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What’s in a Name?
The system biologists use to classify the natural world was developed in Sweden in 1735 by a scientist known as Linnaeus. But now two Yale researchers think they’ve found a better way to catalog creation.
by Bruce Fellman
April 2000
If Noah were to return any time soon to reprise his Biblical mission, he would, at the very least, need a bigger boat. “We’re in a golden age of biological discovery, and the rate at which we’re finding new species is extraordinary,” says Michael J. Donoghue, a botanist and biodiversity expert who is joining Yale’s fledgling ecology and evolutionary biology department as its first G. Evelyn Hutchinson Professor. “Scientists have described more than a million and a half species, and there are an estimated five to ten million species out there waiting to be found.”
Making sense of such diversity, from bacteria to birds, mushrooms to mammals, represents a monumental challenge to biologists. It is also likely to cause monumental headaches, for not only must each newly discovered organism be given a proper Latin name, every one of them has to be classified: assigned its place on the tree of life.
And therein lies a problem.
In the middle of the 18th century, the Swedish botanist and explorer Carl von Linne—Linnaeus, as he is known today—invented the basics of a classification method that bears his name and, in essence, remains in use. Linnaeus based his method of cataloguing creation on a hierarchy of ranks, and its key feature was a shorthand way of describing each species. Before he published Systema Naturae in 1735, a discreet kind of plant or animal would be known by an unwieldy string of Latin words; under the Linnaean system, the name of a species could be reduced to a binomial like Musca domestica (the housefly) or Acer saccharum (the sugar maple).
But though this classification method, the backbone of modern biology, has worked well enough in the past, it is in danger of collapsing under the weight of recent scientific advances, says Donoghue. “The Linnaean system is simply not up to the task of handling the sheer amount of information we’re amassing about diver- sity,” he explains. “We think there’s a better way to classify the natural world.”
At scientific meetings and over the Internet, Donoghue and an increasing number of rebel biologists are voicing their support for a heresy put forth in a series of research papers written in the 1990s by Yale’s Jacques Gauthier, a paleontologist and professor of geology and geophysics, and Kevin de Queiroz, a vertebrate biologist at the Smithsonian’s National Museum of Natural History. As graduate students in California in the 1980s, the researchers had been collaborating on a study of the evolution of lizards, but the more they tried to tailor their findings about relationships to a Linnaean hierarchy, the more they felt stymied. The ranks kept getting in their way, recalls Gauthier, and, in frustration, the scientists simply stopped using them.
“The sky didn’t fall,” says Gauthier.
The researchers were able to figure out an adequate alternative method of describing their discoveries, and as they pondered their success and its implications on taxonomy—the science of classifying the natural world—they came to a bold conclusion. It was not enough to tinker around the edges. “It’s time to abandon the Linnaean system,” says Gauthier. “We need a thorough housecleaning.”
Gautier believes that while there are a number of practical reasons to move away from this classification strategy, the main argument against it is philosophical. The Linnaean system was born more than a century before Charles Darwin published The Origin of Species, and it doesn’t reflect the evolutionary viewpoint that lies at the heart of biological thinking. Says Gauthier: “We’re attempting to complete the Darwinian revolution.”
To be sure, a way of doing business that has survived 250-plus years has tremendous staying power, and museums have not started to rearrange their shelves of specimens. But professional taxonomists are certainly taking note of a set of rules and regulations known as the PhyloCode.
“This is a pretty profound new idea, and I’m looking forward to testing it,” says Peter C. Hoch, secretary general of the International Botanical Congress. For more than a century, Hoch’s organization has met every six years to update the procedures which, by general agreement, govern the way plants are named and classified. (There are also regular international nomenclature gatherings to fine-tune regulations for animal and bacterial taxonomy.) “We’ve had a radical change in our understanding about relationships between organisms, and some people feel we need a nomenclatural system that reflects this new knowledge.”
