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Biotech News

Identifying World's Species With Genetic Bar Codes 156

Posted by samzenpus from the scan-the-fish-first dept.
Fokker writes "Reuters reports that scientists from around the world launched a project on thursday to genetically identify species using bar codes. By taking a snippet of DNA from all the known species on Earth and linking them to photographs, descriptions and scientific information, the researchers plan to build the largest database of its kind."
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Identifying World's Species With Genetic Bar Codes More

Identifying World's Species With Genetic Bar Codes

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  • what about the zebras? (Score:5, Funny)

    by Suburbanpride ( 755823 ) on Thursday February 10, 2005 @03:11AM (#11627631)
    Wont this hurt the self esteem of the animals that already have barcodes?

  • Why? For Check out lines? (Score:5, Funny)

    by DanThe1Man ( 46872 ) on Thursday February 10, 2005 @03:12AM (#11627633)
    "Could I get a price check on a large brown marsupial?"

  • The result will be (Score:5, Interesting)

    by hashish ( 62254 ) on Thursday February 10, 2005 @03:14AM (#11627642)
    that we will find more unique animals that we didn't know were unique. We are still identifying more unknown species every day, now with DNA species we thought are related will now be determined not to be.
    • i wonder which specific DNA sequence they use, since it should be present in all species and sufficiently divergent to discriminate between species.

      another thing that might be problematic, is the dicrepancy between different classification methods... sometimes morphological or biochemical classifications do not coincide with DNA based classifications.

      i like the effort, but i have to see it work before i am convinced of the merits. the article is a bit vague regarding implementation.

      • Re:The result will be (Score:5, Informative)

        by extensis ( 665596 ) <mdjones&ualberta,ca> on Thursday February 10, 2005 @04:26AM (#11627867) Homepage
        I have to admit i ahve yet to read the article, but did write a lengthy report on the subject last semester...
        The region of DNA they are using as a barcode is a 561 bp stretch of the cox1 gene, which encodes Cytochrome C Oxidase subunit 1.
        The gene is found in the mitochondrial DNA in all animals and plants, and many homologues are in bacteria and other forms of life.
        There are some great resources out there

        http://barcodinglife.com/ [barcodinglife.com], The official site.
        Or for the geeky, http://www.ncbi.nlm.nih.gov/ [nih.gov], GenBank, search for cox1, it's the second most sequenced gene on the planet,
        you'll find it's sequence and other info you can play with 'bioinformatically'.

        If anyone is interested Cytochrome C Oxidase is the final protein in your electron transport chain.
        It is the enzyme that reduces oxygen in your body (try breathing in!), and is found in 'nearly' all life that lives in oxygen.

        • The depressing bit is, that all made sense to me :(
        • " There are some great resources out there
          http://barcodinglife.com/, The official site."

          thanks, that site was informative and good instead of the shallow PR story linked in the main article.
        • Actually, according to the "Citation" link on the site, barcodinglife.org [barcodinglife.org] is the preferred address of their site, though the .com version works too. If they're a noncommercial project, .org is more logical.
        • ... or does it bug other people that mitochondria have their own DNA and reproduce asexually? It's like we have this second species living inside our cells. We're utterly dependent on them, but they're just coasting along, evolution wise. I predict trouble, 4 billion years from now. Ok, maybe 5.
      • "i wonder which specific DNA sequence they use, since it should be present in all species and sufficiently divergent to discriminate between species."

        True if they actually want to infer a phylogeny of all those species (the so-called Tree of Life [tolweb.org]). Choosing the adequate data is only one of the problems for those seeking to do this, among other you have huge computational problems (give use faster computers please!) as well as biological problems such as: is the history of life adequatly represented by
        • oh man... i'm aware of all these things you mention.

          a unique identifier for each and every species needs a DNA sequence that is present in all these species and divergent enough, whether they want to use phylogeny or not.

          if they use different features as well, there needs to be some kind of mapping between the differences they observe based on these features, and the DNA sequence of said gene, right?

          hence, we *are* in the realm of classification. not as a goal, but as a means to an end.

