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Data Storage Biotech

Data Storing Bacteria Could Last Millennia 252

Posted by samzenpus
from the written-in-the-genes dept.
PetManimal writes "Computerworld has a story about a new technology developed by Keio University researchers that creates artificial bacterial DNA that can carry more than 100 bits of data within the genome sequence. The researchers claimed that they encoded "e= mc2 1905!" on the common soil bacteria, Bacillius subtilis. The bacteria-based data storage method has backup and long-term archival functionality." The researchers say "While the technology would most likely first be used to track medication, it could also be used to store text and images for many millennia, thwarting the longevity issues associated with today's disk and tape storage systems ... The artificial DNA that carries the data to be preserved makes multiple copies of the DNA and inserts the original as well as identical copies into the bacterial genome sequence. The multiple copies work as backup files to counteract natural degradation of the preserved data, according to the newswire. Bacteria have particularly compact DNA, which is passed down from generation to generation. The information stored in that DNA can also be passed on for long-term preservation of large data files."
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Data Storing Bacteria Could Last Millennia

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  • A Must (Score:2, Insightful)

    by kraemate (1065878)
    We *will* need a Beowulf cluster of these, seriously.
    • Re:A Must (Score:5, Insightful)

      by nmb3000 (741169) <nmb3000@that-google-mail-site.com> on Thursday March 01, 2007 @02:39AM (#18191446) Homepage Journal
      You mean a Biowolf cluster.

      Talk about an interesting way to sneak information out of a company/country... transcribe it into the DNA of an infectious bacteria or virus, and then infect yourself with it. You walk out the door with a sniffle and 10 million dollars worth in classified secrets.

      "New company policy is no isolinear chips, holocubes, or antiquated 'flash' drives on the campus. Additionally, all employees must submit to a biological cleansing and surrender their belongings for baryon sweeping before leaving the building."

      At least they might cure the common cold as I side effect to preventing data theft.
      • by Kadin2048 (468275) <slashdot@kadin.xoxy@net> on Thursday March 01, 2007 @03:21AM (#18191606) Homepage Journal
        This definitely brings with it some possibilities, but I think that the technology is available right now to allow any determined person to sneak data past all but the most intensive biomedical screenings.

        You can fit an awful lot of data in something the size of a Tylenol gel-cap, and aside from the unpleasant recovery aspect, nothing less than a X-ray is going to detect that (maybe not even an X-ray, if you were careful about the components used). Of course, your digestive system only gives you a window of opportunity measured in (at most) days; if you wanted to go longer than that, you're talking about implants. But that would get you through most transit checkpoints.

        I'm not really even sure this is a new development: spies and other folks with resources have had microfiche and microdots for years. Cement one of those to your nether regions, or swallow one, and it would take a pretty determined search to turn one up. Or if you wanted, you could probably even sprinkle them over an unwitting mule's clothes, and then recover one on the opposite end.

        It doesn't seem like data theft is really something that you can realistically try to stop at any border, anymore. If someone has the data in a format that they can load on their person and take to the border, it's gone. If you can get a person across, you can get data across. Certainly if you are allowed to take any type of electronics, it should be considered information-porus; there are so many ways to disguise information using steganography, that it's not practical to try and sanitize it.

        Certainly by the time that biological information storage becomes widely practical, all but the most backwards nations and companies will have realized that stopping the flow of information with physical checkpoints at the border is a losing game. At best, you might be able to make it a little easier or harder, but real information security depends on limiting hostile parties' access to information in the first place, not trying to limit their transportation of it afterwards.
      • Re: (Score:3, Interesting)

        by bmo (77928)
        "You mean a Biowolf cluster.

        Talk about an interesting way to sneak information out of a company/country... transcribe it into the DNA of an infectious bacteria or virus, and then infect yourself with it. You walk out the door with a sniffle and 10 million dollars worth in classified secrets."

        Vergil I. Ulam did this in Greg Bear's "Blood Music"

        It brought about the end of the world.

