How we can store digital data in DNA | Dina Zielinski

127,131 views ・ 2019-03-21

TED


Please double-click on the English subtitles below to play the video.

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I could fit all movies ever made inside of this tube.
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If you can't see it, that's kind of the point.
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(Laughter)
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Before we understand how this is possible,
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it's important to understand the value of this feat.
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All of our thoughts and actions these days,
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through photos and videos --
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even our fitness activities --
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are stored as digital data.
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Aside from running out of space
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on our phones,
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we rarely think about our digital footprint.
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But humanity has collectively generated more data
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in the last few years
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than all of preceding human history.
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Big data has become a big problem.
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Digital storage is really expensive,
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and none of these devices that we have really stand the test of time.
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There's this nonprofit website called the Internet Archive.
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In addition to free books and movies,
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you can access web pages as far back as 1996.
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Now, this is very tempting,
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but I decided to go back and look at the TED website's very humble beginnings.
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As you can see, it's changed quite a bit in the last 30 years.
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So this led me to the first-ever TED,
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back in 1984,
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and it just so happened to be a Sony executive
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explaining how a compact disk works.
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(Laughter)
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Now, it's really incredible to be able to go back in time
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and access this moment.
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It's also really fascinating that after 30 years, after that first TED,
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we're still talking about digital storage.
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Now, if we look back another 30 years,
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IBM released the first-ever hard drive
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back in 1956.
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Here it is being loaded for shipping in front of a small audience.
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It held the equivalent of one MP3 song
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and weighed over one ton.
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At 10,000 dollars a megabyte,
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I don't think anyone in this room would be interested in buying this thing,
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except maybe as a collector's item.
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But it's the best we could do at the time.
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We've come such a long way in data storage.
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Devices have evolved dramatically.
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But all media eventually wear out or become obsolete.
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If someone handed you a floppy drive today to back up your presentation,
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you'd probably look at them kind of strange, maybe laugh,
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but you'd have no way to use the damn thing.
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These devices can no longer meet our storage needs,
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although some of them can be repurposed.
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All technology eventually dies or is lost,
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along with our data,
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all of our memories.
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There's this illusion that the storage problem has been solved,
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but really, we all just externalize it.
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We don't worry about storing our emails and our photos.
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They're just in the cloud.
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But behind the scenes, storage is problematic.
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After all, the cloud is just a lot of hard drives.
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Now, most digital data, we could argue, is not really critical.
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Surely, we could just delete it.
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But how can we really know what's important today?
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We've learned so much about human history
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from drawings and writings in caves,
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from stone tablets.
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We've deciphered languages from the Rosetta Stone.
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You know, we'll never really have the whole story, though.
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Our data is our story,
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even more so today.
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We won't have our record recorded on stone tablets.
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But we don't have to choose what is important now.
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There's a way to store it all.
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It turns out that there's a solution that's been around
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for a few billion years,
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and it's actually in this tube.
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DNA is nature's oldest storage device.
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After all, it contains all the information necessary
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to build and maintain a human being.
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But what makes DNA so great?
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Well, let's take our own genome
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as an example.
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If we were to print out all three billion A's, T's, C's and G's
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on a standard font, standard format,
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and then we were to stack all of those papers,
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it would be about 130 meters high,
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somewhere between the Statue of Liberty and the Washington Monument.
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Now, if we converted all those A's, T's, C's and G's
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to digital data, to zeroes and ones,
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it would total a few gigs.
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And that's in each cell of our body.
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We have more than 30 trillion cells.
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You get the idea:
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DNA can store a ton of information in a minuscule space.
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DNA is also very durable,
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and it doesn't even require electricity to store it.
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We know this because scientists have recovered DNA from ancient humans
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that lived hundreds of thousands of years ago.
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One of those is Ötzi the Iceman.
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Turns out, he's Austrian.
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(Laughter)
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He was found high, well-preserved,
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in the mountains between Italy and Austria,
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and it turns out that he has living genetic relatives here in Austria today.
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So one of you could be a cousin of Ötzi.
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(Laughter)
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The point is that we have a better chance of recovering information
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from an ancient human
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than we do from an old phone.
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It's also much less likely that we'll lose the ability to read DNA
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than any single man-made device.
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Every single new storage format requires a new way to read it.
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We'll always be able to read DNA.
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If we can no longer sequence, we have bigger problems
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than worrying about data storage.
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Storing data on DNA is not new.
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Nature's been doing it for several billion years.
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In fact, every living thing is a DNA storage device.
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But how do we store data on DNA?
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This is Photo 51.
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It's the first-ever photo of DNA,
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taken about 60 years ago.
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This is around the time that that same hard drive was released by IBM.
