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Data Storage Science

DNA For Information Processing and Data Storage 234

Posted by CmdrTaco from the but-how-many-mp3s-can-it-store dept.
Haydn Fenton writes "Here is an article on using DNA for data storage and even information processing. From the article, "The DNA molecule - nature's premier data storage material - may hold the key for the information technology industry as it faces demands for more compact data processing and storage circuitry. A team led by Richard Kiehl, a professor of electrical engineering at the University of Minnesota, has used DNA's ability to assemble itself into predetermined patterns to construct a synthetic DNA scaffolding with regular, closely spaced docking sites that can direct the assembly of circuits for processing or storing data.""
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DNA For Information Processing and Data Storage More

DNA For Information Processing and Data Storage

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  • ha (Score:1, Funny)

    by Anonymous Coward
    i hope the feds don't find any copyrighted material stored in my DNA...

  • It works on so many levels (Score:5, Informative)

    by antimatt ( 782015 ) <xdivide0@gmail.com> on Monday December 20, 2004 @04:19PM (#11139873) Homepage
    And another thing: chemically, DNA is almost heroically unchanging. It is among the most unreactive, inert molecules in the biological world. That means data integrity, a Good Thing.
    • ... chemically, DNA is almost heroically unchanging. It is among the most unreactive, inert molecules in the biological world. That means data integrity, a Good Thing.

      Good point.

      When DNA does go bad, typically what happens is that the telomeres [nih.gov] wear out, leading to cell death.

      -kgj

      • Re:DNA heroically unchanging (Score:5, Informative)

        by InternationalCow ( 681980 ) <[moc.cam] [ta] [lesneetsnaveciruam]> on Monday December 20, 2004 @04:34PM (#11140082) Journal
        Good point indeed but you misunderstood. DNA inside the cell IS changing all of the time although changes to its chemistry are being repaired all the time. Telomere change is something else, that happens at cell division. Higher-order structure, like folding, also changes. What the parent meant is that DNA, when taken out of the cell, is very very stable with most of its primary and secondary structure remaining intact over a long long time (see extraction from Neanderthal bones). However, the point of using DNA as a scaffold for the assembly of information is not in its stability per se. It's in its ability, per its repetitive structure with lots of nice modifiable side chains available, to direct assembly of other molecules. This is what is meant, methinks.
        • However, the point of using DNA as a scaffold for the assembly of information is not in its stability per se. It's in its ability, per its repetitive structure with lots of nice modifiable side chains available, to direct assembly of other molecules.

          Thanks for the clarification.

          -kgj
        • although changes to its chemistry are being repaired all the time

          How about this for redundancy/error correction? DNA could yield almost inconceivably high storage values. Replication and repair could form a futuristic form of data integrity protection and duplication abilities. Want to copy your dish (petri, that is), have the DNA "replicate" itself - no hardware needed.

          Petri-dish is a joke of course, but one wonders what the optimal instrument for storing such data would be?

    • DNA does not clone perfectly (Score:1, Interesting)

      by Anonymous Coward
      While it is self-repairing, changes do occur from time to time during cell division, introducing errors.

      A 100th-generation copy of your favorite MP3 may sound as bad as a 100th-generation analog copy. Maybe not quite that bad, but the md5's won't match.
    • On the otherhand the world is filled with enzymes called DNase that will willingly eat your TB DNA storage in no time.

      Siliconase however does not exist.

    • D'oh (Score:1, Funny)

      by Anonymous Coward
      That means data integrity, a Good Thing.

      So MySQL won't support it, then---but you can do it in the application layer.

    • Re:It works on so many levels (Score:1, Interesting)

      by Anonymous Coward
      See here. [slashdot.org] The data aren't being stored in the DNA, they're being stored in a magnetic layer on top of the DNA. The DNA sequence just drives the granularity of the magnetic layer. (To be precise, all this should be expressed in the future tense but I don't feel like backteracking...)

