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Earth Science

Naming All Lifeforms On Earth With Hash Functions 97

Posted by timothy 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."
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Naming All Lifeforms On Earth With Hash Functions More

Naming All Lifeforms On Earth With Hash Functions

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  • The actual journal article (Score:4, Informative)

    by Anonymous Coward on Saturday February 22, 2014 @06:46PM (#46313365)

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

    The word hash is never mentioned either :)

    • Re: (Score:3)

      by Fwipp ( 1473271 )

      An important limitation of his approach is that it only works for "all organisms whose genomes can be aligned to each other." (With no mention of how "good" the alignment has to be, nor the fact that alignment is not objective.)

      So, you'd have multiple schemas for each "group" of organisms. I think his idea is possibly applicable to, say, describing multiple samples within a species. It's clearly ill-suited for a universal naming strategy like the article proposes, though.

      • Re: (Score:2, Insightful)

        by Anonymous Coward

        So are every two people who aren't twins going to have a completely different hash function?

        Perhaps a better scheme would be to assign a function that describes the genetic similarity between two organisms. Well, we kinda already have that. We can use percentage. and if all organisms are 90 percent similar and only vary by ten percent, for instance, we can narrow our function to those ten percent. Create a new scale from 1 to 100 where the genetically most similar organisms would be grouped next to each oth

        • Re: (Score:2)

          by Fwipp ( 1473271 )

          Your method is actually pretty close to what the paper describes. The idea is that '00060000000D' and '00070000000F' are closely related, but '38439FDCA' and '921938312C' are not.

          • Re: (Score:2, Insightful)

            by Anonymous Coward

            and the idea is nothing new except he is adding more digits and making it more confusing for us by removing the intuitive base ten that has been the scientific standard since the metric system and replacing it with something worse (kinda like how the 'standard' system is worse than the metric system).

            • Re: (Score:2, Informative)

              by Anonymous Coward

              (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

      • (With no mention of how "good" the alignment has to be...

        Chaotic good suffices.

        • To the truly chaotic a good alignment is impossible.

          • To the truly chaotic a good alignment is impossible.

            Depends. The standard alignment grid uses cartesian coordinates. It's "natural" shape is a square where law-chaos and good-evil axis are separate, and ordinal alignments have a greater magnitude of difference from neutrality. On the other hand, the Great Wheel uses a polar alignment system where the type and magnitude of alignment form the axis, thus chaotic good is both less good than neutral good and less chaotic than chaotic neutral of same magnitude.

      • Re: (Score:3, Informative)

        by Frosty Piss ( 770223 ) *

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

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

      • Re: (Score:1)

        by Anonymous Coward

        Yep! Sorry, I haven't read the article ... but I do know that there's really no such thing as a strain, meaning, a collection of genetically identical organisms. (Note: yeah, I know a virus may not fit strict definitions of "organism;" I'm using the term loosely.)

        Viruses mutate continually -- which is why a "strain" is actually a collection of "closely related" organisms, that vary within some limit of permitted (by the classifier) of point mutations.

        • Re: (Score:2)

          by pepty ( 1976012 )
          But a strain isn't a collection of genetically identical organisms; the closest you would get to that would be clones. A strain refers to a group with a similar genotype or phenotype.

    • I'd totally hash that!

    • Hash would be a horrible way to do it (and I doubt it's what's proposed).

      A single bit error in reading the DNA would lead to a completely indistinguishable, unrelated hash value.

      Even if we could sample DNA and get a 100% accurate reading of its content, which we can't, DNA sampled from your left hand would come up with a different value from DNA sampled from your right hand - just due to insignificant genetic drift, tiny transcription errors, etc.

  • Names are for communication (Score:5, Funny)

    by Chemisor ( 97276 ) on Saturday February 22, 2014 @06:49PM (#46313381)

    I think I'll go hunt some af7caaf1e73a2d24924371a370b4ef9b so I can feed my 362842c5bb3847ec3fbdecb7a84a8692 and a nice quiet evening with my 34b46c8cf192431e84ea81109660367b, chatting about the difficulty of talking about a474fb23f886eeaa16223eba872e53b1 that some socially inept scientist decided to name with a hash function.

