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Naming All Lifeforms On Earth With Hash Functions

Posted by timothy on from the sort-of-a-nickname dept.

First time accepted submitter ssasa writes "A Virginia Tech researcher is proposing a new naming system for all life on earth [based on each organism's] genetic fingerprint — basically something like a hash function of an organism. Hash functions are in common use in software development. Hopefully it will pass some time before we see a hash collision between a cat and some dinosaur."

6 of 97 comments (clear)

  1. The actual journal article by Anonymous Coward · · Score: 4, Informative

    For those that want to read the actual journal article
    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089142

    The word hash is never mentioned either :)

    1. Re:The actual journal article by Frosty+Piss · · Score: 3, Informative

      An important limitation of his approach is that it only works for...

      Those who pay the licence (since it's being patented)?

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      If you want news from today, you have to come back tomorrow.
    2. Re:The actual journal article by Anonymous Coward · · Score: 2, Informative

      (same author)

      I just read the article (I know, I should have read it before posting anything earlier instead of relying on the often misleading Slashdot summary) and while I don't really understand what he's doing it does seem to make more sense than what the Slashdot summary shows.

      and, no, my original idea does not seem to be what the article proposes (my original idea is an obvious improvement over what the misleading Slashdot summary proposes but next time I should read the article before posting).

      I agree that the current way organisms are named and classified can be inconsistent and confusing. A lot of time the usefulness is based on whether a particular bacteria produce a specific enzyme (enzymatic tests can be done to determine this and then substances that inhibit an enzyme can be used to stifle the bacteria). but what I found interesting about the article is that

      "

      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 genome sequence, 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 article is kinda vague and I would like to see more detail on exactly how it works but it does seem like it has potential.

  2. No success by Sven-Erik · · Score: 4, Informative

    Not so sure this will take off since they have applied for a patent and wants users to pay a license fee to use it.

    --
    - "Every demand is a prison, and wisdom is only free when it asks nothing." Sir Betrand Russell
  3. The most obvious problem with this approach by Anonymous Coward · · Score: 4, Informative

    This kind of thinking has a tremendous problem with it. Presently, organisms take the name of a previously described species if and only if it is a member of the same species as a particular type specimen from which the species is described. This holotype serves as the reference specimen for each species. This system has worked extraordinarily well for more than 200 years and has promoted nomenclatural stability.

    The biggest problem with attempting to identify species on the basis of their genetic "fingerprint" or bar code is that unless you have some other means to establish that the specimen from which the genetic material is in fact from the same species as the holotype, then the genetic fingerprint will simply misidentify the specimen. This is a major problem for much of the genetic data in GENBANK, for which, more often than not, there is no longer a means of associating the source of the genetic material with a specimen, whose identity can be established independently). because the original specimens are seldom vouchered or saved. Consequently, the actually identity of the species that has been sequenced, remains uncertain, even if alignments of the code are "perfect". As for the patent, the rules of Zoological Nomenclature forbid the commercialization of names used in science. These guys can make up their own naming scheme, but scientists, who must rely on having their work, at least in principle repeatable and refutable, will be unable to use it for the purposes of science.

  4. Not sure how similar this is to hashing by fozzy1015 · · Score: 3, Informative

    I first thought the genetic sequence of an organism would be the input to a hash function, but reading further that doesn't seem to be the case.

    "Using Vinatzer's genome sequence, 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."

    The output name would still show ancestry using identical values, when one of the key properties of a hash function is that small changes in the input result in a completely changed output.