back to article New DNA 'hard drive' could keep files intact for millions of years

Researchers at the University of Washington (UW) and Microsoft have managed to write data directly onto DNA, a format with dramatic storage densities and a very long life. The team wrote 200MB onto strands of synthetic DNA, including video footage of the band OK Go, the Universal Declaration of Human Rights in more than 100 …

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What could go wrong?

Could your data center be used to produce real viruses now? Who do we trust with these things?

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Re: What could go wrong?

Not sure if serious.

You'd need the code for a real virus to start with, and some clue as to how to make it more dangerous.

If you think that a real, dangerous virus can be created by accident as a by-product of data storage, then you are not the person with that clue.

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Re: What could go wrong?

Who said anything about accident?

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Pint

Re: What could go wrong?

Dave actually wrote without realizing, "If you think that a real, dangerous virus can be created by accident ..."

Creationism much?

The world, if not the entire Universe, is chock-a-block full of viruses. Apparently all created 'by accident'.

: If the conditions are right, it's inevitable.

:-)

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Re: What could go wrong?

Infinite monkeys with DNA synthesizers.

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Re: What could go wrong?

Synthetic biology is old tech. The first virus was in 2002, and first bacterium in 2010.

As far as accidents go, you get to try this at home for fun. Just paste everything from '#!' to 'done' into a text file called random_virus_machine, make it executable (chmod 755 random_virus_machine), and run it (./random_virus_machine).

#! /bin/bash

while true; do

dd if=/dev/urandom of=/tmp/virus bs=1024 count=4 2>/dev/null

chmod 755 /tmp/virus

/tmp/virus 2>/dev/null && exit 0

done

I expected the chances of success to be small. Although it possible to squash a binary executable into 45 bytes the chances of those bytes being a valid ELF file are tiny. It is also possible to create a valid executable by starting with '#!' followed by the full path of an interpreter, followed by code valid for that interpreter. There are a few interpreters in /bin, so the required prefix of '#!/bin/' reduces your chances to 1 in 7x10¹⁶. It turns out if the file does not match any other pattern, the Linux kernel gives the file to one of the shells to chew on.

Shells have an insane default feature. If a line of shell script is complete gibberish the interpreter outputs "syntax error near unexpected token '%c'" and try to interpret the next line. There is a real chance that random_virus_machine will actually do something (probably harmless, but don't blame me for rm -r ~).

The DNA decoding machinery inside cells have similar default features. IIRC, they chug along until they find a start code, then take three base pairs (6 bits) at a time as an opcode. 21 of the 64 possible opcodes have a useful meaning. (I think the other 43 are 'unexpected symbol error, look for the next start sequence'). Microsoft's error correction code could easily insert invalid opcodes at regular intervals to prevent the creation of anything dangerous. If you fool the software into thinking that your raw file has already been through the error correction filter, then you can have the file->DNA machine create the DNA sequence for a virus (the small ones are only a few K). Normally viral DNA needs to be packed into a phage to be infectious (there are exceptions, ask a biologist). The chances of random data happening to be a valid sequence for an infectious virus are tiny. random_virus_machine is just as likely to output the code for ninvaders.

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Re: What could go wrong?

>The world, if not the entire Universe, is chock-a-block full of viruses. Apparently all created 'by accident'.

Hiya Jeff!

No, not 'by accident', but by a series of accidents interspersed by selection. Or rather, the natural selection of randomly occurring mutations.

If one were to merely transcribe a cat video into DNA, there would be no process of selection, no realisation of biological traits that could be tested against a selection pressure.

Of course, it is possible that transcribing an encrypted file into DNA would result in a virus, in the same way that it possible for a monkey at a typewriter to tap out the works of Vonnegut. Possible yes, but very unlikely. With 'very unlikely' being an extreme understatement.

Hehe, I made a comment which is text book Darwin, and I'm a creationist!

: )

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Re: What could go wrong?

Viruses are for pansies anyway. Godzilla or go home.

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Boffin

Re: What could go wrong?

The thermodynamic stability of DNA follows an Arrhenius equation. From the statements in the article, the DNA's data retention at room temperature can be estimated to be about a year. That's from thermodynamic stability. It's shorter if any organism has a chance to eat it.

So "What could go wrong?". Well, this long term storage needs long term refrigeration.

Of course, read & write speed must be horrible.

So when is this "great work" going to make it through peer review?

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Re: What could go wrong?

Better to ask, "What could go right?"

http://www.schlockmercenary.com/

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UA

Re: What could go wrong?