        Read it. Really good. Trust me.

        *bmo goes out to buy sunlamps*

        --
        BMO
    • Mankind (Score:5, Insightful)

      by theuedimaster (996047) on Thursday March 01, 2007 @05:00AM (#18191938)
      Pretty soon we're gonna find out that human DNA was just supposed be storage for Alien pornography.
      • that's 4^3000000000 potential values in terms of data.
        (compared to a gigabyte hard drive which is 2^8000000000 potential values)

        Not much storage capacity.
        • Hmmm... As each base pair can only be constructed one way I would say that the (theoretical) 3 billion bases pairs = 3 billion bits. Which works out to be about .35G [google.com] little of a third of a Gig, call it a 400G Hard drive. Which if you work it out is .35G per DNA/20TB per LoC ~= .00001705 DNA/LoC Then multiply that by 29x10^6 number of books per LoC ~= 494 books. Meh, still a lot of data in plain text.

          Sera

          • by RDW (41497)
            You can have any of the 4 different base pairs at each position, though, so each base is equivalent to 2 binary digits, e.g.:

            T = 00
            C = 01
            A = 10
            G = 11

            (the paired base on the other DNA strand doesn't add any information, of course, since its identity is specified by its partner).

            In fact, 2 bit binary formats are commonly used to represent large DNA sequences in a compact way, as in UCSC's .2bit format:

            http://genome.ucsc.edu/FAQ/FAQformat#format7 [ucsc.edu]

            This makes (e.g.) whole human genome BLAT alignment searches mana
      • by saskboy (600063)
        ... Which would explain why we have sex, and invented latex and hand cuffs.

        This DNA modification sounds scary though. Are we not going to unleash a superbug when we cause an encoding error while trying to write Grandma's canning process on bacteria?
  • Shareware (Score:5, Funny)

    by Harmonious Botch (921977) * on Thursday March 01, 2007 @01:12AM (#18190974) Homepage Journal
    This is the ultimate distribution system for OSS. New distros are released every flu season.
    It's also not a bad way to distribute movies. Let the RIAA sue a bunch of bugs for file sharing.
    And windows could be distibuted on anthrax bacteria, so users would learn to be appropriately wary.
  • longevity issues associated with today's disk and tape storage systems .

    What about the longevity issues associated with the readers?
    • by goombah99 (560566) on Thursday March 01, 2007 @01:19AM (#18191030)
      It's not enough to store the data, you also have to make the data recognizable. After all 100 years from now how do you know where to look to read the data? The biggest problem is that non-coding dna is not selectively preserved.
      • Re:Longevity Issues (Score:5, Interesting)

        by David_Shultz (750615) on Thursday March 01, 2007 @01:57AM (#18191252)
        The biggest problem is that non-coding dna is not selectively preserved.

        Actually, genetic sequences which are irrelevant to the survival of the entity (as these sequences presumably are) spread through a population and thus are preserved. It is not as rapid as if it provided a benefit, but they spread nonetheless. In a 5th year AI class I actually did experiments with evolutionary computation, looking at genetic changes which had no affect on the fitness of the individuals. The purpose of the experiments was actually to explore whether variation in a population, even if it didn't have any effect of the fitness of the individuals, was a good thing (basically) -turns out it is. But I also learned that even without selection pressure, mutations/new genetic information, spreads (actually rather quickly) through a population.
        • amendment: I realize I may have misinterpreted the previous poster. They are right to worry about the preservation of code in the absence of natural selection insofar as the information will degrade via mutation. While the information will spread throughout the population, there is nothing to keep it from gradually degrading.
        • ... in the biological world.

          Yes in a computer system you can make genes that are truly adaptively neutral. Even so they are subject to genetic drift.

          But in a biological system the organism must expend energy to maintain and duplicate DNA. Therefore every codon has a small but implicit fitness cost. If the benefit of the gene does not overcome the fitness cost of carrying it around and copying it, natural selection will quickly eliminate it.