    • Possibly, but not necessarily so. There is no "species" defining gene of course. And the dream of one (such as COI) that will provide all answers, is just that, a dream. A barcode is a unique identifier for an *already identified object*. If you don't know what your species are in the first place, you can't give it a barcode. Genetic differences can alert one that there might be a new species there, but they can't recognize the presence of a new species without supporting evidence. Most upper year e

  • Um... GenBank? (Score:5, Informative)

    by davidstrauss ( 544062 ) <david&davidstrauss,net> on Thursday February 10, 2005 @03:18AM (#11627653)
    That project, minus the insignificant addition of photos, is already widely underway at GenBank, a part of NCBI, which is in turn part of NIH. Most major biological journals require submissions of sequences to GenBank prior to consideration for publication. Combined with NCBI's taxonomic system, I don't see the value of this new project.

    I work in this lab [utexas.edu]. Specifically, I'm working on objective analysis of RNA sequence alignment heuristics.

    • I too am somewhat confused about the project too, since this is more or less done already today. Isn't 16S ribosomal DNA the standard "genetic bar code"?

      But I think the project is about actually sampling the bar code from every known species. To some extent we are getting spoiled with all the genome data coming out, gene discovery projects, whole genome sequencing, gene expression data, et.c., and at least I have more or less come to expect to find the gene data I would like to have. However, the sequenci

      • 16S ribosomal DNA the standard "genetic bar code"?

        No not really. That just types your mitochondria and is a quite bad marker. You're better off sequencing the complete mitochondrial genome, which is what we do. http://phylo.gen.lu.se/ [gen.lu.se]

        However, the sequencing is not uniformly sampled: It is concentrated to the important model organisms and then patched out over the animals that some researcher has had an interest in.

        The field is still quite young and high throughput techniques are not that old. But compl

    • Actually, most biological journals require submission to either GenBank (U.S.), EMBL-Bank (European), or the DNA Data Bank of Japan. The members of the International Nucleotide Sequence Database Collaboration exchange data every night, but that doesn't mean they are the same thing, or that it is run by NIH.
    • NCBI's taxonomy is widely regarded to be.. well suspect by people working in the taxonomy field. In fact there is NO common taxonomy system, contrary to popular belief. Like many other areas of science it is beset with individuals who *talk* co-operation and fail to do it.

      I have seen taxonmy comparisons from various sources and NCBI's is by no means definitive.
      • NCBI's is by no means definitive

        Not definitive? Dead wrong, grossly misleading, and similar descriptions apply.

        Entire phyla which are now strongly supported by multiple solid analyses are simply missing, broken up into bizzare arbitrary groupings.

        They seriously need some new taxonomy work. Who's supposed to be doing that for them anyway?

      • Exactly right. NCBI's taxonomy could use a lot of improvement. For a course I took last year we had to figure out whether the Quagga (an extinct horse/zebra relative) was closer to the horse or the zebra according to mitochondrial DNA samples. Well, let's just say that the taxonomy data for the Quagga in NCBI's db was pathetic - it was listed as at least two different species.


    • 1) Genbank taxonomy is notoriously horrid, as any practicing systematist knows. 2_ Anyone can submit any sequence to genbank and call it what they want, without any measure of quality control. Of course the errors can be caught, and annotated, but this is not the type of system you want for barcoding.
      • Anyone can submit any sequence to genbank and call it what they want, without any measure of quality control

        Wrong. GenBank aligns submissions against existing data and requires submitters to validate any possibly errors.



        • Whoa. Your obviously a bit of a GenBank newb. There are papers where whole *organisms* were missequenced and identified incorrectly then submitted to Genbank under misidentifications. And not just minor problems, but across phyla (fungi identified as insects for example). Just because Genbank aligns your data and suggests there might be errors has absolutely nothing to do what you call it or how it gets submitted. We have several projects we are working on 20 percent or more of sequences we retrieved

  • I have never heard of a technology more.. (Score:3, Interesting)

    by ciroknight ( 601098 ) on Thursday February 10, 2005 @03:22AM (#11627662)
    ..based on something from Star Trek. This is the very kind of thing I think of when they pull up their tricorder to some alien race, and poof, a strand of their DNA is up on one of those pretty LCD monitors behind them.