The traditional method that the phylocoders propose abandoning has been to fit every newly discovered organism into a hierarchy composed of distinct ranks. Linnaeus, building on a view of nature developed some 2,000 years ago by Aristotle, grouped organisms into a five-rank system. The broadest category was the Kingdom: There was one kingdom reserved for plants and another for animals. (Depending on which authority you consult, there are currently either four or five kingdoms.) Both kingdoms could be divided into a number of classes, each of whose occupants shared certain common traits—for example, a backbone in the case of the Class Vertebrata, and certain flower characteristics in the plant classes. Again, based on shared traits, the classes could be further subdivided into orders, the orders into genera, and the genera into species.
Over the years, taxonomists have expanded the Linnaean hierarchy, and they currently recognize seven basic ranks—kingdom, phylum (botanists substitute the term “division” for this category), class, order, family, genus, and species. To accommodate new knowledge and theories, scientists have, at times, split each of these groups into further categories such as the subspecies or lumped them into entities such as the superclass, but this additional cubbyholing aside, a taxonomist would look at a human being and say that basically we belong to the kingdom Animalia, the phylum Chordata, the class Mammalia, the order Primates, the family Hominidae, the genus Homo, and the species Homo sapiens.
So it goes with every organism, and at first glance, the methodology appears to be neat, clean, and quite capable of cataloguing creation. “It’s a very simple and efficient filing system,” says Raymond J. Pupedis, who manages the vast insect collections of the Peabody Museum of Natural History.
But Gauthier, Donoghue, and their colleagues are asserting that such order, however impressive, is, to borrow a line from Macbeth, “sound and fury, signifying nothing.” Gauthier explains that all these hierarchical ranks might have been useful in the past, but not now. “They’re not real because they don’t reflect the evolutionary process,” he notes. “This means that the taxonomy we’re using actually gets in our way when we try to answer one of our most basic biological questions: How are groups of organisms actually related to one another?”
The solution that these scientists have proposed is a system called phylogenetic taxonomy. This classification method groups creatures together based on common ancestry and descent rather than on similarity, which is the hallmark of the traditional way of doing business. Under the terms of the PhyloCode, the Linnean ranks simply disappear. Gone would be the angst of schoolchildren (and many scientists) who have had to commit “kingdom, phylum, class, order, family, genus, and species” to memory, and then relearn everything when a creature’s place in the Linnaean universe changed in the face of new discoveries. Also gone would be the philosophical baggage inherent in ranks and hierarchies.
“Naming things is the oldest form of science and one of the first human activities, and in looking for similarities in plants and animals, Linnaeus sought to discover God’s plan,” Gauthier explains. “But the categorical ranks he used were more than just the formalization of the folk taxonomy of western Europe. The hierarchies were an expression of where you stood on the ladder of creation, with slime molds on the bottom and white European males on top.”
The new system would replace this pyramid notion with an updated version of an ancient metaphor: the “tree of life.” A tree is essentially a collection of diverging pathways. There is a main trunk that splits off into major limbs, each of which divides into branches. These may subdivide again and again into increasingly smaller branches and finally, into twigs.
The basic currency of the PhyloCode is each branching point and all the branches that diverge from it. The phylocoders call this fundamental unit a “clade,” and it consists of a group’s common ancestor and all the species that descend from it. Just like the branching pattern of a tree, says Gauthier, there can be “clades within clades within clades.”
Cladistics, as this method of organizing creation is known, was developed in the 1960s by Willi Hennig, a German biologist who attempted to classify insects on the basis of common ancestry, rather than on how similar they were to one another. Generally these two notions track well together, and plants and animals that look like each other are indeed closely related. But over the past couple of decades, as biologists started to use increasingly high-tech methods (one of which, molecular taxonomy, was developed at Yale) to examine organisms, it’s become clear that, according to Gauthier, “similarity is not always an adequate proxy for relatedness.”
Taxonomists have long been aware of a phenomenon known as convergent evolution, in which creatures separated by time, geography, and lineage may, if they have the same kind of lifestyle, come to resemble one another. A classic example is the outward similarity that has evolved between the “wolves” of Australia, which are marsupials and carry their young in pouches, and their North American counterparts, whose young are matured through a placenta.