          Junk DNA isn't "junk". It has a purpose, otherwise we would hav
      • Re:Longevity Issues (Score:5, Informative)

        by Ibag (101144) on Thursday March 01, 2007 @01:59AM (#18191266)
        Exactly. The fact that the data is preserved by being copied every 20 minutes is entirely counteracted by the fact that reproduction is inherently error prone. Many species of bacteria regularly swap DNA to get around the fact that their reproduction is mostly asexual, but even then, mutations can and do occur. Without some mechanism to kill the bacteria when there is a mutation with the encoded data, this is a horrible long term data storage solution. There are interesting short term tracking applications, but data storage? No.
      • It's not enough to store the data, you also have to make the data recognizable.

        So true! And the prerequisite to looking for recognizable data is the recognition that such data might be present.

        Which is only now public.

        So how long will it be before someone claims that some common sequence in human junk DNA is actually the copyright notice for the species?

        Disclaimer: this isn't an original thought. I came across something like this in an SF novel years ago, but I don't recall the author. Phillip K Dick? Connie Willis? Hmmm, it's odd to see those two names next to each other...

    • Re: (Score:2, Funny)

      by g4sy (694060)
      I can see a movie coming on: Indiana Jones and the Lost Bacteria. After a long race to figure out what the sequence means, he is forced to shoot (from an airplane) an unsuspecting Mexican maid (who he had fallen in love with) when she pulls out the AntiBacterial soap on the last remaining specimen in his hotel room.
      Or something like that. I might not be the best at futuristic thrillers.
  • by Statecraftsman (718862) * on Thursday March 01, 2007 @01:13AM (#18190980) Homepage
    It's hard enough keeping track of all these CD's and DVD's.
  • by zappepcs (820751) on Thursday March 01, 2007 @01:14AM (#18190984) Journal
    But how many Libraries of Congress will a bathroom drain hold?
  • Overwriting? (Score:5, Insightful)

    by CoolGopher (142933) on Thursday March 01, 2007 @01:14AM (#18190986)
    So, has anyone tried working out if various junk DNA already holds information that we'd be overwriting with this technique?

    I mean, there are plenty of theories about "seeding" of life on earth after all... maybe we already have a wealth of untapped knowledge?

    (Personally, I think it's extremely unlikely, but that doesn't mean that it wouldn't be prudent to check anyway)
    • Re: (Score:3, Funny)

      by king-manic (409855)
      We're problably someones tape back up. When the main server goes down they'll be coming to vivisect us.
    • by truckaxle (883149)
      The same thought popped into my head. After spending some time following the Bible Code [wikipedia.org] story I wonder maybe they were looking in the wrong place - maybe instead of Genesis they should be in looking into prokaryotic junk DNA.
    • If there were encoded data, a good place to look might be the DNA rainbow [dna-rainbow.org]. It was covered on Slashdot less than a month ago [slashdot.org], complete with comparisons to the Bible code [slashdot.org].
      • "Turing test - tell the computer to simulate Alan Turing, then ask him if he's "just a simulation"."

        **Tester** - Speaking into mouse (ala Scottie) - "Computer. Simulate Alan Turing."

        **Computer** - "I am Alan Turing, would you like to chat?"

        **Tester** - "Are you just a simulation?"

        **Computer** - "Depends on what you mean by "just a simulation". Why do you ask?"

        **Tester** - "Because it's a test."

        **Computer** - "What's a test?"

        **Tester** - "This is, it's a Turing test."

        **Computer** - "I
        • Gah, I've had that sig literally for years (at least 6) and this is the first anyone's commented on it. (Conclusive proof that it sucks and needs to be changed.) Apparently I got it from this page [demon.co.uk], which is a super-nerdy treatise on Star Trek. I was about to claim they copied it from me, but considering it was written in 1993, I probably got it from them.
    • by mapkinase (958129)
      Nice try, but you have absolutely no idea what you are talking about.
  • organic computing (Score:5, Interesting)

    by notgm (1069012) on Thursday March 01, 2007 @01:14AM (#18190988)
    stories like this one, and the story earlier today about the graphene transistor, make me wonder how far off truly organic computing is - and whether or not we'll eventually be indistinguishable from computers. or they from us.

    who's to say that our bodies/brains aren't some elaborate computer design ala douglas adams' design?

