Scientist proposes revolutionary naming system for all life on Earth

Feb 21, 2014
Boris Vinatzer has developed a naming convention based on genome sequencing to enhance the way organisms are classified. Credit: Virginia Tech

A Virginia Tech researcher has developed a new way to classify and name organisms based on their genome sequence and in doing so created a universal language that scientists can use to communicate with unprecedented specificity about all life on Earth.

In a paper published in the journal PLoS ONE, Boris Vinatzer proposes moving beyond the current biological naming system to one based on the genetic sequence of each individual organism. This creates a more robust, precise, and informative name for any organism, be it a bacterium, fungus, plant, or animal.

Vinatzer, an associate professor in the College of Agriculture and Life Science's Department of Plant Pathology, Physiology, and Weed Science, suggests a new model of classification that not only crystalizes the way we identify but also enhances and adds depth to the naming convention developed by the godfather of genus, Carl Linnaeus. Scientists worldwide have used the system that Linnaeus created for more than 200 years.

"Genome sequencing technology has progressed immensely in recent years and it now allows us to distinguish between any bacteria, plant, or animal at a very low cost," said Vinatzer, who is also with the Fralin Life Science Institute. "The limitation of the Linnaeus system is the absence of a method to name the sequenced organisms with precision."

Vinatzer does not propose changing the naming convention of existing biological classification. Instead, the new naming system is meant to add further information to classify organisms within named species and to more rapidly identify new ones since the process depends solely on the organism's genetic code.

A genome-based naming system could be particularly helpful to public health officials who live in an age of constant vigilance against biological threats. In his paper, Vinatzer used the anthrax strain that appeared in the wake of the Sept. 11 terrorist attacks as an example of the limitations of the current taxonomy-based system.

Weaponized anthrax frustrated officials as the powder found its way to offices in the United States and the ensuing investigation took months for law enforcement to identify the origin of the original pathogen as the Ames strain.

More than 1,200 strains of anthrax—or Bacillus anthracis—exist. Each one possesses an arbitrary name chosen by researchers that does nothing to illuminate genetic similarities.

With the naming scheme developed by Vinatzer, the name of every single anthrax strain would contain the information of how similar it is to other strains. Using Vinatzer's , the Ames strain used in the bioterrorist attack would, for example, be known as lvlw0x and the ancestor of this strain stored at the U.S. Army Medical Research Institute for Infectious Diseases would be known as lvlwlx.

Vinatzer's naming convention would also give researchers the ability to name new pathogens in a matter of days—not months or years—based on their similarities to known pathogens.

The proposed naming process begins by sampling and sequencing an organism's DNA. The sequence is then used to generate a code unique to that individual organism based on its similarity to all previously sequenced organisms.

The advantages to Vinatzer's method over the Linnaeus system are many.

Coded names could be permanent, as opposed to the shifting of names typical in the current biological classification system. Codes could also be assigned without the current lengthy process that is required by analyzing one organism's physical traits compared to another's. Lastly, the sequence could be assigned to viruses, bacteria, fungi, plants, and animals and would provide a standardized naming system for all life on Earth.

Vinatzer cites one plant pathogen—Ralstonia solanacearum—as an example of the roller coaster of rotating name changes that exists in the world of plant pathogens. The pathogen went through three costume changes of names and was originally called Bacillus solanacearum, which then became Pseudomonas solanacearum, and then Burkholderia solanacearum before finally resting on Ralstonia.

Vinatzer has previously used genome sequencing with great success. In 2009, he and a collaborator were able to trace a pathogen that was devastating kiwifruit crops around the world back to China.

Virginia Tech is submitting a patent describing the naming scheme. Vinatzer and his collaborator Lenwood Heath, a professor in the Department of Computer Science in the College of Engineering founded This Genomic Life Inc., which will license the invention to develop it further.

Heath oversaw the development of the bioinformatic pipeline to implement the system. He was interested in collaborating with Vinatzer because of the potential to empower scientists to communicate accurately with one another about biological systems.

"I work in computation, so having the opportunity to impart my knowledge by ordering the organic world through numbered sequences of DNA was fascinating," Heath said. "The mathematical world and the living world are a lot more closely related than we think."

Explore further: Reinventing the high court of organism names

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User comments : 21

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AntonKole
5 / 5 (3) Feb 21, 2014
"Virginia Tech is submitting a patent describing the naming scheme.....which will license the invention to develop it further."

So will scientists then need to pay a fee, in order to name an organism?!
What about needing to pay a fee, just to mention a newly named organism in a Paper..... mmmmm??
I don't believe there's a Patent on the currently used Linnaeus naming system.
Not so sure about this one.
TegiriNenashi
1 / 5 (5) Feb 21, 2014
This seems like almost trivial problem. With phylogenetics method, given a genetic sequence of a specie, its location in the tree of life is well defined. Now, a specie name is nothing more than a path navigating the tree from the root to a leaf. Something like
left,left,right,left,right,left,...
Is there more to it?
Returners
2 / 5 (4) Feb 21, 2014
This is essentially a patent on the base 4 numbering system, which is completely ridiculous.