    That being said, I think this is a brilliant use of computer technology. Catalogs and databases of this kind are what we need, especially while going through the jungles of various continents in search of miraculous wonder cures. Besides, if we had done this before with the Dodo and other animals that went extinct, we could rebuild the strands of DNA, and make the animal again for study. I tend to think more and more as we corrupt the planet with roads and sidewalks that research and food will be the only reason to have living stuff around, and knowing that we have a computer database of all that is alive and the ability through cloning to reproduce any of it is at least a comforting thought.

    end rant.
    • This has nothing to do with cloning animals, the basis of identification is only small piece of the DNA (like the one gene, COI, that is currently in the discussion, although the primers suck). At least for this project, the complete DNA of the organisms is not needed, or kept. But I seem to remember a project that had the aim of freezing DNA of all kinds of animals.
    • I'm pretty sure they aren't sequencing the whole organism. Just a few spot checks.

      Sequencing is still pretty expensive - up for a few dollars a read (where a read is 500-1000 bp), and you've got to do a whole genome (say...3 billion bp for humans.) We're talking millions of dollars, minimum, plus LOTS of work for people to assemble all of that data (I have friends over in the finishing group at the Broad Center for Genome Research - I work in the medical and population genetics part of the Broad...)
    • No, this is exactly NOT what we need. This is something a geek needs. You can't compare species with their DNAs. This is a great misbelief. An animal is more than just a little DNA (the same as a human). But this is one further example of throwing some technology and money at a subject, which it doesn't need this and destroying it therefore.

      • You can't compare species with their DNAs. This is a great misbelief. An animal is more than just a little DNA (the same as a human).

        I don't exactly know what you put in the word "compare" here but using the common understanding then that is what we do for research. http://phylo.gen.lu.se/ [gen.lu.se]

        You can perfectly well compare the sequence of two homologous genes from two species and knowing the function of one you can guestimate the function and domains of the other.

      • Is this based on an anti-reductionist belief on your part, or is this just a gut feeling?

        First off, yes you can do some interesting inter (and intra) species comparisons; you say an organism is more than "a little DNA", but all proteins are clearly encoded by DNA (or RNA in the case of some simpler life-forms, and certainly the vast bulk of a species' distinctive characteristics are down to DNA.

        However putting that to one side; your comment is not really relevant to the project in question - they are not


    • > ..based on something from Star Trek. This is the very kind of thing I think of when they pull up their tricorder to some alien race, and poof, a strand of their DNA is up on one of those pretty LCD monitors behind them.

      But that's a few hundred years in the future. Right now the Federation still uses the older Anal Probe (tm) technology, to the great mortification of species all around the galaxy.

    • I've been to several debates regarding this technology. In fact, the "kicker" slide used in these talks is a mocked-up little tri-corder like gadget which you insert your leg/organism/leaf etch into. The tri-coder sequences the bit rapidly, and spits out the pertinent data. Of course this is just a vision of the future, but its funny that they make no qualms about presenting the potential tool as a tri-corder or star-trek like gadget.
  • I've got a better record stuck to the bottom of my fishing boots...how do people get paid for this stuf?

  • The hard part is... (Score:4, Informative)

    by Lynx0 ( 316733 ) on Thursday February 10, 2005 @03:23AM (#11627671)
    ...actually finding and agreeing on the locus (piece of DNA) to use for this. It has to be present in all species, i.e. in gnat and cow and jellyfish, but also has to be variable enough to be able to differenciate between, for example, the Tennesse gnat and Alabama gnat.
    The main problem is that the locus must contain two regions to the right and to the left of the sequence of interest that must be highly invariable. This is necessary so that the same PCR [wikipedia.org] primers can be used to amplify the sequence in most species. The amplification step is necessary for sequencing.
    • If you had some sequence to the left and right to prime off of that was constant over many organisms, I'd say that was an extremely highly conserved, and thus very important (and interesting) region.

      You aren't amplifying more than 500 or so bp (what's the reasonable limit on sequencing now? Is it up to a KB yet?), and finding two very highly conserved sequences with sufficent variation would be...interesting.

      I'd love to see how they pick regions to sequence for this...
    • Well since they're going for a barcode it sounds more like the results of electrophoresis than the sequence of a particular gene. This would be closer to how DNA fingerprinting(that we've all heard so much about on tv) is done. There are actually several different ways of going about it. One method involves just creating two random primers. These primers will produce PCR products of varying lengths, depending where the endpoints lie within the genome by chance alone. Electrophoresis is run on the PCR a

  • how long until (Score:2, Insightful)

    by mirko ( 198274 )
    sombody thinks about determining human species based on their DNA ?