    • Names are indeed for communication, but 'name' here is mostly bad terminology, or at least The Fine Article leads me to believe these are meant more as serial numbers to supplement the existing system of nomenclature than anything else.

      Which is actually somewhat useful. Any research project starts by looking at what other research has already been done. It's no good if your search terms don't bring up the relevant papers. I suppose this might be somewhat like the nomenclature system for chemistry, in whi

      • I don't think they're like serial numbers. A serial number should be just that - assigned serially to whatever is produced/discovered next. These will have meaning embedded in them.

        I generally don't like identifiers with meaning. Yeah, let's give the females odd employee numbers and the males even ones. And while we're at it, make the 3rd digit indicate their grade and the 5th their education level...

    • Different forms of communication. You wouldn't say "I'm going to feed my Felis Cattus some Gallus Gallus for dinner." The Linnaeus system is already too specialized to fill in those mad libs blanks, you just use the common names for organisms you deal with regularly. This is for when the Linnaeus system isn't specialized enough. Say you discover through DNA sequencing that your sample of mud from the bottom of the ocean has ten new species of microbes in it. You're probably not going to come up with ten

    • ["dog\n", "deer\n", "wife\n", "animals\n"] ... People would find these names easier to understand if you used "echo -n".

  • No success (Score:5, Informative)

    by Sven-Erik ( 177541 ) on Saturday February 22, 2014 @06:54PM (#46313401)
    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.

    • 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.

      Much like Dewey Decimal [wikipedia.org].

    • For those that did not RTFA:

      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.

      • Re: (Score:2)

        by pepty ( 1976012 )
        If the licensing terms are expensive or onerous they won't get many users ... so the name will probably also contain a paid advertisement ;). Actually; I'd guess the license would ask users to submit a copy of the name and other useful info to This Genomic Life's database and then they will charge institutions a fee to search it.
  • A higher form of life.

  • Biology and Computer Science Two Way Street (Score:5, Insightful)

    by utkonos ( 2104836 ) on Saturday February 22, 2014 @07:14PM (#46313451)
    Last month, at ShmooCon [shmoocon.org] a talk [archive.org] was given about spatial analysis [shmoocon.org] of malware samples. The technique is borrowed directly from bioinformatics. This is a great example of techniques from Biology being used effectively in the IT security realm.

    I hope that the researcher involved in naming organisms based on hash algorithms chooses context triggered piecewise hashes (CTPH) AKA fuzzy hashing [dfrws.org] or a similarity hash algorithm [princeton.edu] rather than an algorithm like SHA512. Google's simhash [wwwconference.org] or at least the ideas of this type of algorithm would lend itself much better to the naming of organisms.

    FYI: a FOSS implementation of fussy hashing is called ssdeep. The project site is here [sourceforge.net]. This is an implementation that is widely used in open source malware analysis tools like Cuckoo Sandbox [cuckoosandbox.org].

    • Re: (Score:2)

      by dirt ( 1129 )

      Thanks for those links. Comments like yours are why I continue to read /.

    • Last month, at ShmooCon a talk was given about spatial analysis of malware samples. The technique is borrowed directly from bioinformatics

      Haven't read it yet but from the abstract, it sounds very much like the approximate word matching/text indexing method I prototyped almost a decade ago, matching pieces of text by mapping them onto sets or multisets of their constituent trigrams. (And I'm pretty sure I wasn't the first person ever to have done that.)

  • I think we're a little late to the game [deviantart.com] on this one.

  • A few years back there was an eruption of expensive "premium short message services" that offered gullible people to provide their "Manga character name", their "hero name" and other ridiculous stuff like that - based on a hash-function that picked a name from a name library according to the hash sum over some arbitrary data (like real name, phone number or whatever) the gullible customers provided in their short message.

