system. There’s been no analysis by those sages of the real consequences of what they’re proposing.”

If the PhyloCode were adopted, biology textbooks would have to be rewritten, museum collections reorganized, legislation revised. The cost of rewriting the Endangered Species Act alone “could range in millions to billions of dollars,” according to one recent article in the journal Taxon.

Even the PhyloCode’s staunchest detractors admit there are problems with the current system. The zoological code alone is more than 170 pages long, and its rules and regulations can bog down the day-to-day work of taxonomy. Yet they believe the PhyloCoders are trying to tear down a house that at most needs a new paint job. “It’s what you might call an end run,” says botanist Kevin Nixon of Cornell University. “This would be very similar to a set of politicians who decided to bypass the Constitution to create a whole new set of laws.”

And they may well succeed: The PhyloCoders plan to start publishing papers using only their naming system. If they were just a bunch of hacks, no one would pay them much mind, but several are leaders in their fields. Carpenter calls their publishing plan “completely confused nonsense.” He compares it to an old joke about a communist bureaucracy: The leaders wanted drivers to switch from the left side of the road to the right, “but because this was a very complicated and delicate matter, they would begin on Monday with only party members switching sides, and everyone else would drive as before. Well, that’s exactly what’s going to happen.”

Carpenter assumed the editorship of Cladistics, the Willi Hennig Society’s house publication and one of the more influential journals in evolutionary biology, this past January. “As editor, I have every intention of outlining that our journal’s policy is to follow [the existing] codes,” he says. “You will do that or your paper will be rejected. It won’t even be considered.” Gauthier and de Queiroz call this censorship. “If they have to resort to that, they must feel threatened,” de Queiroz says. “Really bad ideas don’t have to have policies against them.” Gauthier is less circumspect: “They wouldn’t get away with that. It’s so unscientific. Hey, let it compete in the marketplace of ideas. If it sucks, people won’t use it.”

Scientific journals usually have rules requiring that authors adhere to the standard nomenclature, but few enforce them. As the PhyloCode gains publicity, however, more and more journals may return papers to scientists, demanding they follow the traditional system. One postdoc at the PhyloCode conference complained that he had shopped a paper around for more than a year before a journal agreed to publish it.

Gauthier says that Carpenter’s dire predictions of runaway costs are “scaremongering.” Costs, he adds, would be more than made up for by the benefit of no longer having to constantly rename taxa to accommodate new discoveries. He believes the PhyloCode’s improvements are so obvious that scientists will have no choice but to adopt it. “I can’t believe, once people realize the sky isn’t falling, that this won’t catch on,” Gauthier says.

Meanwhile, the movement does suffer from a recruiting problem: Most of its proponents are vertebrate paleontologists, a field particularly bedeviled by the old Linnaean system. Few, if any, study insects, fungi, or bacteria—groups that include far more than half of all described species—and getting those researchers on board will take a while. “It’s not going to happen in one generation,” says botanist Michael Donoghue, director of the Peabody Museum of Natural History at Yale University.

Like other PhyloCoders, Donoghue worries that jumping on an uncrowded bandwagon could hurt his career. He has had grant requests criticized, he thinks, because he supports the new system. “If a young person came to me and said, ‘Do you think I should really get into this?’ I’d have to say, ‘Maybe you’d better wait on that. Go publish some other stuff.’ ” Gauthier disagrees: “You’re a scientist. You’ve got to stand up and take the shots. Nothing ventured, nothing gained. This trail may ultimately prove a dead end, but that’s the name of the business.”

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