    • Re:how long until (Score:3, Interesting)

      by espressojim ( 224775 )
      Well, you may want to look up Admixture mapping to start. We don't really have species, but we have people from various backrounds with differing genetics that cluster by location due to population movements, bottlenecks, and migration.

      Or: Yeah, you can tell the difference between say...chinese and japanese people by looking at the frequency of various single nucleotide polymorphisms.
    • The barcodes are coming! The barcodes are coming!

  • Pet store efficiency (Score:5, Funny)

    by Orgadam ( 850974 ) on Thursday February 10, 2005 @03:29AM (#11627685)
    Does this mean the pet stores of the future will allow a cashier to swipe an animal across an electric eye, greatly increasing the efficiency and speed with which people can buy large quantities of animals? Such a system could greatly help out my habit of buying as many mice as I can! Although, it becomes a problem when geneticists demand that barcodes be placed on individual fruit flies so that they, too, can be bought quickly and efficiently.

    Yeah, I know the barcodes won't be put on the animals... but maybe after a trial run, customers will demand it!
  • Will they call it Project Titan?
  • What picture will they use for humans?

  • A Few Less Species (Score:4, Insightful)

    by _Hellfire_ ( 170113 ) on Thursday February 10, 2005 @03:39AM (#11627712)
    The sad part is that by the time they get around to barcoding all of them, we'll have a few less species around to bar code.
  • Pig and elephant DNA just won't splice!
  • ...barcode 666!

  • I wonder... (Score:1, Interesting)

    by Dragon Rojo ( 843344 )
    From TFA

    The initiative will begin with three projects. One will provide barcodes for the 10,000 known species of birds by 2010, another will tackle the 23,000 types of marine and fresh water fish and a third will genetically label the 8,000 kinds of plants in Costa Rica, Central America.

    When they will be able to classify the 2,000,000(estimate number of known species) species??

    And who will be the poor soul that have to carry the weight of the task(An intern maybe??)


    • > When they will be able to classify the 2,000,000(estimate number of known species) species?? And who will be the poor soul that have to carry the weight of the task(An intern maybe??)

      It would save a lot of trouble if we just used the boarding sequence numbers from Noah's passenger manifest.

  • Open Directory (Score:5, Interesting)

    by wces423 ( 686579 ) on Thursday February 10, 2005 @03:47AM (#11627747)
    Wikipeople have free online directory of species WikiSpecies [wikipedia.org]

  • lets say they actually do it... (Score:2, Interesting)

    by Anonymous Coward
    ... the find ever species and make a bar code for it. Then what ? Call me dumb - but the point of a barcode is to easily scan it .. last time i checked, frogs dont have barcodes on them.

    You find a weird insect .. 'oh - i'll just check the barcode database! oh wait, it doesnt have one .. damn'

    scrap the barcode thing .. just build the database (perhaps spending more time (and cash) on it you could have the full DNA sequence .. not just a scrap)

    So next time we wipe out some endangered swamp monster we have
  • ...they could also add 'women' to the index so we know how to identify one. Some list of suggestions for handling procedures might be welcome too as an appendix.
  • Could this help find unknown species or help determine what *could've* happened in the evoultion of animals had things gone differently? i.e. presumably there is a finite number of genetic "bar code" combinations, so there would be a finite number of species that could exist... no? yes?

  • Partially useful (Score:5, Informative)

    by onco_p53 ( 231322 ) on Thursday February 10, 2005 @04:32AM (#11627901) Homepage Journal
    The fragment of DNA that they are sequencing is located on the mitochondria and is part of the cytochrome c oxidase gene (COI). http://en.wikipedia.org/wiki/DNA_barcode [wikipedia.org]

    I am a taxonomist and can tell you this is of limited usefulness, sure we will be able to see some differences between organisms, but this is already done is many studies with the control region of the mitochondria.

    The problem could be if people just rely on these sequences alone to delineate species, we learnt this years ago in bacterial taxonomy that you simply cannot rely on any one particular gene (There is evidence of horizontal gene transfer in 16S genes if someone was going to counter with that).

