Store Digital Files For Eons In Silica-Encased DNA

If there’s one downside to digital storage, it’s the short lifespan.  Despite technology’s best efforts, digital storage beyond 50 years is extremely difficult. [Robert Grass, et al.], researchers from the Swiss Federal Institute of Technology in Zurich, decided to address the issue with DNA.  The same stuff that makes you “You” can also be used to store your entire library, and then some.

As the existence of cancer shows, DNA is not always replicated perfectly. A single mismatch, addition, or omission of a base pair can wreak havoc on an organism. [Grass, et al.] realized that for long-term storage capability, error-correction was necessary. They decided to use Reed-Solomon codes, which have been utilized in error-correction for many storage formats from CDs to QR codes to satellite communication. Starting with uncompressed digital text files of the Swiss Federal Charter from 1291 and the English translation of the Archimedes Palimpsest, they mapped every two bytes to three elements in a Galois field. Each element was then encoded to a specific codon, a triplet of nucleotides. In addition, two levels of redundancy were employed, creating outer- and inner- codes for error recovery. Since long DNA is very difficult to synthesize (and pricier), the final product was 4991 DNA segments of 158 nucleotides each (39 codons plus primers).

Codon Wheel

Accelerated aging experiments, where the DNA was exposed to sustained temperatures up to 70ºC for 1 week, compared DNA encased in silica to DNA on other dry mediums, like paper or polymer. After one week, significant degradation occurred in all but the silica-encapsulated DNA. The silica provided complete isolation from the external environment. [Grass, et al.] noted that adding a layer of titanium dioxide to the silica adds protection from light, especially UV.  Thus, only the DNA from the silica was sequenced and decoded. Decoding began with the inner code, correcting any individual base errors. Sorting the sequences by index followed. Outer-decoding then corrected any errors in whole sequences or the recovery of lost ones. The overall results showed that not only did silica preserve the DNA the best, the error-correction allowed perfect retention of the original data.

The duration of the accelerated aging test corresponded to 2000 years. Additional testing suggested that storing the DNA in silica at -18ºC (such as at the Global Seed Vault) could stabilize it for over 2 million years, longer than mankind has existed. Potentially, all the information we’ve ever generated as a species could be stored in a soda bottle.

While the published article is only available for purchase, the supplemental information is publicly available and goes into a great deal of depth. We are simply blown away by this research.  One thing’s for sure: we’ll never have to worry about the Archimedes Palimpsest reading like bad fanfiction to our descendants!
[via Reddit]

58 thoughts on “Store Digital Files For Eons In Silica-Encased DNA

  1. According to wiki the “human genome has approximately 3.3 billion base-pairs”. If these are the same as the mentioned segments here, and if we know that the human dna contains plenty of redundant information, it would be more practical to create an information-virus, and let it replicate. Then we could all have all the information as long as mankind last.

    1. I was thinking along the same lines. We can “store” information in organism’s DNA. As long as the organism we choose pass on it’s DNA to it’s offspring the information is retained. Now we just need to find and catch one of these things to read the data. Haha. Who knows there might be a message in a bottle in our own DNA.

    2. the danger in this is that those virus cells replicate, and make mistakes while doing so. You wouldn’t want a virus that was made to infect every human to evolve a lethal trait to humans.

      1. Lethal traits tend to negatively impact viral fitness. The common cold (rhinovirii) has a high mutation rate, quite a bit of diversity, and is (true to its namesake) quite common. It’s likely to be an order of magnitude more serious a problem than a hypothetical engineered virus designed to not be a weapon.

        It’s odd that we’re afraid of genetically engineered virii, which will probably be medically useful with a little more work. I think guns are more frightening and have fewer medical applications!

        Anyway, genetically engineered virii do make OK movie plots, and all the much scarier stuff is sort of too complicated for 90 minute action films.

    3. I for one would personally make sure that anybody involved with making such a virus would be either executed or put in jail for the rest of their lives. And not a too pleasant a jail.

        1. It’s 2015, you have information about all the people who made internet statements and the followed through, from islamic idiots through russian rebels to the white house.

          Although you are 99.9% likely to be correct in my case. But you have no way of knowing that in advance. In fact I don’t even know, but if the US started to fuck with people’s DNA I’d seriously don’t know how mad a person would get. I mean that’s messing with the very fundamentals of both the people and their offspring, present and future.