    • And it's really fun to make backups.... (Score:1, Funny)

      by Anonymous Coward
      Sex as a backup device!!!! That's way cooler than tape drives.
    • Disclaimer: IANA[Molecular Biochemist/Geneticist]

      I'm not so certain that's something to brag about in this case. DNA may be stable, but DNA replication is not always reliable and accurate. Genetic mutations are common - they are the result of random errors in the replication process. Some organisms have turned really rotten replication accuracy into an advantage (e.g. HIV, which mutates so fast that it has demonstrated an amazing ability to survive everything science has thrown at it). Other organisms
      • Well I quite certain they will not use 1 dna strand to store the data... they will use lots. See it as RAID but then with really cheap disks... and millions of them. As long there is no heavy selection on the replication (there is a bit of selection: AT bonds only have 2 H-bonds while CG has 3), it should be very accurate.

        btw HIV is RNA (retro) virus

      • Re:It works on so many levels (Score:4, Interesting)

        by jhoger ( 519683 ) on Monday December 20, 2004 @05:00PM (#11140388) Homepage
        The solution to such problems is redundancy. One efficient form is padding with extra bits to add error correcting codes.

        Science fiction may have an answer too. I believe the Slavers [Niven, Known Space series] engineered giant food animals (with intelligence just because the Slavers were really mean) that had specially engineered DNA so that they would not be impacted by radiation. As you say, mutation is necessary in evolving systems, but if one were engineering a system, you'd want to take that out of the equation.

    • Viruses (Score:5, Funny)

      by goombah99 ( 560566 ) on Monday December 20, 2004 @04:41PM (#11140170)
      So the equivalent of a SQL, insert field command, will be a retro-virus? Will my database be down...with a cold?
    • It is among the most unreactive, inert molecules in the biological world

      The backbone of DNA is very stable, but the bases definitely do not fit your description (indeed, I smell troll). Bases can be oxidized (drink your anti-oxidants), thymines can be fused (UV light causes this), etc. The reason DNA retains such high fidelity over such a long time is because there are enzymes in the nucleus that are specifically designed to repair these unwanted changes (for example, 8-oxoguanine is repaired to guanine

  • 640K DNA molecules... (Score:3, Funny)

    by GillBates0 ( 664202 ) on Monday December 20, 2004 @04:20PM (#11139887) Homepage Journal
    ought to be good enough for anybody.

    -GillBates0.

  • So how long... (Score:5, Interesting)

    by JossiRossi ( 840900 ) on Monday December 20, 2004 @04:20PM (#11139889) Homepage
    How long until Religious Nuts start claiming to see hidden messages encoded in our DNA telling us to love Jesus?
    Or
    How long until spies pass messages along in the form of biological matter by sneezing into a tissue?
    Or
    How long until we can buy books in readable vials full of liquid?

    The possibilites are endless and cool but of course it will probably just be used to sell us Coca Cola... so much wasted potential.

    • Re:So how long... (Score:5, Funny)

      by savagedome ( 742194 ) on Monday December 20, 2004 @04:27PM (#11139972)
      How long until Religious Nuts start claiming to see hidden messages encoded in our DNA telling us to love Jesus?

      Each DNA strand is a number. Like the Hebrew A, Alef is 1. B, Bet is 2. You understand? But look at this. The strands are inter-related. Like take the Hebrew word for father, 'Ab' - Alef Bet... 1, 2 equals 3. Alright? Hebrew word for mother, 'em' - Alef Mem... 1, 40 equals 41. Sum of 3 and 41... 44. Alright? Now, Hebrew word for child, alright, mother... father... child, 'Yeled' - that's 10, 30, and 4... 44
      • 9:32 Restate My Assumptions.

        Been too long since I've seen Pi =) So the 3 word quote I gave is probably wrong.

