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Biotech Data Storage Science Technology

Scientists Store Entire Textbook In DNA 160

Posted by timothy from the ok-but-where-are-the-tiny-spectacles? dept.
sciencehabit writes with this mind-boggling bit from Science Magazine: "When it comes to storing information, hard drives don't hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare. All of this has been mostly theoretical—until now. In a new study, researchers stored an entire genetics textbook in less than a picogram of DNA — one trillionth of a gram — an advance that could revolutionize our ability to save data."
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Scientists Store Entire Textbook In DNA More

Scientists Store Entire Textbook In DNA

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  • HOSTS file would have prevented this. (Score:1)

    by Anonymous Coward

    nummynuts

  • I am sorry. I opened Pandora's Box.

    • Re:Brewster you've screwed us all! (Score:4, Funny)

      by butalearner ( 1235200 ) on Thursday August 16, 2012 @04:07PM (#41016761)
      I am disappointed that nobody has pointed out that we can now measure human mass in terms of Libraries of Congress. For example: Americans can now proudly proclaim that we carry, on average, at least ten million more Libraries of Congress than citizens of any other country. Or: I really shouldn't have eaten those atomic wings, I just dropped two million Libraries of Congress from spending so much time in the bathroom.

      • Why did the scientists do this?

        Are they planning to add a EULA, manifesto or wiki-backup to some biological creation?

        It could be handy if DNA was well-commented source code. Hidden jokes anyone?

        Better that than cookie storage.

  • Take it one step further (Score:5, Interesting)

    by Intrepid imaginaut ( 1970940 ) on Thursday August 16, 2012 @02:33PM (#41015319)

    Store data in DNA, then figure out a way for our brains to interpret it as knowledge. Imagine being born with the combined understanding of all of the major fields of science, history, languages, crafts, trades, from day one.

    • Re:Take it one step further (Score:5, Insightful)

      by Dyinobal ( 1427207 ) on Thursday August 16, 2012 @02:35PM (#41015349)
      Knowledge but not understanding. I think it is important to remember that those are two different things. Still it would be pretty neat.

      • Re: (Score:1)

        by Anonymous Coward

        If you could do it with knowledge, you could also do it with understanding.

        • Comment removed (Score:4, Interesting)

          by account_deleted ( 4530225 ) on Thursday August 16, 2012 @02:48PM (#41015551)
          Comment removed based on user account deletion

          • Re: (Score:2)

            by icebike ( 68054 ) *

            At what point would individuality be replaced with fabrication?

            At what point would our library of congress stored in DNA mutate into something totally different?

            When the Gettysburg Address starts sounding lib Bob Dylan or worse yet, mutates into a hand with 7 fingers?
            Or would you simply call that evolution of knowledge, and line up for your smart-shots at the local library?

            • At what point would individuality be replaced with fabrication?

              At what point would our library of congress stored in DNA mutate into something totally different?

              What evolutionary benefit would a mutation of encoded history serve? Any distortion would simply be part of random noise and wouldn't take over the general population. Moreover, I have a feeling someone would consciously notice if they thought the Gettysburg Address started "Three score and..." when everyone else said otherwise. Encoded knowledge wouldn't preclude the ability to obtain knowledge during your lifetime.

          • good point. anyone with enough money to make this happen is going to give you the version of history that they wrote.

          • Re: (Score:2)

            by Kismet ( 13199 )

            At what point would individuality be replaced with fabrication?

            Isn't that what our mass-production consumer society does already? The question is, how much of who we think we are is due to some sort of fabrication?

          • Probably at the point when the man with the goatee leaves an origami crane outside our apartment.

        • Re: (Score:2)

          by sjames ( 1099 )

          How? We have yet to manage such a task in any form. We know how to lead a person to understanding with varying degrees of success but it has never been directly transmitted before.

      • What's it like to have knowledge that you don't understand? That concept doesn't make sense to me.

        • Re:Take it one step further (Score:4, Insightful)

          by __aaeihw9960 ( 2531696 ) on Thursday August 16, 2012 @02:50PM (#41015573)
          Knowledge with no understanding = Memorization. I can memorize the parts of the brain with no understanding of how they work. To do anything useful with the information you have to be able to apply it.