It should be rejected, and if not, somebody should file a lawsuit against the patent office until it is rejected.
Mimath224
2 / 5 (4) Feb 21, 2014
@Returners, ridiculous? I'd say it a bit stronger than that. What about all those researchers that spend a lfetime finding a new species and manage to get just one named after them. The present system reflects a species name as they are seen with the naked eye and that means everyone can study it. This article is just another way to deny us info without paying for it...'rights' people should follow this one.
Skepticus
3 / 5 (2) Feb 22, 2014
I guess it wouldn't wash with people who egos are pumped up by the prospects of their names of which will be eternally enshrined and in association with a particular nasty virus, bug or obnoxious weed..!
Howhot
1 / 5 (2) Feb 22, 2014
Lets all hope that the patent is denied for being arbitrary.
manifespo
not rated yet Feb 22, 2014
This could be useful when we have handheld devices that are able to instantly identify species in the field through tiny DNA samples (hair, leaf, biofilm, fasces, et cetera).
Mimath224
3 / 5 (2) Feb 22, 2014
@Skepticus, Not a matter of egos...on that basis all recognition is 'ego based', qualifications, Knighthood, Nobel Prize etc. I look upon it as a small appreciation for all those things that can't be paid for.
axemaster
5 / 5 (1) Feb 22, 2014
Yeah I've been working on patenting some stuff, and in all my reading I've never encountered the notion of patenting a naming method. Given that it's not a product, or part of a product, I'm not sure what the point would even be. Could you actually make money off such a thing?

Not to mention it's obviously unethical.
Lex Talonis
1 / 5 (1) Feb 22, 2014
Is it unethical?

Provided that it's reasonable and not greedy - because it will take a considerable amount of resources to implement probably the best system ever.

My own concern is that in order to survive over the centuries - is that it needs a paper and pencil fall back system - and a way to reinterpret DNA when the tech age ends.
Grallen
not rated yet Feb 22, 2014
The patent is probably more to retain control than to monetize. Also to prevent it from being cherry picked by patent trolls.

Until the patent system is removed and replaced by a new and better system(One that may not yet be conceived of), everything you do will need a paper shield that costs a fortune, just to avoid getting sued for existing.
alfie_null
not rated yet Feb 22, 2014
Since you can't patent algorithms (wink, wink. nudge, nudge!), they are probably trying to patent a "system" such that those employing similar "systems" should take care (or get a license that addresses indemnity, just to be safe).

Hey, the duration's only for the next 20 years or so, anyways.

TheGhostofOtto1923
1 / 5 (2) Feb 22, 2014
Will this system still work when we see the advent of things like this?
http://www.slashf...-galaxy/
Protoplasmix
not rated yet Feb 22, 2014
So if I call it water there's no fee, but if I call it hydrogen hydroxide it's gonna cost me? The idea actually sounds like something obvious to anyone skilled in the art. Considering the security aspects mentioned (i.e., anthrax, other natural pathogenic threats), the world's governments are obliged to implement a global standard forthwith, if not sooner.
Noodle_Naut
not rated yet Feb 22, 2014
Patent? Fee? Horrible! A sure way to become a forgotten scientist. Someone else will develop a similar but sufficiently different method and give it to the world. They will become famous, while Boris Vinatzer, no doubt a brilliant scientist, stands a good chance of being forgotten.

I suppose this is a rather negative prediction...there are other possibilities. If the money is used to sequence 100,000's of organisms and the fee is sufficiently small...maybe all will be fine. Scientists would have to receive back something, to be sufficiently worth it over a rival free encoding system like access to a large genome database, photos of organisms in various life stages...
Mimath224
3 / 5 (2) Feb 22, 2014
Maybe Boris Vinatzer is thinking of possible microbes etc on Mars (and elsewhere) eh? Gosh that might bring in a few $ eh?
Z99
1 / 5 (1) Feb 23, 2014
"species" is a construct, a function of time and a maybe a statistical population. It will be interesting to see how this "system" handles mutations, variable length genes, not to mention non-coding sequences. How many individuals need be profiled in order to establish a particular "name"? Obviously, there won't be 100% sampling of any but the most specialized (lab) populations. Amer.Chem.Soc. used a first in, first out, numbering system for new chemicals (CAS RN) since at a certain level of complexity "similarity" is meaningless, as are (except in the very simplest compounds) "classes". I doubt if biological organisms are capable of having an internally consistent, meaningful, nomenclature....The meme, "species", is well past the date we should have relegated it to paleontology.
I just can't see how a "linear" (word-like) code can possibly work. DNA often isn't linear...isn't well ordered: XY comes before XX, right? Too much sex for this to work (gene swapping).
dtxx
not rated yet Feb 23, 2014
I think no one here has done actual work in mycology. I disocovered a new species, but a) thats as common in mycology as sneezing and b) the recognized mycologist I was working with got the credit. That's fine. Only finding a new genus will net you any recognition, or anything I would find worth making a dispute.
jimbo92107
not rated yet Feb 23, 2014
"A genome-based naming system..."

How about "genom." Gets the gen and the nom in one word, nice and short. Could even abbeviate it to GN: [stuff]. One good thing about Boris Vinatzer's innovation is that it can also be an appended to the traditional goofy name, so you please the geezers and also include info that's handy for genetics.

As for Boris Vinatzer patenting his idea, why not? He's just created an industry. Let the guy cash in for awhile, it's his retirement nest egg.
tadchem
not rated yet Feb 28, 2014
Sounds to me like a plan to bar-code everything alive. ;)
FastEddy
1 / 5 (1) Mar 05, 2014
"All science is either physics or stamp collecting." - Ernest Rutherford - "the "father" of nuclear physics"

He also said: "An alleged scientific discovery has no merit unless it can be explained to a barmaid."

Oh, well. Back to the origin: swahili.