      • Re:So how long... (Score:4, Insightful)

        by leroybrown ( 136516 ) on Monday December 20, 2004 @05:17PM (#11140576) Homepage
        For the love of god, who in the hell thought this was anything but funny? Look people, the universe does not give a rat's ass that we count to ten. That is, the fact that we have ten digits in our numbering system is COMPLETELY arbitrary. So is the fact that we have 26 letters in our alphabet. I guarantee you all that if we had four fingers on each hand like the Simpsons characters, we'd be counting in octal. Anyone that manages to apply any sort of relation between letters and numbers to come up with some sort of code which bears any sort of relevance is deluding themselves.

        Think about it this way... the Bible was originally written in Hebrew. The Hebrew alphabet has 22 letters. Do you really think that the Christian God (should he exist) thought far enough ahead to include people in the bible who numerological name conversions would apply in English? No, that's absolutely absurd.

        This is why I swerve to hit these wacky numerologists out there. They're so blissfully ignorant of the arbitrariness of our numbering system and number of letters in our English alphabet that they try to apply some grandiose scheme to letters in order to convince people that they're some kind of mystic.

        • Do you really think that the Christian God (should he exist) thought far enough ahead to include people in the bible who numerological name conversions would apply in English?

          Although I absolutely agree with you in regards to these crackpot code schemes, your reasoning here is flawed. The Christian God, as taught in the Bible, is omniscient (all-knowing) as well as sovereign (in control). He is outside of time and knows exactly what the future holds. Therefore, He certainly could think "far enough ahead

          • So, do you believe in the omniscient God, or not? If so, why did he make man to fall?

            • Yes, I do believe in an omniscient God.

              If so, why did he make man to fall?

              Quite honestely, I do not know. Why did He create the universe at all. It is not as if He needed it. I suspect the truth relies somewhere in the realm of creating a being that could choose to follow Him and so that He could communicate and relate with them -- somewhat like a RPG developer. It would be much more thrilling to be able to create a truly AI game character that you could talk to and relate with rather than a scripted

              • I don't see how God could be omniscient and still think the choices we make are interesting, since he to him they appear scripted just like bad RPG NPCs. But the moment he makes the script interesting, with some fuzzy or random or chaotic function, then the devoloper loses his omniscience, since he can't possibly know what his own creation will do next.
          • Christianity went through a period very early (from about 150 AD to a time a little past Constantine's conversion, say 350 AD at the latest), when the biggest heresy was called Gnosticism. The Gnostics were big on hidden messages, secret meanings only the elect could know, codes and symbols, and so on.
            The basic reason for rejecting their ideas was when those ideas were reduced to simplest common assumptions, the Gnostics believed in a God who would damn all the stupid people just for not being smart eno
            • For a comment on a geek playground (read "Slashdot") that is a pretty good description of the God's purpose for the Bible. You are the first person, I've seen on Slashdot that seems to have any knowledge of church history. I would agree with you and I don't think the Bible was meant to be a history, math, cryptography, astrology or sociology manual. It pertains only to God's relationship to humanity, faith and salvation. It discusses and mentions specific places and names but overall that is not the purpose
    • Or
      How long until someone injects this crap into themselves and brings about the end of the world?
      [cough]Darwins Radio[/cough]

      How do you use here w/o the damned site censoring out the funny fake HTML tags.
    • When the DNA could be carried as data in ones body, I'd be be super-paranoid about viruses. If you were captured, it could carry the 2900AD version of "this message will self destruct" causing you to crap your pants, go blind, mute, and then expire...

      Integration of technology and biology has scary possiblities... especially in nanotech.
  • I'll take a 5TB kidney and a 9TB heart please. Oh and while you are at it, staple my stomach and squeeze all of the storage you can from the excess. I'm sure you'll get a decent amount.
  • I remember hearing about this originally nearly 10 years ago now. I remember bringing it up in a discussion on Usenet, engendering many "It will never happen" trolls...still seems a few years off though from consumer product?