Scientists, by examining the entire animal, would not be tricked into classifying both as close relatives (their evolutionary paths diverged more than 65 million years ago), and as researchers turn increasingly to molecular biology and genetics to help determine who’s related to whom, they’re less and less likely to be deceived by outside appearances. Donoghue, for example, recently published in Science research that used both molecules and morphology to suggest a new way to envision how plants are related to one another. But while he’s confident of his research conclusions, Donoghue has little hope that his view of plant lineages will make it into the textbooks any time soon.
“We’re failing to reflect all the discoveries we’re making on a daily basis because of the burden of the current nomenclatural system,” Donoghue asserts. “It’s just too cumbersome.”
The problem is what the scientist terms the “downstream consequences” of rewriting relationships: Under the rules imposed by the Linnaean system, reassigning an individual species to a new group requires that it be renamed. Changing the groups around means even more name changes, and when it comes to major revisions, such as the one Donoghue is suggesting for plants, the impact could be so great that few scientists would push for accepting a classification scheme that might involve providing and learning new names for more than 100,000 species.
“The beauty of the PhyloCode is that there’s no fear of downstream consequences,” says Donoghue. “Even if research shows that you belong in a different clade, our system doesn’t necessarily require that you change your name.”
According to the tenets of the PhyloCode, those two-part Latin names would lose their special significance and become simply a convenient means of identification. But they would not, as some critics have feared, disappear. “We could just as easily call a plant or animal ‘Bob’ or ‘1234567,’ but people are used to the Latin names, so at least for now, we’re going to keep them,” says Donoghue.
When it makes its formal debut on the Internet this spring, the PhyloCode will address one central theme: how to throw out the Linnaean ranks and replace them with properly named clades. The phylocoders couldn’t agree on the ultimate fate of the Linnaean terms, so they opted to leave them untouched.
There are, however, several possibilities under consideration. One idea is to hyphenate the two-part names, and so our species, Homo sapiens, would become homo-sapiens. Another solution, and one that has special appeal in the dot-com era, is to write the name as homo.sapiens. A third proposal is to use the species designation followed by a unique registration number, and so we would forever be known as, say, sapiens7523.
This last strategy, which would require a name change, is probably the least likely to be adopted in its entirety. Sapiens7523 doesn’t, after all, lend itself too well to conversation, but Donoghue expects that some kind of registration number will be required. “This is the way the world’s going, with so many research papers online that are part of searchable data bases,” he says. “I envision this ultimate database we’ll be able to tap to find any and all information about a species or a clade. To access it, you'd need a number.”
In any event, a hyphenated, “dot-com,” or numerical designation would fulfill the uniqueness criterion established by Linnaeus, and the names would never need to change, even if they were at some time assigned to a new clade. This would take, admits Donoghue, a lot of getting used to. “We’re asking people to change their way of thinking,” he says.
Kathleen A. Kron, a researcher at Wake Forest University who studies the relationships among plants such as blueberries and rhododendrons, has taken Donoghue up on his challenge. “I was skeptical until I tried it on my own, but I’ve found that the PhyloCode has the flexibility a researcher needs to quickly incorporate new information about the tree of life,” says Kron. “It’s important to distinguish between traditions that are helpful and those, like the current nomenclature system, that are inhibitory.”
For the foreseeable future, the phylocoders expect both systems to coexist, perhaps peacefully, perhaps not, as biologists compare the two methods and assess advantages and disadvantages. And Yale, with two of the most prominent phylocoders on its faculty, will be at the center of what promises to be a taxonomic storm.
Eventually, Gauthier and his colleagues figure that the reward of what they believe will be a simpler, more stable, and more nimble classification system will be worth the turmoil inherent in abandoning so much taxonomic tradition. “We set out to evolutionize the Linnaean system, to reinvigorate the old-time religion,” says Gauthier. “We’re going to let this system evolve. We’re not done, this is a work in progress.”  |
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