        1. The issue here is not building custom stuff, the issue is the concept of forcing that on the world population without asking them. I call that an act of violence of extreme proportions.I would find the thought extremely offensive, and I’m sure half of the world population would agree. And some of those have big armies and nukes and what not.I remind you. I don’t imagine china and russia for instance would be thrilled to hear the US was spreading viruses to splice crap in human DNA. And I don’t think the EU would either, (but those are so under control by the US that it might have them grovel anyway.)

          And inf fact I think even the majority of the US would find it offensive. Especially if it’s scientific knowledge indicating evolution exists and such. So that religious madness might work in a positive way for a change.

          1. I was maybe a bit careless with my words, I did not meant to imply that we force the information-virus on everybody. I suppose in Switzerland you can put it up for vote if the population wants to keep official data in themselves or white bottles. There are ways for viruses tailored to groups or even single persons. So the fun would be carrying your OWN relevant data with you – or the family tree and all ( I mean birth certificates, wedding pictures and such ) literally in the family. AFAIK you can carry all your mp3s in your blood. Maybe it would make the copyright industry happy as your music collection would die with you. Of course you would be banned from giving blood for the rest of your life :D.

            I beg to differ, that it would be scientific knowledge indicating that evolution exist. You can interpret it so that DNA is a program ( which it is anyway ), that could be written by programmers and that tips the scale to the side of intelligent design ( as far as programmers are intelligent ) – explains all the overlapping/common sequences as well – would YOU prefer to write fresh code from the first line separately to every living organism, or just reuse as much code as possible and have a nice long coffee break? Junk code? Look into your Windows! Sorry, my wrong that’s not junk code, that’s there for a purpose :-).

            On a personal note I am – as someone who grown up reading early sci-fi – pretty much fed up on the general mentality of people – instead of seeing new possibilities, frontiers to go for, ideas to fool around even here on hackaday most commenter comes up with the don’t-s, even in such a silly hypothetical polemy. I didn’t even know what I was talking about when I mixed “pairs” with “segments”. I just brought up an idea I thought worth a laugh, and some constuctive criticism.

            I mean this place is hackaday! Instead of misinterpreting my half/barely intelligent words as planning a global plague and talking about prison sentences, you should post – or at least f*cking THINK – about solutions. If we would be on the level of creating anything like my idea, we would be on the level to create the vaccine at the same time. So you can undo at will. Is it defies our original purpose ( of having data safe to keep )?

            What cells? Most things we suffer as viruses are in the wet parts aren’t they? Like flu in blood/mucus, or herpes in the nerves. So what if you can put your code so that it only target HAIR cells? NAIL? How an mp3 player looks like which can read the files from your beard? I suppose hair and nail changes at a different rate than blood. So how fast a writing would be? If you can “program” hair cells, can you program the color/shape/length? We just got ourselves a blooming new industry! New expressions – as natural blonde, dyed or programmed.

            Disclaimer: As long as your upset and offendedness is your OWN, I deeply respect your personal opinion. But if you form your opinion as part/SJW of any crowd ( like for example liberal, democrat, republican, materialist, religious, health&safety, feminist, animalrightactivist, whitesupremacist etc. ) you can take your opinion turn it sideways and shove it up – and so is your crowd. I see you in the nasty prison you sent me when the itunes pandemic I created hits. Until then try to think for yourself.

          2. When I was commenting it was about the concept of injecting DNA into a virus that was spread to the general population, the idea that was put up was that it would survive a million years because it would be replicated infinitely. I responded from my viewpoint and I’m not sure there even where others rejecting the concept of such rudeness.

            I get it’s just an idle thought, in fact I don’t even think it’s possible, it’s not like you have long stretches of ‘free’ DNA that you can just put anything in all the while not having it express anything. But that’s what I was rejecting, the mind experiment. And as for reality, I think there is a real risk of certain people, notably the US, in starting to mess with global things, and without caring about the views of the majority of the world population. And I think that is both risky and offensive.
            An example is that idea of creating clouds over the ocean to alter the climate, supposedly to ‘fix’ global warming. That is so wrong in various ways, including that the climate change also benefits large groups of people, but more importantly that plankton is a major CO2 scrubber, and if you make clouds the sunlight penetrates less into the sea meaning a significant loss of the scrubbing effect of plankton/. And all the jokers who think clouds are a solution didn’t even think about that. The point though is that a single nation should not be allowed to mess with the very basic of the planet or the biology of all humans and things like that. And as I said, slowly the possibility that it becomes possible to deliberately do that is becoming a real risk.