    • Re:The things people doubt (Score:2, Informative)

      by Anonymous Coward
      This has (essentially) nothing to do with older ideas of storing data in DNA sequences. The DNA is being used here as a scaffold to lay down a particularly dense array of unformatted storage material.
    • I studied this at uni as part of my (*abortive) MSc degree;

      I was looking into genetic algorithms at first, then decided that to really understand genetic algorithms I should look at nature and went and studied cell bio and genetics. For a comp-sci guy that was a humbling experience... we think that we are so smart with our computers but they have nothing on the simplest of organisms. Anyway, where was I oh yeah

      Leonard Adelman (sp?) did some really interesting work with DNA computing (about 10 years ago, p
      • As I remember- it was the RNA stuff that I read about, basically switching from base-2 to base 4 (GATC) encoding to get extremely dense storage.

        Protists are awesome; our trick, as multicellular organisms, is that we build houses out of lots of bricks. But protists build an entire house out of just *one* brick. I think thats impressive.

        I agree- it's amazing how much is packed into a single cell organism.
        • "I agree- it's amazing how much is packed into a single cell organism."

          they are so sophisticated; one of the things I always wanted to try was putting protists through the kind of cognitive psych tests that they use on rats and pigeons to guage their intelligence and ability to learn from experience. I have a suspicion that there would be some surprises..
          • I wouldn't doubt it- there's got to be some instincts in there somewhere. I seem to remember a theory about mitochondrial memory some time back- wouldn't surprise me a bit if a protist had enough mitochondrial DNA to form some sort of a memory structure to carry that form of information.

  • SCO and DNA (Score:4, Funny)

    by lordsilence ( 682367 ) * on Monday December 20, 2004 @04:22PM (#11139911) Homepage
    Just wait till SCO find infringing code in YOUR DNA..
  • DNA "tiles" that spontaneously assemble in a predetermined pattern to form a sheet of molecular fabric, much like corduroy.

  • Slow Posting (Score:5, Funny)

    by ClownsScareMe ( 840001 ) on Monday December 20, 2004 @04:24PM (#11139931)
    Could people be *gasp* reading the article?

  • base 5 computing? (Score:1, Insightful)

    by Chillybott ( 835894 )
    seems to me that this would be the big benefit, that rather than base 2 for data storage, you could use base 5, with each slot value as 0, 1, 2, 3, or 4 based on having no protien, a, g, t, or c in the "slot" - giving a larger number of values (and therefpre addresses) per slot

    (base 5, would the 'slots' be called "quints" - not sure)

    I would wonder - though, how quickly data transfer would really be....cell replication takes awhile because the DNA splicing takes a long time, right?
    • Your post shows a complete lack of understanding of DNA completely. Please don't post about this again.
    • wow this makes me shiver when I read it.

      1. it's spelled protein.
      2. It can only be a, c, g, t in dna
      3. those aren't proteins they are bases
      4. Proteins are coded by dna, they do not comprise dna in any way.
      5. Dna doesn't get spliced during cell replication. It gets copied.
      6. therefpre isn't a word.

  • Nasty unforeseen consequence (Score:5, Funny)

    by borroff ( 267566 ) on Monday December 20, 2004 @04:24PM (#11139940) Journal
    Unfortunately, when the tune "Jingle Bells" is coded in DNA for storage, it turns out to be a version of the flu...
  • The article states that this technology could be used to allow for faster recognition technologies, but can this be used to create a computer in the more typical sense?

    I find this to be an extremely interesting and inventive process, but from the article I can't really decide if it has, or ever will have the ability to make something that isn't just a repeated pattern. Does anyone else know a little more about this technology?