          • Re: (Score:2)

            by xevioso ( 598654 )

            Perhaps one of the things that can be encoded into the DNA is information on how to apply it. This would "interface" with our own experiences and our background would allow us to make use of some of this information, but contained within the information could be information on how to make use of it.

            • This brings up the problem of incompleteness and ontology.
              You can code every last bit of information that could be found in a car, but can you use that information alone to extract every possible use for a car? You still use your brain to process meaning and application even when you already have complete knowledge. That's how new things come about. If I knew absolutely everything to possibly know about let's say: a piece of piano wire, it still wouldn't contain any application of the piano wire further

          • Best I can figure, the old "knowledge" vs "understanding" is just a discussion of completeness. We like to think there's some kind of magic between the two, but I don't think there is.

        • What's it like to have knowledge that you don't understand? That concept doesn't make sense to me.

          For example, I know that some people hate math, but I don't understand it.

        • Re:Take it one step further (Score:4, Insightful)

          by Urban Garlic ( 447282 ) on Thursday August 16, 2012 @02:59PM (#41015739)

          > What's it like to have knowledge that you don't understand? That concept doesn't make sense to me.

          That would be like if someone told you about a concept, so you knew it existed, but it didn't make sense to you.

        • I can't think of an example from something that everyone should know, but I'll attempt to answer this.

          1) There are two tides each day, one when the moon is directly overhead, and one when the moon is directly underneath. Since the gravitational attraction of the moon causes tides, can you explain why there is a tide when the moon is directly underneath?

          2) The fourier transform converts from time domain to frequency domain; ie - it takes an audio WAV file of amplitudes over time and converts it to a list of

          • Re: (Score:2)

            by tibit ( 1762298 )

            Personal anecdote re.2, and I hope I'm not mixing it up too much. I eventually understood it in linear algebra. The integration happens to work like a dot product of two vectors, if you consider linear vector space of functions. If you think of abstract vector spaces, it becomes (eventually) quite blatant that it must be so. To me the big point was wrapping my head around the fact that "vectors of numbers" are merely representations of abstract vectors in a certain base, and that the abstract vectors are ju

          • Re: (Score:2)

            by Plunky ( 929104 )

            There are two tides each day, one when the moon is directly overhead, and one when the moon is directly underneath. Since the gravitational attraction of the moon causes tides, can you explain why there is a tide when the moon is directly underneath?

            Except that your statement is not actually true.. some places only have one tide per day, and even when there are two it is not directly aligned to the moon as the tides are caused by the water slopping back and forth, rather than following the moon around the p

        • You can memorize the multiplication tables up to 10*10, but if you don't understand why 10*10=100, you probably won't be able to do 15*34 or any higher numbers.

          You can memorize a few words so you can fill out a resume, but unless you know how to read, the you'll never be able to enjoy a good book.

        • Information is not knowledge. Knowledge is not wisdom. Wisdom is not truth. Truth is not beauty. Beauty is not love. Love is not music. Music is the best.

          -- Frank Zappa

      • Because we don't need the information in our DNA that is already present?

    • Re: (Score:2, Interesting)

      by Anonymous Coward

      Knowing mankind, they would use it so we're born with knowledge about who's in charge, the limits of our freedoms and the religion appropriate for your country.

    • Knowledge encoded in DNA would be cool, but it's not a very reliable method. DNA has a bad habit of denaturing if it gets too hold, or produces errors if not cloned properly (leading to a runaway cancer cell in some cases). DNA works "well enough" to get an organism to 15 years old & procreate itself to the next generation, but is far from perfect.

      • DNA works "well enough" to get an organism to 15 years old & procreate itself to the next generation, but is far from perfect.

        Even worse, it works well enough because there is a strong evolutionary pressure to keep it intact - any disabling change in the DNA removes the individual from reproduction, thereby keeping the population mostly clean of genetic problems. Unless the stored data participates somehow in introducing evolutionary pressures, it will degrade fairly quickly for sure.

    • Re:Take it one step further (Score:5, Insightful)

      by jader3rd ( 2222716 ) on Thursday August 16, 2012 @02:56PM (#41015691)

      Imagine being born with the combined understanding of all of the major fields of science, history, languages, crafts, trades, from day one.

      Isn't that what made the goa'uld so evil?

