Binomial Nomenclature Is Failing Us

Binomial nomenclature, the genus-species system of naming all living things, is older than the United States and hasn't changed a whole lot since Carl Linneaus invented it back in the 1750s. And it’s no longer good enough to keep up with a field that's increasingly relying on DNA sequencing to make new discoveries, says one Virginia Tech researcher.

It’s not necessarily time to kick Linnaeus to the curb, though he could probably take the host of species named after famous people (the Frank Zappa bacteria!, the Bob Marley fish parasite!, the Obama lichen!) with him and we’d be no worse off. But the level of intraspecies diversity that can be observed through genetics has become so great that it’s time for something to complement it, according to Boris Vinatzer, a VT researcher who studies infectious diseases in plants.

“There is a lot of diversity within described species, and there’s simply no general system on how to name bacteria and viruses that belong to the same species,” Vinatzer said. “Different strains of the same species of microorganisms do very different things.”

That’s certainly true—take the flu, for instance. Within the species Influenzavirus A, you’ve got H1N1 (swine flu), H5N1 (bird flu), H1N2 (a pretty standard strain of flu that affects humans), and at least eight others. Those codes are considered “serotypes,” but there’s no guidelines for how to go about naming them. And even within those serotypes, there are differences. The H1N1 that caused the Spanish Flu in 1918 was certainly much different than the one that caused the 2009 swine flu outbreak.

Vinatzer proposes, in a paper published in PLOS One, to create “coded names” using full genome sequences. One strain of Bacillus anthracis (anthrax) would be known as lvlw0x, another would be known as lvlwlx, based on certain code sequences within the strain’s genome. Sure, those “names” or codes don’t exactly have a ring to them, but they would be useful to researchers who study pathology—strains that are closely related to each other would have similar (but not exact) codes, ones that are more distantly related would have codes that are much different.

“If I’m a researcher and need to identify the source of a food-borne salmonella outbreak, it’s very confusing right now,” he said. “But if I had the code, I know exactly how similar it is to other outbreaks.”

His convention, of course, requires the full genome sequencing of millions of species (and smaller groups within those species). That’s a huge task—one that the Smithsonian Museum of Natural History is already working on—but as new species are identified and as genome sequencing becomes much faster and much cheaper, it’s becoming a much more likely scenario.

And it’s not just viruses and bacteria that it’d be useful for: In plants, you’ve got different cultivars that remain in the same species but are still very different (consider all the different types of apples and peaches), in dogs and cats there are hundreds of breeds. Vinatzer says his naming system could even be useful for humans.

“You have lots of people who are interested in their ancestry. With this, you could tell how closely related you are to different populations around the world,” he said. “We think it’d be interesting if there were a company who analyzed your DNA and gave you a genome code. Then you could look  at someone else and say ‘Hey, we have similar ancestry.’”

I’m not so sure we want to necessarily open that can of worms—you can easily imagine discrimination against the “strain” of inherently disease-prone 0x8r2 humans or something—but Vinatzer does have a point when he suggests that the way we name and classify species has jumped leaps and bounds from how we did it back in the days of Linnaeus. Morphology, physical traits, and behavior are being used less and less to distinguish between species, and the latest papers describing new species are filled with examples of species that can only be told apart once you drill down into their genetics. There have also been many examples of species being reclassified once they’re named due to new genetic finds. Vinatzer’s system would, theoretically, be permanent. Once a species’ genome changed enough to give it a new code, it would simply become a new “strain” of that species.

“This code system is completely independent of phenotype. We don’t need descriptions of phenotypes, and within a few days—in a year or two it’ll be a few hours—you can automatically code something,” he said.

Getting fellow scientists to hop aboard and adopt the new naming system is going to be an uphill battle, one made much more difficult considering that Vinatzer is trying to patent the system, meaning he could theoretically charge for or restrict access to the technology necessary to generate a code.

“I think it’ll take a while, but taxonomists will see things that don’t make sense within a described species and decide what we have is not precise enough,” he said. “We think that scientists who work with bacterial genomes will start using it and that’s going to give us an immediate advantage in terms of studying disease.”