            Meanwhile there are groups who seek to put protection in place in advance of the development of real sentient AI’s. Which I think will be much longer term thing to actually come about.
            But also to think ahead and limit the use of autonomous robots on the battlefield. Which seems timed right to me.
            And I think there’s nothing wrong with thinking about such things in advance, and to not have the insane megalomaniac view that we (humanity) are so incredibly wise and flawless and entitled.that we can just go ahead and it will magically all be OK and not abused and can’t go wrong.

            But it’s a bit odd to say you just throw something out for discussion, and then complain if people discuss it with a (theoretical) fierceness. The alternative is to just joke around until these things are done for real and then all the jokes have made it seem acceptable and people are confused and think that it’s too late to seriously object and just silently think it’s very wrong while letting the politicians green-light the madness.

          3. But it won’t be replicated indefinitely. Viruses lack mechanisms to repair their own DNA (or RNA in some cases), and so will mutate and corrupt the data over time.

  2. Paper tape has pretty long shelf life too. Even without error correction. It takes a lot stronger of a magnetic field and orders of magnitude more cosmic radiation to cause a bit flip.

      1. Gold foil then? :D

        That reminds me of the gold (instead of aluminium or dye) plated CDs…maybe if the carrier was made out of glass they could have similar long term storage capability?

  3. Its possible there is already messages or data hidden in earths genetic code, especially if the universe is infact a hologram; and crazy as it seems the sighs seem to be pointing more and more in that direction as our ability to examine and understand its structure.
    I mean the ancient alien scene could spend an hour on the History channel reinforcing the point.
    we may just now be at the beginning of understanding how to decode this info, consider the small percentage of our genome we actually use, the rest of our DNA just lays dormant.
    an interesting thought anyway.

      1. Yeah im gonna go ahead and ignore that link. Try finding one that isnt arguing an unrelated point…
        “It may well be that, due to harmful mutations (the consequence of sin and our living in a fallen world), some DNA is genuinely junk—but there is growing evidence that this is a very small part, indicating that yet another argument for evolution is finding its way into the waste bin.”

        1. Most of the articles I found are biased one way or the other. I’d rather an article that argues that DNA was coded by someone than one that argues that it was coded by noone; simply comming into being and improving itself by random chance as if it in itself were some sort of conscious being. And speaking of consciousness… it’s not like we as complex cellular organisms actually have any conscious subjective experiences of qualia, right? I mean that’s of course just an illusion created by chemical reactions in our brain isn’t it? Last I checked there wasn’t any atheistic answer to the Hard Problem of Consciousness (other than just denying it exists).

          Sorry for going off topic BTW. I would wonder however if Memristor technology could also provide a reliable means of long-term data storage (aswell as all its other benefits such as high-speed parallel read/write and random access. I should think it would also be available to the general public long before cheap DNA synthesis)

          1. “simply comming into being and improving itself by random chance as if it in itself were some sort of conscious being.”

            You do not understand evolution.

            Step 1:
            Step 2:
            Step 3:
            If survives, multiply.

            You guys never get step 2.

          2. I agree that the creationism link sucks as a source.

            As for the Memristor thing – there have been studies on phase-change memory data longativity. I think 300 years was the outcome. Look up “Reliability study of phase-change nonvolatile memories” from “IEEE Transactions on Device and Materials Reliability”.

            I don’t think memristors will move as fast as people are hoping they will, but I agree it’ll probably be useful long before DNA storage would.

          3. “Last I checked there wasn’t any atheistic answer to the Hard Problem of Consciousness (other than just denying it exists).”

            Define what “conciousness” means.

            Otherwise the question itself makes no sense and cannot be answered.

          4. > And who creates your creator?
            Basically, anything which has a beginning (ie. the universe) must have a cause for coming into existence (Law of Cause and Effect), but anything that has no beginning (ie. God) never came in to existence, thus no cause is needed.

            I can easily understand micro evolution, where different species are mutated, selected, and if the mutations are benifical, then multiply. However it doesn’t explain how the mechanisms by which they are able to grow and multiply (ie. essential coding for DNA proteins and irreducibly complex cellular mechanisms) came about, all in one step, at the same place and time, in order to form a living reproducing cell, before they dissolved back into the primordial soup they were in.