    • Until we figure out the means to update DNA remotely, this wouldn't be as awesome as it sounds. Your knowledge of history could be outdated as soon as day two. Science and languages would fall out of date only slightly less quickly. Crafts and trades would take longer, but would almost certainly be at least a little outdated by the time you were mature enough to enter the workforce. And all of this would be hard-coded into a person's knowledge, so overcoming that hurdle would likely be very difficult.

    • Re: (Score:2)

      by Gotung ( 571984 )
      How do you overcome knowledge that is hard coded in your DNA? When you go beyond indoctrination, and start implanting knowledge as base instinct it would likely be near impossible for that being to believe anything that was contrary to that implanted knowledge, much of which would be contradictory or turn out to be just plain wrong. I think your being would be mentally crippled and tragic instead of the glorious super genius you imply they would be. Probably more of a super-rainman then a fully functional
    • This would be the equivalent of adding comments into some source code and expecting the compiled program to impart the knowledge. Cool idea, but we won't be programming genius babies this way.

    • Then something happens, random mutation, chemical poisoning, radiation, ... and then cancer starts. A cell containing some obscure text about homicidal geniuses becomes cancerous and spreads to the reproductive organs, and then happens to reproduce before they die. This passes on an overwhelming amount of information to an impressionable brain which then becomes an homicidal genius. Not to tip their hand too soon, they wait to unleash the homicidal nature of their being until they reproduce. Their offsp

    • How much unlearning will you have to do. Will it be worse then learning.

      Just compare our culture and understanding with life 30 years ago. We will be programmed with the latest and greatest Disco Dance moves, The threat ingrained in your system from the USSR. The process of learning is the process of change. Our Text books from a generation ago is rather different then todays text. Things have changed.

    • Or take it only a half step further, breed it, and see the finished product.
      • We just mated the complete Twilight saga with 1000 pages of Harry Potter Fan Fiction...

        There are some things that science should just leave alone.

    • Human engineering is bad not only because of intrinsic moral problems, but also because it would lead to societal catastrophe. Imagine multiple countries engaging in supersoldier arms race.

    • Comment removed based on user account deletion
    • Extraordinarily interesting, +6. Whether that is even vaguely practical is another matter, but it's one of the most interesting SF ideas I've heard in a long time. I'd include religion in there, an outsider's view of the history and theory of religions is a useful thing, and it would be interesting to see how a person's belief system develops with all of the information already there, good and bad.

    • Re: (Score:2)

      by ceoyoyo ( 59147 )

      The old learning by osmosis theory (falling asleep with your head on a textbook) except with a modern trendy biology twist!

  • But could we make backups? Oh, wait, never mind.

  • How fast? (Score:3)

    by cyberjock1980 ( 1131059 ) on Thursday August 16, 2012 @02:34PM (#41015337)

    It appears on the surface that the data isn't quickly(sub-ms speeds) stored or recovered. This technology could be very useful for backing up large quantities of data. The real question is how many MB/GB/whatever per second can be read/written to this new "media"?

    • Re:How fast? (Score:5, Informative)

      by coldandcalculating ( 1311907 ) on Thursday August 16, 2012 @02:56PM (#41015699)
      The fastest DNA polymerases can copy a template at around 250 bases/sec. Chemical DNA synthesis is much slower.

      As for read speeds, DNA sequencing can be done serially (500-800 bases in a matter of hours - 1 cent per base) or massively parallel (100-200 bases per read; 100 million reads; overnight - $1000 per chip by year's end?)

      Tools allowing for rapid synthesis (write) and sequencing (read) of DNA would enable a biotech revolution similar in scope and impact to the computing revolution of the last century. As far as I know, this technology is still incredibly far away, but definitely merits relentless R&D.

      • Re: (Score:2)

        by Cyberax ( 705495 )
        Also, common sequencing techniques require amplification of DNA and read it in very small batches (hundreds of base pairs). These batches then have to be painstakingly assembled - think about assembling a puzzle from a billion fragments, some of which are duplicated, overlapping and/or have errors.

