Researchers Store Computer OS, Short Movie On DNA (phys.org) 95
An anonymous reader quotes a report from Phys.Org: In a new study published in the journal Science, a pair of researchers at Columbia University and the New York Genome Center (NYGC) show that an algorithm designed for streaming video on a cellphone can unlock DNA's nearly full storage potential by squeezing more information into its four base nucleotides. They demonstrate that this technology is also extremely reliable. Erlich and his colleague Dina Zielinski, an associate scientist at NYGC, chose six files to encode, or write, into DNA: a full computer operating system, an 1895 French film, "Arrival of a train at La Ciotat," a $50 Amazon gift card, a computer virus, a Pioneer plaque and a 1948 study by information theorist Claude Shannon. They compressed the files into a master file, and then split the data into short strings of binary code made up of ones and zeros. Using an erasure-correcting algorithm called fountain codes, they randomly packaged the strings into so-called droplets, and mapped the ones and zeros in each droplet to the four nucleotide bases in DNA: A, G, C and T. The algorithm deleted letter combinations known to create errors, and added a barcode to each droplet to help reassemble the files later. In all, they generated a digital list of 72,000 DNA strands, each 200 bases long, and sent it in a text file to a San Francisco DNA-synthesis startup, Twist Bioscience, that specializes in turning digital data into biological data. Two weeks later, they received a vial holding a speck of DNA molecules. To retrieve their files, they used modern sequencing technology to read the DNA strands, followed by software to translate the genetic code back into binary. They recovered their files with zero errors, the study reports. The study also notes that "a virtually unlimited number of copies of the files could be created with their coding technique by multiplying their DNA sample through polymerase chain reaction (PCR)." The researchers also "show that their coding strategy packs 215 petabytes of data on a single gram of DNA."
DMCA on ur DNA (Score:1)
One step closer...
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Re:How many... (Score:5, Insightful)
Actually that did hit me as being jaw-dropping amazing. Yes the technique is slow write and slow read but the information density is about as good as it is possible to get at a molecular level. Even better the stuff is self replicating so backups of your backup are trivial. I am scratching my head as to how this might be used in a practical way at the moment, a bit like a laser in 1970 but the concept itself is staggering. I had no idea that the genetic science had moved so quickly, it seems like only yesterday we sequenced the human genome for the first time. I know one thing, if I was 50 years younger it would be this field rather than semiconductor physics that would be the most interesting physics to get into. Also I have absolutely no doubt that in 50 years time some pretty amazing medicine will be available. Much like 50 years ago a computer was a room full of racks and today it is an Apple iPhone. Today we just cured one child of sickle cell anemia using gene therapy, where is that going to go in the next 50 years? Wow, just wow. (Always assuming we can get pass the current trend towards 0.001% of the population having all the wealth and the rest of us living in a ghetto of course).
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In terms of practical use, the information density means it is excellent for archival purposes. Consider how much space is used to store backups offline (tape or otherwise). I'm thinking things like Amazon S3 Glacier. Now, I didn't read the article, but I'm going to assume it is a bit easier to store these vials then racks upon racks worth of hard drives or tapes. Also consider the cost of moving this stuff, its smaller, simpler, and lighter, which means cheaper in many ways.
Furthermore, unless I'm hugely m
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Furthermore, unless I'm hugely mistaken, this will survive an EMP with no ill effect, so that's an added bonus in terms of resiliency.
The data might, but the gene sequencers will not. Just like I have a box of 9 track tapes with data on them. And the data won't survive ionizing radiation.
What is fascinating is that TFS said they encoded the data and then deleted problematic pairs, which would seem to be a waste. Why not change the encoding so you don't create problem base pairs in the first place?
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I don't know about where you work, but our generator (and every other one I've seen) sits in a giant sheetmetal enclosure.
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Unfortunately, I think the error rate may be higher than typical storage hardware. Enzymes will need to be designed and placed to repair the DNA strands.
That is why they are using such short pieces of DNA. There are already enzymes that replicate short strands with exceptionally high fidelity; it would be much more difficult if we were duplicating very long pieces. There are even DNA polymerases that do their own error-checking that are especially good for this type of work.
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Yes the technique is slow write and slow read but the information density is about as good as it is possible to get at a molecular level.
There are molecules much smaller than nucleic acids that could be strung together. The difference is that sequencing DNA is an existing technology that is paid for by serious users, so is available for cheap for this kind of thing.