            To quote the linked article:
            “Just think about one essential machine that copies the DNA instructions for making each protein. Then let’s take just one protein component of that machine, less than 10% of the total. This protein is 329 amino acids in length. What would be the chance of getting this one protein by chance, assuming that the correct, and only the correct, amino acid ingredients were present? Calculate it this way: 1/20 x 1/20 x 1/20 … 329 times! This is a probability of 1 in 10^428 … a number with 428 zeros after the 1! Even if every atom in the universe (10^80—a number with 80 zeros) represented an experiment for every molecular vibration possible (10^12 per second) for the supposed evolutionary age of the universe (14 billion years=10^18 seconds), this would allow ‘only’ 10^110 experiments—a long, long way short of the number needed to have a ghost of a chance of getting just this one protein to form, let alone the over 400 others needed.”

            >Define what “conciousness” means.
            >Otherwise the question itself makes no sense and cannot be answered.
            The relevant wikipedia article:
            and also

          5. Setting out a method, observing data and then coming to a conclusion based on evidence =/= ‘biased’. No one was talking about consciousness, you were for some reason. And youve missed my point. You made a blatantly false assertation presented as concrete fact and attempted to support it using a website with a vested interest in the outcome being a certain way, which itself is ‘referencing’ a biased book which is also blatantly campaigning against evolution.
            And now you say Youd Rather! Thats not how science works. You dont get to rather anything! All i want is a peer reviewed article or study to support your strangely tangential claim.

          6. At the risk of feeding a troll

            “Irreducible complexity” is a farce put out by YECs backed up by bad logic. Animals don’t “pop” into being fully formed and they certainly don’t “all happen at the same time”. There’s a couple billion years of swirling and mixing and mass orgies that you’re willfully glossing over.

            Do yourself a favor and stop reading sham science. Go to your library and read a science book or a peer reviewed journal instead of web articles put out by people with, largely, no credentials.

          1. Need. More. Reply. Depth. Also edit capability.
            This is to an above post. Dont understand how single celled organisms came about in one step? THEY DIDNT! We can see precellular organic chemical processes happening in hydrogen clouds in deep space. Life is just chemistry, the biological precursors in proteins, amino acids and sugars and stuff mix together outside of cells and they slowly merge until they become self sustaining. And voila! Rudimentary life.
            Sorry everybody bit of a rant and off topic. On topic we saw a while ago scientists developed artificial dna using alternative chemicals, maybe skip a step and code straight into silicon DNA?

      2. Even though the article doesbring up some valid points (i.e. the similaritys in “junk DNA” in different species) it COMPLETELY obliterates every credibility by trying to shove down creationistic views down the readers throat.

        You seem to know of the reputation of creationistic views (why else woul you have shortened the URL in hopes of hiding the source) therefore I must tell you to get lost (or go to your idea of hell, whatever).

    1. Wait a second. You are referring to the same “Ancient Aliens” TV show I am thinking right now? The one manipulating and misrepresenting well known data, omitting everything we know about history, archaeology and anthropology? The one based on works of con artist and charlatans like Sitchin and Daeniken? Give me a brake?

  4. Welcome to the future! Just an inkling of what is in store. Software was the name of a head shop on our courthouse square back in ’68. It will seem so… in that many more years.
    New science shows problems with the standard mouse model and gut biota affects body weight and DNA is code.
    Hack on!

          1. Warm porridge, I went through a stage of eating only that in the morning.

            I am surprised that it was tested on humans without some breach of ethical conduct. In light of this, it seems dubious that it was done, in such a case that it was, it would be interesting to read up on it. This is why I was asking for a source.

    1. The thing about the cockroaches surviving nukes and such is that sure, due to their very slow metabolism and heart rate they might survive for a bit individually, but radiation would still make them sterile and the local population would be gone after a while.

      So that stuff is a bit of an inflated story.

    1. Pictures.

      Presuming that the DNA vials survive the eons, you can include a simple symbolic illustration to instruct how one should arrange the data, like the one they did with the voyager discs that illustrates the scanning format they used for the signal.

      Then it’s a matter of making a picture-dictionary.

    2. Another issue is that any civilization that can read DNA encrypted messages already knows everything we know so far..
      But maybe it’s useful for the NSA to store your e-mails for a million years, just to be sure.

      So in fact the only thing to keep would be unique art/music. And I guess musical notation at least could have a long life, it’s a rather simple linear thing after all that is standardized across the planet.

    1. DNA already does that, your body constantly rejects and kills bad cells and bad DNA, every second of the day. But unfortunately nothing is foolproof,a and some diseases are actually cause by the very system evolved originally to self-protect.

Leave a Reply

Please be kind and respectful to help make the comments section excellent. (Comment Policy)

This site uses Akismet to reduce spam. Learn how your comment data is processed.