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So really, our understanding of digital storage and of DNA have coevolved.
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We first learned to sequence, or read DNA,
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and very soon after, how to write it,
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or synthesize it.
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This is much like how we learn a new language.
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And now we have the ability to read, write and copy DNA.
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We do it in the lab all the time.
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So anything, really anything, that can be stored as zeroes and ones
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can be stored in DNA.
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To store something digitally, like this photo,
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we convert it to bits, or binary digits.
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Each pixel in a black-and-white photo is simply a zero or a one.
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And we can write DNA much like an inkjet printer can print letters on a page.
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We just have to convert our data, all of those zeroes and ones,
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to A's, T's, C's and G's,
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and then we send this to a synthesis company.
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So we write it, we can store it,
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and when we want to recover our data, we just sequence it.
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Now, the fun part of all of this is deciding what files to include.
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We're serious scientists, so we had to include a manuscript
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for good posterity.
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We also included a $50 Amazon gift card --
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don't get too excited, it's already been spent, someone decoded it --
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as well as an operating system,
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one of the first movies ever made
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and a Pioneer plaque.
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Some of you might have seen this.
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It has a depiction of a typical -- apparently -- male and female,
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and our approximate location in the Solar System,
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in case the Pioneer spacecraft ever encounters extraterrestrials.
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So once we decided what sort of files we want to encode,
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we package up the data,
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convert those zeroes and ones to A's, T's, C's and G's,
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and then we just send this file off to a synthesis company.
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And this is what we got back.
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Our files were in this tube.
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All we had to do was sequence it.
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This all sounds pretty straightforward,
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but the difference between a really cool, fun idea
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and something we can actually use
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is overcoming these practical challenges.
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Now, while DNA is more robust than any man-made device,
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it's not perfect.
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It does have some weaknesses.
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We recover our message by sequencing the DNA,
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and every time data is retrieved,
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we lose the DNA.
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That's just part of the sequencing process.
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We don't want to run out of data,
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but luckily, there's a way to copy the DNA
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that's even cheaper and easier than synthesizing it.
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We actually tested a way to make 200 trillion copies of our files,
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and we recovered all the data without error.
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So sequencing also introduces errors into our DNA,
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into the A's, T's, C's and G's.
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Nature has a way to deal with this in our cells.
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But our data is stored in synthetic DNA in a tube,
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so we had to find our own way to overcome this problem.
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We decided to use an algorithm that was used to stream videos.
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When you're streaming a video,
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you're essentially trying to recover the original video, the original file.
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When we're trying to recover our original files,
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we're simply sequencing.
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But really, both of these processes are about recovering enough zeroes and ones
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to put our data back together.
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And so, because of our coding strategy,
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we were able to package up all of our data
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in a way that allowed us to make millions and trillions of copies
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and still always recover all of our files back.
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This is the movie we encoded.
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It's one of the first movies ever made,
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and now the first to be copied more than 200 trillion times on DNA.
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Soon after our work was published,
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we participated in an "Ask Me Anything" on the website reddit.
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If you're a fellow nerd, you're very familiar with this website.
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Most questions were thoughtful.
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Some were comical.
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For example, one user wanted to know when we would have a literal thumb drive.
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Now, the thing is,
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our DNA already stores everything needed to make us who we are.
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It's a lot safer to store data on DNA
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in synthetic DNA in a tube.
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Writing and reading data from DNA is obviously a lot more time-consuming
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than just saving all your files on a hard drive --
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for now.
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So initially, we should focus on long-term storage.
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Most data are ephemeral.
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It's really hard to grasp what's important today,
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or what will be important for future generations.
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But the point is, we don't have to decide today.
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There's this great program by UNESCO called the "Memory of the World" program.
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It's been created to preserve historical materials
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that are considered of value to all of humanity.
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Items are nominated to be added to the collection,
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including that film that we encoded.
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While a wonderful way to preserve human heritage,
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it doesn't have to be a choice.
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Instead of asking the current generation -- us --
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what might be important in the future,
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we could store everything in DNA.
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Storage is not just about how many bytes
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but how well we can actually store the data and recover it.
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There's always been this tension between how much data we can generate
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and how much we can recover
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and how much we can store.
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Every advance in writing data has required a new way to read it.
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We can no longer read old media.
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How many of you even have a disk drive in your laptop,
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never mind a floppy drive?
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This will never be the case with DNA.
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As long as we're around, DNA is around,
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and we'll find a way to sequence it.
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Archiving the world around us is part of human nature.
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This is the progress we've made in digital storage in 60 years,
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at a time when we were only beginning to understand DNA.
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Yet, we've made similar progress in half that time with DNA sequencers,
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and as long as we're around, DNA will never be obsolete.
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Thank you.
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(Applause)
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