    Now this "pick name based on hash over genes"-proposal does not sound that different

    • Re: (Score:2)

      by PPH ( 736903 )

      I hope this doesn't invalidate my family coat of arms which I paid good money for some years back.

  • From now on, please refer to me as "ed35073e47a38fbbcc66c1c69058b9c3"

    This system has more uses beyond categorizing life on earth. My favorite movie line: "77b0ba27c2fcfa0e02793671c27afb38"

  • Individials of the same species have (Score:3, Insightful)

    by Anonymous Coward on Saturday February 22, 2014 @07:47PM (#46313591)

    differing genetic code.

  • The most obvious problem with this approach (Score:4, Informative)

    by Anonymous Coward on Saturday February 22, 2014 @07:56PM (#46313617)

    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.

    • I think you''re mostly correct, except for the case of organisms with horizontal gene transfer such as bacteria and archaea. The current naming convention breaks down when it is applied to this type of organism.

      • Yes, this approach makes far more sense for bacteria, whose phenotype is not that far removed from its genotype.

      • I should have also added that if you have evidence that horizontal transfer of genetic information has occurred then you probably already have information about the distinctiveness of two putative species. Otherwise, how would you tell?

        • There may be cases where a single "species" of bacteria has a varying rate of horizontal transfer based on its host species. It may have more exposure to a different species of bacteria that it is able to trade genes with because that other species is exclusive to one of the two hosts rather than both. In cases like these, you could name each by its code. I think the ultimate goal is to make clear naming distinctions that reflect actual differences in populations of organisms.

    • There are problems with the current system, though. The one I'm most familiar with runs like this:

      1. Species was named a while ago, with the type specimen kept. Name, say, Foozy yanner. Specimens are collected from several places over time.
      2. Then we realize that those specimens represent more than one species (very possible just with old-fashioned naturalist observation, and happens also with genetic analysis).
      3. So some of the specimens now are officially Foozy tanner -- but we aren't allowed to rename Fo

  • ... my genius!!
    How the fuck am I now supposed to have an "angel'o'sphere" in the middle of a the name of a beetle?

    They just gave a beetle the name of Darwin and a stupid musician ... and I'm lost.

    (* cry *)

  • are, if he (women can't be this stupid) thinks that a hierarchical naming scheme is anything like a hash function.

  • At the rate we are driving species extinct a much simpler system of naming the few surviving will be sufficient.

    • If anything, killing the big, fuzzy, charismatic ones and leaving nothing but horrid insects and burbling bioslurry probably makes the naming challenge substantially more difficult. Back in the good old days, when 'biology' consisted of going out, shooting things, having the servants stuff them, and then deciding which ones looked most like the other ones, you could get away with all kinds of sloppy naming because there just weren't that many species on the table.

      Now that we have these kids with their fa

      • shooting things, having the servants stuff them [...] there just weren't that many species on the table.

        Ah. When you said "stuff them" I thought you were referring to taxidermy, and not the herbs and breadcrumbs kind.

        • More than a few noted biologists also came to this conclusion. A major theme in Charles Darwin's "The Voyage of the Beagle" is his constant quest to document, and devour, every goddamn novel species he could get his hands on. And he got his hands on quite a few.

        • In reply to your subject: did you know about the hippo farming plan? Apparently it was a big deal like a hundred years ago when we had a "meat problem" in the united states.

          Random link: http://www.wired.com/wiredscie... [wired.com]

  • You don't want a hash function for this, where the hash is effectively random. You need a function that derives a unique value for each input, but retains the relative distance of the original value. i.e. two values that are very similar yield an index that is similarly close. That way the 'hash' can be used to determine how closely related two species are. Randomising in the way a true hash does is of no real value.

    • Randomising in the way a true hash does is of no real value.

      There's nothing random about a hash function. It has to be deterministic; the same input will always result in the same output.

      • I know that; you know that; everyone on Slashdot presumably knows that. I didn't mean 'random' as in truly random, I meant that the spread of values produces by the hash must be effectively random. In the context of the article, you don't want anything like random, you want both deterministic and a function that maintains distance. A hash is completely wrong.