    • Re: (Score:2, Interesting)

      by Monoliath (738369)
      I think you raise an interesting issue, had I any mod points I would have modded you up.

      Nano-technology is the missing link in the current bio-tech field, in my opinion, between the ultimate symbiosis of hardware and human flesh, it will allow us to work at levels far too minute at this point, to make the proper kind of medical advances that would allow effective cohesion of man and machine.

      I can't wait for it, even though I hope the day never comes...heh ;D
      • by mike2R (721965)

        Not sure why, but this reminds me of some of my favourite SMAC quotes:

        I think, and my thoughts cross the barrier into the synapses of the machine, just as the good doctor intended. But what I cannot shake, and what hints at things to come, is that thoughts cross back. In my dreams, the sensibility of the machine invades the periphery of my consciousness: dark, rigid, cold, alien. Evolution is at work here, but just what is evolving remains to be seen.

        Commissioner Pravin Lal
        "Man and Machine"

        The Warrio

    • It's interesting that when you apply computer science to biology at their most fundamental levels, you simply confirm the feasibility of solutions long since developed by what we believe to be completely natural evolutionary processes.

      The Universe is a giant computer. Or a simulation [simulation-argument.com] running inside another one. Either way, it doesn't matter.

  • by gr3kgr33n (824960) on Thursday March 01, 2007 @01:16AM (#18191002) Homepage Journal
    My backup chemistry thesis mutated; granting me a degree in forensic anthropology.
  • So do you feed them instead of plug them in?
  • by king-manic (409855) on Thursday March 01, 2007 @01:26AM (#18191092)
    But as always, a virus can still eat your data.
  • by trainsnpep (608418) <mikebenzaNO@SPAMgmail.com> on Thursday March 01, 2007 @01:26AM (#18191096)
    Funny how a virus will still corrupt your data.
  • by BronsCon (927697) <social@bronstrup.com> on Thursday March 01, 2007 @01:29AM (#18191110) Journal
    Can you spray them with Lysol to erase them in an emergency? (The remainder of this post assumes a YES.)

    This could be great for military/government intelligence archival, or, really, any situation where the data needs to be used once and destroyed.

    The longevity, coupled with ease of total erasure, would be great for digital storage of any document with personal information on it, as well. I could see using these discs to submit job/credit/lease applications, recieve bills and in any dealings with the government or IRS. They'll last for as long as needed and can be completely erased before disposal.

    If they're rewritable, as well, all temporary storage related to the files on the disc could be placed on the disc as well, completely keeping that sensitive data off of any other, possibly recoverable, media. If this is the case, perhaps, once these become available, any business or govenrment entity storing personal information should be required to store it on these discs and only these discs.

    ---

    Yes, the entirity of this post, excepting this line and the first, is entirely speculative; keep that in mind when moderating (insightful?)
    • A quick spritz of Lysol isn't going to affect the DNA of the bacteria much, if at all. Denaturing the DNA is not how antiseptics kill bacteria. I think that data stored in this fashion would actually be a lot harder to destroy than magnetic storage. After all, they can extract (fragments of) DNA from fossils.
    • Can you spray them with Lysol to erase them in an emergency?

      The information is included in the bacteria's DNA. Lysol will kill the bacteria, but leave the DNA intact.

      I'm not sure what is in Lysol, but rubbing alcohol will not destroy DNA (at least not initially). Rubbing alcohol is one component in your Kitchen DNA Lab [utah.edu].