Just a small correction: All 64 codons are usefull, yes there are only 20 amino acids that can be derived from these 64 (3 base) combinations, which means multiple combinations result in same amino acid. This is nature's way of error correction or fault tollerance, as a mutation of only one base in 3 base codon likely results in same overall translation.

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Re: What could go wrong?

DNA Foundries wont produce viruses as they blast your sequences to prevent you from doing these things.

And it is a bit sad that yesterday was SynBioBeta activate on Edinburgh, openning of a DNA foundry in Edinburgh and Synthetic Yeast 2.0 annual meeting also in Edinburgh, and no news about it.

Also, I do not want to diminish the excellet work at UW, but you could name the DNA manufacterer, they are quite proud about being able to fulfill the DNA order from Microsoft.

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Boffin

Re: What could go wrong?

Nothing in your script requires bash extensions, so you should use #!/bin/sh for maximum portabiliy -- I only know of Linux systems that have bash in /bin , but sh is universal amongst unix(type) systems

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Meh

Re: What could go wrong?

@Jeffy, ah yes, the old abiogenesis is well known, well understood and demonstrated. NOT. Aside from Sol3 there is still only wishful thinking about life elsewhere. And no, Drake Equations and the appalling self-contradictory nonsense in New Scientist sometime in 2015 about earthlike planets and life elsewhere simply demonstrates another post western cultural myth is thriving in an age of superstition and wishful thinking.

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"a mutation of only one base in 3 base codon likely results in same overall translation."

Mostly.

IIRC there are 2 amino acid codes that have only 1 codon pattern.

Mutate one of those codons and you are guaranteed to make a new amino acid.

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Re: What could go wrong?

Infinite monkeys with DNA synthesizers.

I used to enjoy a bit of prog rock in the 70's

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Just think, all the drivel we produce today (Facebook, Twitter) could be preserved for millions of years. Kind of blows your mind.

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But all those records of our dinners will be invaluable for future archeologists who will no longer have to dig about in fossilized dung.

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Anonymous Coward

Future archeologists

Will go mad if they have to sift through zettabytes of twits and posts to fund anything even remotely useful.

On the other hand the humanities may have some interesting* PhD theses in the future:

"On the interactions between rival beeotches on New Jersey in the XXI century, as measured by a particular nasty sequence of tweets and comments from their friends at their community college and tanning salon, and what that reveals about their feeding and breeding habits" - Dr LaShaWanna Frito Rodriguez McNakamoto III.

*not really.

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invaluable for future archeologists

Pity the poor ET, millions of years into the future, who lovingly recreates a sample of life from long-dead Sol 3, only to find that (s)he's cloned Facebook.

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Unfortunately the discoverers of this old data won't have the key.

I've been doing some work for the Drive Trust Alliance (http://drivetrust.com), so I'm tuned to the Full Disk Encryption / Self Encrypting Drive technology. By the end of 2017 nearly all storage will be using it.

So now I foresee a distant future when , after the collapse of human civilization, our successors, having risen to sentience and culture and having a robust archaeological science, discover this trove of human data in the Lunar Long Term Data Repository that we kindly left for future generations.

Unfortunately, all the data is encrypted, and the key is lost. Or there's a typo in the docs.

Thus speaks to a fundamental problem - such a data trove undoubtedly must contain secrets that should not be available to just anyone. But how to assure that the data is truly available in the distant future?

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Re: Unfortunately the discoverers of this old data won't have the key.

People have worked out various mechanisms for Time Release Encryption, but the issue is trusting the required 3rd party server.

Such a 3rd party server would have to be honest, and also in existence x years into the future.

If anyoine knows of work done to sidestep those issues, I'd love to hear them.

(The idea came to my attention when I thought of the uncaptured oral history available from people of a generation that don't blog. Whimsically, I thought of placing microphones in a pub, with everybody knowing that recordings couldn't be listened to for 100 years. )

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Anonymous Coward

"at 10 degrees Celsius the DNA won't degrade for around 2,000 years, and at -18 degrees it could last for millions"

Can we have some baseline comparisons so we can tell if that's good or bad? How long would a DVD-ROM last if you stored it at -18 degrees? What about magnetic tape, or punched cards and paper tape? QR codes etched into titanium sheets?

The latter I think would be far easier to decode by future civilisations, and could be read in a non-destructive way.

Also, there is no risk that you'd accidentally drop the entire world's knowledge into your tea thinking it was a sugar lump.