Even better the stuff is self replicating
Uhhh, no.
where is that going to go in the next 50 years?
"Fixing one child" is to "today" as ? is to "in 50 years"? This is a very scary question. In no more than 15 years we will probably be fixing genetic diseases. It won't be much longer than that before we "fix" other things. Eugenics ain't just for chickens, you know.
But
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In no more than 15 years we will probably be fixing genetic diseases.
That's rough... 20 years ago, that was only 10 years out.
It won't be much longer than that before we "fix" other things.
We're running out of time to find the dusty VHS tapes of the '700 Club' warning us about the horrors of "designer babies" before they degrade. They could save humanity!
Seriously, this is like hearing about the imminent danger posed by AI from the Kurzweil nuts. It's science fiction, old science science fiction, that's got you worried. Relax. There are real monsters, like greed and lust for power, that are far more likely to cause you harm in the i
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We're running out of time to find the dusty VHS tapes of the '700 Club' warning us about the horrors of "designer babies" before they degrade. They could save humanity!
I'm sorry that you think that eugenics through direct genetic manipulation is not a bad thing. Are you as unconcerned about the current "eugenics through abortion" system, too?
It's science fiction, old science science fiction, that's got you worried.
Every technological advance is science fiction until it happens. Prior to the Manhattan Project, nukes were science fiction, too.
that are far more likely to cause you harm in the immediate future
Ahhh, got it. You are only concerned about things which will cause you immediate personal harm, and ignore anything that may be harmful to future generations of other people.
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Not quite. I'm not generally afraid of imaginary things, nor am I concerned with their ethical implications.
I'm also not worried about alien invasions, evil AI, or careless time travelers.
When I see silly science fiction doomsday proclamations that call for my attention or action, I look at it the same way you might look at a Chick tract.
You, in contrast, seem genuinely worried about these sorts of things. I wonder if you've called your insurance company to have 'mad robot damage' added to your homeowners
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PCR makes it self replicating. Polymerase chain reaction (PCR) is a technique used in molecular biology to amplify a single copy or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
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Using PCR to make copies is not self replication. You still need to add all the machinery, including the DNA Polymerase protein, to do the replication.
To make this self replicating you'd have to add the sequences to a bacteria like E-Coli, and somehow ensure that the cell doesn't just kick the useless (for it) DNA out again.
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To make this self replicating you'd have to add the sequences to a bacteria like E-Coli, and somehow ensure that the cell doesn't just kick the useless (for it) DNA out again.
Tack it onto a gene for antibiotic resistance so that it's not useless. It'll be the typical movie piracy scenario played out on the microscale: not only does this version of Arrival of a train at La Ciotat not have any DRM, but it has kanamycin resistance thrown in too!
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> a bit like a laser in 1970 but the concept itself is staggering.
> a computer was a room full of racks and today it is an Apple iPhone
And by 1985 I bought a CD player, which course contained a laser, and I was 10 years old. Even before that, we had a computer in the living room that was more powerful than the room-sized computers my mother programmed just a few years before.
> assuming we can get pass the current trend towards 0.001% of the population having all the wealth and the rest of us
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I agree that 'progress' continues to increase the standard of living of the masses. However it is said that it is the public's distress at the status quo which has led to the election of a disruptive president. This suggests that their security is declining, their share of wealth has definitely declined dramatically since the 1970's. It is unlikely that eliminating all H1B and migrants alone will change this given that AI automation will likely devalue the workforce at a faster rate. So the question is wha
Perfect choice of words (Score:2)
> However it is said that it is the public's distress at the status quo which has led to the election of a disruptive president.
Perfect choice of words there. "A disruptive President", I like it. It'll be interesting to see what happens with Trump because he's certainly different - on the one hand he's not at all diplomatic or "politically correct" or whatever you want to call it, on the other hand he's not completely *dependent* on big donors like most politicians. I won't even try to predict, it'll
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We've seen this movie hundreds of times, and we still forget the ending.
Others seem to keep forgetting that point in the middle of the movie where things get really bad for the masses until something is done to improve their lot before it boils over into a revolution (or sometimes nothing is done and heads roll).
Perhaps if we could be a bit proactive this time (since we HAVE seen this movie before) we could avoid all of that and get on with the happy ending.
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Science Fiction Predicts Science (Score:1)
https://www.fourmilab.ch/documents/sftriple/gpic.html
A Pioneer plaque? I was reading the above when this article pinged on my RSS feed. I'm still giggling.