  • goatse (Score:5, Funny)

    by doubtless (267357) on Thursday March 01, 2007 @01:35AM (#18191140) Homepage
    "it could also be used to store text and images for many millennia"

    Imagine a Scientist from the 37th century scanning a particular bacteria's DNA sequence and hit Goatse
    • by soft_guy (534437)

      Imagine a Scientist from the 37th century scanning a particular bacteria's DNA sequence and hit Goatse
      He would be so p0wn3d!!!11!
    • Imagine a Scientist from the 37th century scanning a particular bacteria's DNA sequence and hit Goatse

      For all you know, by the 37th Century humans will have evolved freakishly distended assholes, so Goatse will seem normal to them.

      Ugh. Can't believe I wrote that. Must remember to tick "Post Anonymously" option...

  • by Duncan3 (10537)
    DNA that isn't functional has a high rate of change.

    If it's wrong and functional it dies, and only correct copies live on. If it's just data, being wrong does nothing and just keeps degrading further. This is also how we figure out how far distant relatives or species are apart as well, the "junk" DNA will diverge at a fairly steady rate over time.

    So, cute trick, but that's all.
    • DNA that isn't functional has a high rate of change. If it's wrong and functional it dies, and only correct copies live on. If it's just data, being wrong does nothing and just keeps degrading further. This is also how we figure out how far distant relatives or species are apart as well, the "junk" DNA will diverge at a fairly steady rate over time. So, cute trick, but that's all.

      C'mon, give it a fair chance! Let's say that the researchers surround the message in a contiguous block of text meant simpl
  • by flanktwo (1041494) on Thursday March 01, 2007 @01:59AM (#18191268)
    100 bits ought to be enough for anybody.
  • by Anonymous Coward
    I haven't seen a single post by a biologist yet pointing out that if you start inserting arbitary data
    into "spare" DNA then sooner or later you are going to create a lethal pathogen - purely on the basis
    of probablity and statistics.

    Of course you can be sure the one that wipes out all life on Earth will turn out to be an Mp3 encoding
    of a Britney Spears tune.
  • They are talking about storing digital data on bacteria, so how are people millenia down the track meant to decode it? Like do we store pictures as Jpeg? Do we encode text as Unicode? What I would really like to see is bacteria that I could store all my pictures onto, and to look at them all I have to do is throw some bacteria on a wet floor and wait for them to appear. For a slideshow think of a Conways Game of Life effect. You could control the speed of the slide show by controlling the temperature.
  • Uh oh (Score:3, Funny)

    by AndroidCat (229562) on Thursday March 01, 2007 @02:09AM (#18191322) Homepage
    Don't tell AOL about this. I, for one, do not welcome all the envelopes full of "starter" bacteria.
  • Old news (Score:4, Informative)

    by gessel (310103) * on Thursday March 01, 2007 @02:29AM (#18191414) Homepage
    Joe Davis did this more than 17years [viewingspace.com] ago.

     
  • "Jimmy clean your room! Its disgusting!"

    "What! And lose all my data!?"
  • Compact DNA (Score:5, Interesting)

    by DrKyle (818035) on Thursday March 01, 2007 @02:51AM (#18191486)
    Bacteria, due to their rapid rate of replication (short generation time) are very prone to selection. There would be a fitness decrease to carry around this useless DNA, especially in redundant copies. Because of this, over time the mutants which had this "data" deleted would replicate slightly more quickly and these footprints in the sand would be washed away. This is the whole reason bacteria have compact genomes, redundancy and garbage are a waste of energy to replicate every generation making them weaker than their optimized counterparts.
    • by Viol8 (599362)
      Quite. These guys might know information storage retrieval theory but they seem to know jack sh1t about natural selection. Perhaps they're based in Texas? :)

      Seems to me this is a 3rd rate solution looking for a problem anyway not to mention the fact that since DNA used base 4 why store the data in binary base 2? You're wasting 75% of the storage ability.
  • It occurred to me...Could this encoding be vulnerable to a sort of 'buffer overflow' type attack? i.e., if the data encodes for the duplication of the 'data' DNA, wouldn't it be possible, by artfully crafting the data, to compel the bacterium to produce an altered copy that would do other than its designers intended? It seems like this could be very useful, or potentially very dangerous.