        And such assembly is definitely not an easy process if you don't have a reference genome to help you.
    • Given the machine they used in the paper to read the data back, it would take about 10 DAYS to read out the data they encoded. The problem is that it takes that time to get any data at all. So they could parrallelize it to get better MB/sec (or realistically MB/hr), but with current tech, the latency is 10 days, with a theoretical maximum of 100gigabits of uncompressed data read out in that time, (but realistically much less since they rely on redundancy to reduce error, and have overhead for their encoding

  • In other news, they are now sued for copyright infringment. :-)

  • Genetically-Modified Schoolbooks? (Score:1)

    by Anonymous Coward

    Soon, students will be able to claim that their homework ate them!

    • Re: (Score:2)

      by Tablizer ( 95088 )

      Soon, students will be able to claim that their homework ate them!

      The assignment was about Soviet Russia, no doubt.
         

  • Man, are the educational publishers going to get cheesed about this.

  • "I still don't want your DNA anywhere near me, nerd!"

  • Skip the Library of Congress for once. Why not go for a small country, like Wales (no, not Jimmy or his deed). That would be an effort worth bragging about!

  • I would think that copying errors and degradation would be a serious issue if attempting to use DNA for arbitrary data storage. In organisms, we can even observe some segments of DNA(like those that code for elements of vital metabolic processes) are highly similar across a broad range of organisms, while non-coding or minimally important regions can vary wildly from individual to individual or even cell to cell; because the penalty for getting them wrong is so low...

    Unless the data you are interested in also have, by some impressive coincidence, vital biological importance cruft buildup(or even substantial deletion) could be quite rapid. DNA isn't without self repair mechanisms; but one of the big ones is 'mutants dying' rather than something more elegant.

  • Just in time (Score:4, Funny)

    by arielCo ( 995647 ) on Thursday August 16, 2012 @02:53PM (#41015629)
    The answer to the last Ask Slashdot: Protecting Data From a Carrington Event? [slashdot.org]:

    I've been wondering: is it actually possible to store or protect data in such a way that if such an event occurred, data survives and is recoverable in a useful form? Optical and magnetic media would probably be rendered useless by a large enough solar flare, and storing source code/graphics in paper format would be impractical to recover, so Slashdot, short of building a Faraday cage 100 km below the surface of the Moon, how could you protect data to survive a modern day Carrington event?"

    So, kactusotp, there you have it: splice it into as many mice / E. coli as needed, release into the wild.

    • Re: (Score:2)

      by Hatta ( 162192 )

      The real question is how you guarantee data integrity. If there's no selective pressure maintaining the data, mutations, insertions, deletions, etc, *will* occur. How do you checksum DNA?

      • The real question is how you guarantee data integrity. If there's no selective pressure maintaining the data, mutations, insertions, deletions, etc, *will* occur. How do you checksum DNA?

        Huh? DNA is being use as a storage medium. There is a chance for the protein strains to deteriorate or denature but DNA is no different than any other strain of proteins. You are assuming that this is being stored in a organism of some sort which could "evolve" or that is it laid out in any sort of helix pattern with a self-replication mechanism intact.

  • Meh (Score:2)

    by Artraze ( 600366 )

    Cool achievement, to be sure, but for data storage? There are a great many ways of achieving ultra high density data storage that have been performed in the lab and are 'only 10 years away'. The trouble always is the engineering: how expensive, how fast, how much, how reliable? One strand isn't too big a deal, but it'll only store maybe 1GB. Now you need thousands of strands and a way to page through them. And maybe a way to seek within them. Etc.
    Again, really cool accomplishment, but I can't see it b

  • What sort of textbook can you write with nothing but G, A, T, and C?

  • encoded an entire genetics textbook in DNA...

    Fundamentalists did the same thing. Here is the decoded version:

    G O D . D I D . I T

    • Re: (Score:2)

      by Empiric ( 675968 )
      Nah, anything that has specifically 23 pairs of chromosomes is expected to be able to infer it.

  • Another great high school excuse bites the dust.

  • Fovr sc9re+and sexen ypars agz ovr f{theRs bromght fprth *n th2s cont&nent a ne= natin, congeived in lkbprty, and dWdicmted tx the pr;pos|tion thqt alll mvn are creyted equap.

  • Star Trek (Score:3)

    by SuperTechnoNerd ( 964528 ) on Thursday August 16, 2012 @03:27PM (#41016179)
    There was a star trek episode where this klingon could inject himself with encoded top secret files. I see reality is catching up with sci-fi
  • You are now just getting deleting unneeded files.
  • You code inject secret message into pigeon DNA ...