    A speciation event is driven by some environmental pressure (change in temperature say). The genes that are under selection of this pressure will change at different rates to one under no direct pressure (COI).

    I could rant on but, I think this project is of some use only if combined with traditional taxonomy. The danger is that a large flashy project like this will steal research dollars away from traditional taxonomy.

    • That is a good wikipedia link you gave. I recommend it to people interesting in this thread.

      I could rant on but, I think this project is of some use only if combined with traditional taxonomy. The danger is that a large flashy project like this will steal research dollars away from traditional taxonomy.

      It is not like the field of taxonomy is without flashy projects. Consider the Tree of life project [phylo.org] for instance.

      Given the information in the Wiki you referred to, wouldn't you say that the barcodes cou

      • Given the information in the Wiki you referred to, wouldn't you say that the barcodes could provide a starting point for good taxonomy projects?

        Yes it could well be, but it would be a "fishing expidition" you may well find nothing of significant interest. Spending dollars on focused projects is probably more useful.

        My concern over funding really relates to New Zealand where we have a very restricted research budget. Moving dollars to barcoding would mean that people will actually loose jobs (we are curr

    • Re:Partially useful (Score:2, Interesting)

      by Lynx0 ( 316733 )
      The barcode sequence will only be a means of identifying the species, not to find new ones or do taxonomy on them. The first connection between the sequence and the actual animal will be done by traditional taxonomy, because there is of course currently no other way do differenciate between many species than by the help of a specialist for the group.
      But once this is done, if I find the beetle (or something) again, I can identify the species by myself with a PCR and sequencing, and don't have to mail it to a

      • You wouldn't try to understand your Ramen noodles by looking at its barcode, but the barcode does help the computer to identify the noodles.

        As far as I can tell, that's all they're proposing here, as well. This would allow a student researcher (or other less educated researcher) to help a more experienced biologist by figuring out whether an animal actually is species X or whether it just looks like species X to a relatively untrained eye. And, in this case I imagine the experienced biologist will be very

    • The problem could be if people just rely on these sequences alone to delineate species, we learnt this years ago in bacterial taxonomy that you simply cannot rely on any one particular gene (There is evidence of horizontal gene transfer in 16S genes if someone was going to counter with that).

      Hrmm, I had to google to find out that 16S genes reside in the mitochrondria. One thing that was interesting is that apparently part of these genes may come [oupjournals.org] from the nucleus (at least in some multicell organisms lik

      • Sorry about not explaining 16S, you become quite insular during a PhD.

        16S rRNA is widely used in bacterial taxonomy, and has been for a very long time, even before sequencing was available (as restriction patterns - fingerprints). Wiki on non-coding RNA [wikipedia.org]

        The homologue in human cells is 18S rRNA, however the rRNA in mitochondria in our cells is 16S, as mitochondria and bacteria share a common ancestor.

        Side note: I am so used to Wikipedia I started linking like [[this]].

        I agree with you next point, mayb

  • one use for this technology (Score:5, Interesting)

    by hengist ( 71116 ) on Thursday February 10, 2005 @05:03AM (#11627990)
    Where I work, a group is using this technique to identify insect pest species.

    If, for example, a group of insect eggs, or even just some parts of an insect like the legs, were found in a shipping container, then it can be extremely difficult to identify the insect species by morphology. By sampling and barcoding the DNA in the eggs or fragments then it can be determined which insect was present, and therefore whether a potential pest was present in the container.

    For a country that depends on agriculture, like New Zealand does, this is a very important technology.

  • Taxonomic debates? (Score:3, Interesting)

    by Claire-plus-plus ( 786407 ) on Thursday February 10, 2005 @05:24AM (#11628040) Journal
    Maybe projects such as this one might solve some taxonomic debates such as the old chestnut about whether Megachiroptera (fruit bats) and Microchiroptera (insectivorous bats) are acutally closely related [udel.edu].

    For those of you who don't know the debate is as to whether Megachiroptera are closer related to primates than they are to the Microchiroptera. I personally believe that fruit bats are flying monkeys. Therefore, fruitbats are the only primates native to Australia (besides Homo Sapiens obviously).