    • Friend, why not admit it? Like the rest of us, you're trying to understand what went so wrong in Anna Nicole's and Britney's lives.
  • if you combined them into a RAID array, would that give you better performance, or just wipe out all your data?
  • Good grief. It takes long enough to restore data from a tape backup. I have a hunch that it could take the resources of a "CSI: Las Vegas" crime lab to approach a reasonable restoration rate.

    "The bad news is that the flooded data center is covered in black mold. The good news is that the DNA of the mold contains our backup so we'll have the center up and running in a year or two! Less if you're willing to put up with some minor upper respiratory issues."
  • Well I guess you need alot of error checking and all that, and lets simplfiy it by saying that all of those 100b can be used to store data. That would mean about 7 Terbytes of data stored in 2^40 (10^24) bacteria, if you put these bacterias in a long single line you will get something that's 11 kilometers long.

    Bacteria diameter: 0.1 micrometer
    Sequence ID (SID): 40 bits
    Databits (D): 60 bits
    Maxstorage: 2^SID*D about 7680 Gigabytes

    this is not even pseudoscience.. ;-)
  • Cleaner mistakes the bacteria store for some mold and sprays it with a disinfectant....

  • It becomes schlock! [schlockmercenary.com]



    OK, that being on topic kind of scared me.
  • Copyright 2008, All Rights Reserved

    Copying Illegal.

  • All your base pairs are belong to us!
  • This idea was already proposed by (at least) Jaron Lanier of Virtual Reality fame. In 1999 The New York TImes asked for submissions by various tech-notables and others to design a "time capsule" that would be filled on Jan 1 2000 and opened (hopefully not before then) on Jan 1 3000. I believe the winner would see the design actually built.

    Anyway Mr. Lanier proposed only party tongue-in-cheek that they encode the data in the most indestuctrable, pervasive, consipcuous organism around (at least in New York)
  • Surely the encoded information (although useful to us) is completely useless in terms of increasing the likelihood of survival. So surely it would naturally decay away due to mutations etc. i.e. There would be no selection pressure for keeping the sequence.
  • Wonderful, now instead of my myspace antics just wrecking my next job interview, they can haunt my great-great-great-great-great-great-great-great-gr eat-great-great-great-great-great-great- great-great-great-grandkids, too!
  • http://www.schlockmercenary.com/d/20011216.html [schlockmercenary.com]

    In a few million years they will become sentient, and very violent.
  • 25 terabytes inside, between the potato salad and the stuff in the cool whip container (whatever it once was,) and gigabyte ethernet out to the rest of the house.

    got that already, all I need is to put the network card in the icemaker slot...
  • 42 (Score:3, Funny)

    by Alchemar (720449) on Thursday March 01, 2007 @11:40AM (#18194554)
    They can actually store 7 x 6 in a DNA sequence for furture generations to read? I wonder what the question would read in about 3 million years. The power of DNA is to corrupt itself slightly.
  • by guruevi (827432) <evi@smokingcCOFFEEube.be minus caffeine> on Thursday March 01, 2007 @12:12PM (#18194962) Homepage
    ...bacteria store YOU... especially if you are addicted to the Intarhweb
  • ...bugs with buffer overruns. Imagine writing DNA to somewhere one shouldn't be writing.
  • by dantho (1070282)
    well, this is not news really. joe davis (MIT) suceeded doing this several years ago. he recoded E.COLI bacteria - taken off of space detritus. read more: Scientific American [viewingspace.com]

    dont wanna click: here is some nice info about him:
    * Expelled from three high schools and two colleges: for writing about atheism, refusing a haircut, making a still (which exploded), being elected student body president on a "free marijuana" platform and working on an underground anti-war newspaper.

    * Walked into the M.I.T. Cente

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