    I think this was a plot of Star Trek TNG episode: some ancient part of our DNA had a message from our long, lost Creators.
  • Big Brown Bear?

  • Encode the data into DNA, then splice the DNA fragment into a self reproducing organism and release into the environment. You end up with trillions of copies of the original data distributed all over the world. (error correction codes would deal with transcription mistakes)

    Future generations, even future sentient life forms millions of years later would the be able to decode the data. It would be very obvious as soon as they had sequencing technology: organisms with large parts of their DNA that don't code

    • Re: (Score:2)

      by Jahava ( 946858 )

      Encode the data into DNA, then splice the DNA fragment into a self reproducing organism and release into the environment. You end up with trillions of copies of the original data distributed all over the world. (error correction codes would deal with transcription mistakes)

      Future generations, even future sentient life forms millions of years later would the be able to decode the data. It would be very obvious as soon as they had sequencing technology: organisms with large parts of their DNA that don't code for anything useful...........

      It's a cool thought. Another possibility, though, is that evolution would, within a few (relatively speaking) generations, completely reject the the superfluous DNA as inefficient and/or unfit. Duplicating it costs energy and matter, and transcription errors and/or cross-gene sharing may actually ruin critical parts of the animal. Given evolution's tendency towards optimization, it seems almost inevitable that the information wouldn't survive in even the short (again, relatively-speaking) term.

      Another indep

      • You've made a few errors in your fun theoretical musing:

        1) Most of our DNA is, in fact, superfluous, as far as we can tell. Less of is superfluous than we thought a few years ago, but more than we thought ten years ago.
        2) Evolution does not tend towards optimization. It trends towards "good enough". Extra DNA only matters if you're a bacterial cell, and the rate-limiting step in your growth is the replication of your entire cellular DNA. In many ways, for a human, noncoding DNA is beneficial - random er

        • Re: (Score:2)

          by Jahava ( 946858 )

          You've made a few errors in your fun theoretical musing:

          Oh goodie, someone who talks like this...

          1) Most of our DNA is, in fact, superfluous, as far as we can tell. Less of is superfluous than we thought a few years ago, but more than we thought ten years ago.

          Sounds like we've got it right this time, though! Assuming you're referencing Junk DNA [wikipedia.org], there's a world of difference between "no discernable function" and "superfluous". Additionally, even with an upper bound in DNA functional density, there's no reason to assume there isn't also an optimal upper bound to superfluous-to-functional DNA ratio. Adding a massive chunk of DNA to an organism is going to have some effect, you have to agree, and with no functional purpose t

      • Just to continue the musing...
        IF our (or some other species) did have data intentionally stored in their DNA it was presumably done in a way to allow it be deciphered after a long period of time, without a key, and with accumulated errors. I wonder if anyone has thought of how you might code such a signal, and what sort of analysis of patterns would let you detect it. Then - has anyone analyzed known "junk" sequences to see if there is encoded data. Imagine finding a prime-number sequence in DNA somewhere

  • If a gram of DNA can hold a Library of Congress we are going to need a new unit of measure here at database when having storage debates.

  • And finally Discovery channel can stop relying on animal sex to sell ratings ...
  • Good luck reading it for less than several thousand dollars. And I thought my textbooks were expensive.

  • I know you guys aren't fond of the metric system , but does data have to
    be measured in "libraries of Congress" ?

    Having never been to said library, this doesn't make much of an impression on me. Any official conversion ratio?
    Google claims 1 LoC = 235 TB.

  • I guess turnabout's fair play. They put a whole genetics textbook into a small amount of DNA. Somehow that seems nobler than the serious error of judgment I committed when I bought my "Victorian Underground Literature" textbook in a used book store. It probably had enough DNA in it to populate a small galaxy.

  • If you wrote the book into someone's DNA, you could be the book.

  • http://www.smbc-comics.com/index.php?db=comics&id=2122 [smbc-comics.com]

    Also, as far as prior art goes, when the New York Times asked a bunch of futurists what they would propose for the time capsule they were building for the year 2000 (this was for the millenial issue), Jaron Lanier (I think) suggested that information be DNA encoded and put into cockroaches. The thinking was that they were indestructible and still be ubiquitous in a thousand years.

    No mechanism for preventing copying errors was described though so it

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