  • I'll be anxiously awaiting them to publish the data on our own species' barcode. I'd be kewl to have one tatooded. :D

  • X5? (Score:3, Funny)

    by Claire-plus-plus ( 786407 ) on Thursday February 10, 2005 @05:51AM (#11628126) Journal
    Well one species already carries it's own barcode. It's always there on the back of their necks and grows back when it's removed. And one of them (X5-452) is a hottie as well.
  • What DNA sequence would be considered as the base pairs of all life forms on Earth are similar?
  • What I don't understand is...we as humans are all different genetically as human individuals and the same must be true within the animal kingdom. Where does the intra-species DNA difference end and the inter-species one start?

  • Barcoding web site (Score:5, Interesting)

    by lovebyte ( 81275 ) * <lovebyte2000&gmail,com> on Thursday February 10, 2005 @06:03AM (#11628157) Homepage
    barcoding.si.edu [si.edu]
    From their DNA barcode page:
    DNA barcode sequences are very short relative to the entire genome and they can be obtained reasonably quickly and cheaply. The cytochrome c oxidase subunit 1 mitochondrial region (COI) is emerging as the standard barcode region for higher animals. It is 648 nucleotide base pairs long in most groups...

    Let us note however that most of our planet's biodiversity is contained in the 60% of the biomass that people don't talk much about: Bacteria. Most of them live in the soil and are difficult to study and are simply unknown. It would seem that this barcoding project does not include Prokaryota ( = Bacteria,Archaea) unfortunately.
  • From the BBC coverage:

    "About 1.7 million species are known - we suspect there are anything from 10-30 million species on Earth," explained Dr Richard Lane, director of science at London's Natural History Museum.

    Wednesday saw the announcement at the London conference of a project to get comprehensive barcode data on all known fish types - currently thought to number 15,000 marine and 8,000 freshwater species.

    The current project is looking to catalogue the world's 10,000 known bird species, the 15,000 mar

  • What just bit me? (Score:4, Funny)

    by wolf- ( 54587 ) on Thursday February 10, 2005 @09:11AM (#11629085) Homepage
    Martha, I've been bitten by a snake!

    Hang on Frank, let me get my barcode reader out..

    *eh* *eh*
    Dang it, frank, hold its head still. Can't get a read.

    *bleep* *bleep*
    There we go.

    Good news Frank, its only a black mamba

    Martha, how is that "good"? I thought they were deadly.

    Frank, the life insurance is all paid up!

  • Do you think this will allow me finally to identify the species of my mother-in-law?
  • This has been bothering me for a while - it seems to me that the linnean classification system (kingdom, phylum, class, order, family, genus,species) is outdated and showing signs of being such. It's a table structure, developed to classigy animals when people thought they were created by God to belong to certain classes (birds of the air, fish of the sea, etc).

    Now with evolutionary theory we have the 'tree of life' model of speciation, which is a tree. Why do we still use the Linnean table structure? You

  • ...but isn't the point the converting genetic information into a number in a database, and not the barcode? I mean, the barcode itself is of utterly no value except as a shorthand for transmitting numeric data.

    They take a sample.
    They convert the genetic information to numbers.
    * they convert the numbers to a barcode *
    They send this data to the database
    * it's backconverted from barcode to numbers *
    The information is checked against what's in the database.

    arent the "*" lines redundant?

    I mean, the 'barcode'
  • Well, I guess this will make my grocery shopping simpler.
  • Wait, I saw this movie [imdb.com] already!
  • I can see it now... drop a piece of hotdog into a scanner, and your PC starts scrolling out DNA matches.

    70% Cow
    10% Pig
    5% Chicken
    3% Rat
    2% Cockroach
    2% Mealworm
    1% Quagga
    1% Housefly
    6% Other

    On second thought, maybe we'd be better off not knowing...
  • Anyone remember the end of Titan AE when they discover the ship with the genetic code for every living thing on earth?
  • Does anybody remember [64.233.161.104] Kevin Kelly's All Species Foundation? Within the last month or so the website has gone down.
  • Next thing is they attach RFIDs to those poor creatures that contain their DNA in machine-readable form in order to use an SHA hash as a key to the species database.

    -- Search is going mobile. [mynuggets.net]

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