  • Damn, now where did I put that strand of DNA with all my pr0n.
  • DNA is just a biologic/chemical process of storing info. The smallest bit of information you could reach has already been hypothesized to be an electron...polarize it one way and make it positive (one) and the opposite (zero). Last time I checked electrons are smaller than DNA. But could we go smaller? Quarks? Neutrinos? Photons?...as the smallest components of information?
    • You can store information on anything, as long as you keep the temperature low enough or the energy high enough. The minimum energy per bit you need is kT/6, where k is Boltzmann's constant and T is the absolute temperature of the medium where your information is stored. Sure, you can store a bit of information as the polarization of a free electron. But unless the temperature is low enough, your information will be quickly randomized by thermal noise. Or else you can have your electron in an atom, inside a
  • Wow, it looks all you need is some velcro and corduroy pants...

  • DNA plus Information Processing equals... (Score:3, Funny)

    by amstrad ( 60839 ) on Monday December 20, 2004 @04:32PM (#11140050)
    ...Eddie, your super friendly shipboard computer.
  • In the I, Jedi book, there was a reference to this type of technology, wherein someone would sequence flowers with DNA that contained encryption keys to a set of data stored elsewhere. Very useful for blackmail. Seriously, though, if we're approaching SW technology, I'm happy. When're the hyperdrives and usable ion drives coming?
  • no more electronic viruses. Now we can have the real thing.

    Not only does your computer get infected....so do you!.

  • Performance Limits on Chemical Computation (Score:5, Informative)

    by tjic ( 530860 ) on Monday December 20, 2004 @04:34PM (#11140083) Homepage
    For those interested in such things, a friend wrote his PhD thesis on defining the limits of achievable DNA computation:

    Performance Limits on Chemical Computation [dyndns.org].

    • Wow, excellent link.

      The Slashdot-relevant portion of the abstract:

      I compare the maximum possible performance of proposed DNA computers from the literature with current commodity electronic computers, and conclude that diffusion-driven, DNA hybridization based computers cannot exceed the performance of current electronic computers by more than a factor of 40,000, and probably by much less.

      This doesn't speak to using DNA as a construction scaffolding, which I am not skeptical of, but DNA computing has never

  • I think This technology wont take off too well... Way too small - "Oh, nuts..I dropped my Unreal 2008 DNA vial..There it goes spewing all over the floor" Or maybe..."Oh no..the cat, it ate my DNA processor!"
  • Well then, if all said is true, then I somehow must find a way to hook a USB 2.0 port into my body! Now, if I put the power wires here, and the data wires here...
  • Heh heh heh. Richard Kiehl. DNA.

    Am I the only one who thought of the MST3k episode where they did "The Human Duplicators?"

  • I would prefer to use RNA (Score:4, Funny)

    by dfn5 ( 524972 ) on Monday December 20, 2004 @04:43PM (#11140190) Journal
    Sure, go ahead and use DNA, if you want your data to mutate.
    I will use RNA (Raided Nucleic Acid) instead.

  • Carl Sagan pointed out in Dragons of Eden (Score:5, Interesting)

    by museumpeace ( 735109 ) on Monday December 20, 2004 @04:45PM (#11140218) Journal
    [late 70s] that DNA was the only persistent data storage media nature had until we apes invented languages that we could symbolically preserve. All that has essentially progressed, and what has been changing rapidly with advances in biotech, is the speed of data access into DNA. 5 yeas ago, the best guess [and the big money of govt and industry] was that it would take us 10 years to transcribe the human genome...and now thats already done. We are getting faster even faster than we expected. [that technological acceleration could be partly attributed to the open exchange of techniques and discovered sequences that the consortium of biochemists had agreed upon at the outset of the project...kind of like developing products in open source]
    When that data access speeds up another 8 or 10 orders of magnitude and is both R and W,[and not much sooner!] we can talk about DNA as if it were magnetic media and seriously talk about its applications...Makes you wonder if the lessons of open source are going to have to be rediscoverd as we further exploit what software engineering has to teach us about handling DNA.