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Re: Future archeologists

"Will go mad if they have to sift through zettabytes of twits and posts to fund anything even remotely useful."

There will probably be a massive artifical archeologist mega-brain doing the analyzing, though.

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Devil

I'll take a potshot* at this.... Can the data only be read by Windows 10?

*It's MS... they need deserve all the potshots we can take at them.

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There's always one in every thread. Now watch the flies come swarming.

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Pint

Well.. it's a dark and dirty job, but someone has to do it. No pay, I even have to buy my own beer.

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Happy

Well, at least it isn't a lonely job.

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Pint

It's all gone horribly wrong...

I sent in my spittle sample to 23&Me. They analyzed it and discovered that my DNA carried sections of object code from 'Grand Theft Auto V'. Now I've received a DMCA Take Down notice demanding that I destroy myself and all copies, and compensate them by $3500.

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@JeffyPoooh Re: It's all gone horribly wrong...

You owe me a new keyboard - see icon.

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Pint

Somebody should make a movie like 'Contact'...

Just replace the alien signal with the data encoded by human DNA.

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Headmaster

Could you sort out your prepositions please?

The data is not written onto DNA. It is written in DNA. That is, only DNA is used for the writting by assembling it from four types of nucleotide bases.

(Compare this with a computer writing data onto words. No! It writes data in words by assembling them from two kinds of bits. That's not a perfect analogy, because we can create bits in many ways: discrete electric charges, discrete magnetic domains, holes in paper tape, etc.)

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Anonymous Coward

Prior art: "Blood Music" :-)

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Still early in the morning?

What with the opening posts and AC's too all I thought about was Prions.

CJD; burning banks; inter-species transmission...

These were all by 'accident'. Now add malicious design and then counter measures. More source material for the sci-fi authors, I think.

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Re: Still early in the morning?

The concept has been around for decades, so sci-fi authors have had plenty of time to use the idea! :) Indeed, Dawkins talks about the information half life in living bacteria in his book The Blind Watchmaker. Obviously this is a different situation, because he was taking into the account of the bacteria's error-correction mechanisms over millions of generations.

As for inactive DNA, studies conduction on bird bones at ambient temperatures (i.e not in a frozen vault) in New Zealand suggest that the inforamtion half-life as being around 500 years.

http://www.the-scientist.com/?articles.view/articleNo/32799/title/Half-Life-of-DNA-Revealed/

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Re: Still early in the morning?

Prions are misfolded proteins, so in that respect at least your heart can rest easy.

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Anonymous Coward

sorry Johnny M...

Sorry Johnny, I guess we didn't need to implant a chip in your brain, we just needed to tinker with your DNA...

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Sci Fi becomes reality

I forgot which SciFi author came up with this idea 20+ years ago. DNA as non-volatile computer memory. It was one of the greats. Not Bova, not Brin. Damn... can't recall it, but the idea is not new.

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Re: Sci Fi becomes reality

Tip of the tongue damn it.

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Re: Sci Fi becomes reality

Philip K Dick's "The Preserving Machine" springs to mind, but (having not read it since, probably, the late 1970s, when I may have been too young to fully appreciate/understand it all) ISTR it was more about turning music into animals as a way of preserving it.

Animals which then began to evolve.

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Re: Sci Fi becomes reality

Philip K Dick's "The Preserving Machine"

No, not P K Dick, it was some space-opera genre series, just cannot recall who wrote it.

It struck me at the time that the idea is quite smart. While writing and reading may be a bit on the slow side, the information density is ridiculous and all the error-correction and repair mechanics already exist in nature.

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Re: Sci Fi becomes reality

In that case, it may be something I haven't read (or something I've completely forgotten about).

Mind you, had the subject come up a few days ago I might not have remembered The Preserving Machine, either. I just happened to be browsing some old titles a couple of days back and remembering which ones I'd read as a child and what they were about.

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millions of years

but how do you preserve the information that explains how to decode this dna data ?

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Re: millions of years

I believe that information may not require such a huge storage density, and could be easily carved in a chunk of reasonably durable material nearby.

Prior art: Voyager's golden LP.

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Coat

Dig up the Past

They should dig up dead musicians and see if they really have' music in their DNA'.

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Re: Dig up the Past

Decomposing composers.

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Joke

I'm afraid...

...that your memory card is showing signs of early-onset Alzheimers.

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Microsoft wants to write something into all our DNA strands. Copyrighted by Microsoft

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