        • I meant that the spread of values produces by the hash must be effectively random. In the context of the article, you don't want anything like random, you want both deterministic and a function that maintains distance. A hash is completely wrong.

          Of course a hash is wrong. That's why you use a locality-sensitive hash [wikipedia.org] for that.

      • Re: (Score:2)

        by Nutria ( 679911 )

        It has to be deterministic; the same input will always result in the same output.

        Correct. OP is conflating "random" with "one-way".

        • I think he's conflating random with meaningless. A well constructed hash shouldn't give clues about the contents, i.e. if you change a single e to an f in "War & Peace" the results should be totally different.

    • Not only that, but DNA varies from ape to ape just as much as from ape to humans. So unless they use a hash function like you specify, it would be impossible to tell if you're looking at the hashed-DNA of two members of the same species or two members of different species.

      IMO if they're trying to use hashes to provide a unique identifier for species, they probably don't care about the ability to measure the similarity between species. It would probably be difficult to write a hash function that would have f

    • You don't want a hash function for this, where the hash is effectively random. You need a function that derives a unique value for each input, but retains the relative distance of the original value. i.e. two values that are very similar yield an index that is similarly close.

      Certain hash tables for search functions are built around hashes exhibiting the very type of behavior you describe -- Not to mention current 'reverse' image search technologies. A "hash" function is not required to have a seemingly random output. Cryptographic hashes try to produce high entropy deterministic output, but other types of hashing can and do have different goals, namely with far less entropic outputs.

      I would ask you to turn in your geek card, but the standard for issuance is far lower nowadays

  • Not sure how similar this is to hashing (Score:4, Informative)

    by fozzy1015 ( 264592 ) on Saturday February 22, 2014 @08:46PM (#46313775)

    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.

    • You are equating "hash function" and "cryptographic hash function" with your assertion "one of the key properties of a hash function is that small changes in the input result in a completely changed output". Not all hash functions are cryptographic hash functions. Inside operating systems you may see a hash function that is no more than a simple masking of bits because that is all that is required.
      • No, cryptographic hash functions have certain strong guarantees, but all(*) hash functions are supposed to mimic independent, uniformly random, behaviour of inputs. Since in the physical world, inputs often come from processes, and processes tend to evolve continuously, the inputs to be hashed by a computer system often have some amount of similarity if they occur close together in time. Thus to transform consecutive inputs into a pair of independent uniformly random hashes, it is desirable that small chang

  • Might as well just use shorthands for now. If the nomenclature may have to be changed someday because of collisions, you might as well use something more friendly today. Until we understand DNA well enough to reject nonviables, the potential for namespace collision is too high to expect to be able to use today's scheme forever.

  • It is impossible to make a hash function that gives one hash to a set of similar genes, because there will always be too many near ambiguities.
    There are however other ways of doing things that behave like hashes. I made the best method for this for fingerprints, so I should be contacted for stuff like this.

  • A hash doesn't provide any taxonomy. It would be better to use something like an OID [wikipedia.org] so you see how the organism relates to other organisms.

  • In a way isn't a genetic fingerprint a hash by itself.

    A hash is an form of ensuring the (genetic) code is exactly the same.
    You could basically see every living being as a walking collecting of genetic hashes. Some of these hashes we share others are unique to a species or sub-species or unique to a single person.

    The only difference is that we do not understand the genetic code well enough to use them in the same way as a hash code.

  • The comic page cartoonists are happy people, finding joy in simple things and daily events happening around them. They are amused by such little things they lead a happy contented life. The only reason they share their joy, in whatever little morsels, with lesser mortals like us is, someday they will have a louse or a worm or bacteria named after them. Without an incentive like this they will throw away their crayons and pencils and walk away.

    I will support naming organisms by hash functions when hash fun

  • At the rate we're killing organisms off, we'll only need two of these soon ... one for humans, and one for soylent green ... whatever that stuff is made from!!!!

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