  • DNA computers (Score:4, Interesting)

    by wronski ( 821189 ) on Monday December 20, 2004 @04:46PM (#11140228)
    There has been some discussion about using DNA as a massively parallel computer. Suppose you encode data in a DNA sequence (input), then somehow act on it (running a program), and then read the resulting altered DNA. You have a computer, albeit somewhat slow and not terribly practical. Now imagine you start with not one but *billions* of different DNA sequences.You "run" the program over all these inputs simultaneously, and obtain billions of possible outputs. You can then use some chemical tag that binds itself to the 'correct' answer. You now have a massively parallel computer with negligible power consumption in a test tube.

    This sort of DNA computer could be useful for a number of problems that involve a lot of trial and error, such as protein folding. In a paper some years ago some scientist managed to solve a traveling salesman problem using one such computer. They generated different strands corresponding to each city, and let them mix in a tube randomly to produce different candidate 'paths'. Then, they used some chemical selector (the tricky part) to eliminate the strands corresponding to invalid paths. Left in the tube were all valid paths, which could then be easily replicated using PCR.

    I couldn't find the original paper, but a pretty good explanation can be found here [howstuffworks.com]
    • Heck, if you want to use DNA to study protein folding, why not just code the protein in DNA, mixit up with some transcriptase, some ribosomes, some RNA and some amino acids and fold the darn thing?

  • I can just hear it now... (Score:3, Funny)

    by Bhasin_N ( 838449 ) on Monday December 20, 2004 @04:47PM (#11140254)
    "In Breaking news, a minor short circuit has caused a freak mutation at Genetic Information Inc. causing all the chips to asexually reproduce and take over the coffe machines"
  • Art imitating life: In ST:TNG a Klingon was found to be stealing secrets by reading information off some chips. The raw data was encoded into inert DNA chains and eventually injected into a person. In effect anyone could become a roaming hard drive and not even know it.
  • First of all, it is super-twisted. That means that you've massive latency in accessing it. Secondly, it is linear, which means that finding the Nth "word" is going to be HORRIBLY slow. Thirdly, the existing duplication system is "good enough" only on a large scale. Finally, the protein generator has no exception handler, so if the raw materials aren't available, there is no means of handling the exception.

    Having said all that, if you've massive archives where you're less interested in immediate access as

  • I just finished reading Richard Dawkins' The Selfish Gene, and was thinking about some stuff like this. Note that I'm a computer engineer and don't know much about this stuff:

    Evolution has worked for billions of years. I'd say it's worked out quite a few of its bugs. So why don't we copy it when doing computing? I think the book stated (VERY generally, I assume), that there are 4 bits that get used to build with DNA - A, T, C, and G... obviously this has advantages, so why are we using binary computers

    • The reason we use binary computers is because computers are based on transistors operating in saturation mode, and long-term storage is based on alignment of magnetic materials or optically reflective pits. I suppose we could have computers whose basic unit of data had more than two levels, but it would be a lot less reliable than our current technology until some significant problems could be solved (such as getting these non-saturation-mode transistors to work well at very, very high speeds).

      On the othe
  • The technology could help computers identify objects in images with something approaching the speed of the human eye and brain

    Man, always thought my computer had no trouble winning against my brain in terms of speed.

  • By the way, if you want some good info on home hacking of DNA, proteins, etc. check out DNAhack.com [dnahack.com].
  • Imagine yourself: a beowulf cluster of these things.
  • To think that when I was born, the idea of using DNA to identify suspects at a crime scene was unheard of, but now criminals have to be mindful of hair loss, dandruff flakes, and any sort of DNA they might accidentally leave lying around that could incriminate them.

    Computers used to cost the government and corporations huge amounts of money. The desktop computer competition brought these fees down tremendously and even when governments, companies, and universities find a need for something different, they

  • Will applications released for free use with DNA RAM be known as 'Open Wound'? [makes hurried exit]

  • hmm... (Score:2)

    by Siva ( 6132 )
    "Solylent RAM is people! It's people!!!"

    hmm...maybe not...

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