No surprise since DNA is digital (Score:5, Interesting)
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The real news in this story is that we now have companies that can create designer DNA from scratch.
Where have you been the past decade or two? This technology is working with DNA strands that are ~200 nucleotides long. We've been able to generate sequences of that length on demand in commercial apparatuses for years already.
Every once in a while (Score:5, Insightful)
a story here makes me go WOW!
If this is legit it would be one. Time will tell though.
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Replication doesn't happen on its own. If it did, we wouldn't have cells, and hell, viruses wouldn't need them to replicate either.
The question you are probably asking, that I don't know the answer to, is "what are the odds that a given one of these strands contains instructions that, when put in some kind of cell, would end up creating a virus". I'd imagine the odds would be really steep... but hey, you'd only need one part to behave like that, right?
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I'd imagine the odds would be really steep...
I think the odds are very high that an existing virus or bacterium would incorporate bits of the DNA and start replicating it. Even the cell itself would probably do that.
Imagine using this system to store a movie, and the MPAA comes after you for having pirated copies of their property in your genes.
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I'd imagine the odds would be really steep...
I think the odds are very high that an existing virus or bacterium would incorporate bits of the DNA and start replicating it. Even the cell itself would probably do that.
I can tell you that the odds are actually very, very, vanishingly small. The reason being that it is energetically costly for a cell or virus to pick up DNA from the environment and incorporate it into its own genome - hence there needs to be a good reason for this to happen in order for it to occur. The DNA strands on their own won't be bringing with them machinery to incorporate themselves into a genome, and they would not be long enough to present any advantage for the cell or virus to warrant incorpo
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The question you are probably asking, that I don't know the answer to, is "what are the odds that a given one of these strands contains instructions that, when put in some kind of cell, would end up creating a virus". I'd imagine the odds would be really steep
Rather astronomically steep, actually. Being as the DNA is being designed to carry a message in nucleic acid space, the sequences would likely be highly nonsenical when translated into amino acid (protein) space; meaning they would almost certainly be of no utility to living organisms. And being as they are dealing with very short strands of DNA, if these were transfected into a living cell the target cell would almost certainly see them as food and treat them as such.
Immediate practical use (Score:1, Insightful)
The obvious immediate practical use for this technology is for Monsanto to digitally sign their GM crop seeds, to prove without a doubt that those pesky organic farmers next door have stolen their IP.
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You are correct, sir.
Scientists decode ancient virus DNA (Score:2)
From Nature:
The rich fossil record of virii in equine species has made them a model for evolutionary processes1. Here we present a 1.12-times coverage draft genome from a virus found in horse bone recovered from permafrost dated to approximately 560–780 thousand years before present (kyrBP)2,3. Using polymerase chain reaction (PCR) DNA decoding techniques described by Erlich1 et al, [DNA Fountain enables a robust and efficient storage architecture] we recovered a total of 2.14 × 106 bytes in DNA
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Pretty obvious you have some bit flipping going on and hence data is worthless.
Unlimited funding! (Score:4, Funny)
The $50 amazon gift card was a genius idea. With PCR they will become infinitely rich off of those alone!
Don't need a cranial implant... (Score:2)
To be a pnemonic courier with this tech.....could probably encode it into your bloodstream or implant a capsule under your skin...
A message for future generations... (Score:2)
Ruminations (Score:5, Funny)
Someone ping Hollywood (Score:3)
For an updated Johnny Mnemonic remake.
Genetic Recombination (Score:2)
If I fertilize a complete operating system with a french film, what will the offspring look like? Plan 9, or Windows Bob?
Encoding is not enough (Score:1)
That's the reason for life (Score:2)
Some species stored their porn in DNA, which got dumped somewhere and was the basis for life as we know it today.
Pseudo-profound Bullshit (Score:2)
It has all the hallmarks: It is written "in the code of life", it is an "OS" and a "movie". At the same time it is completely and utterly worthless, because DNA is not a digital storage medium by nature, but a blue-print storage that is limited in what it can store by the reading mechanism to very specific things. Most binary sequences on it are just completely meaningless. May as well put a movie into the pattern of stones used to pace a sidewalk. Possible, but utterly meaningless.
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May as well put a movie into the pattern of stones used to pace a sidewalk.
That... is a really cool idea. When I have to repave my driveway, I'm doing that. Not a movie though. Not enough space, even with a fairly small particle size. Maybe a family photo, as a jpg. I'm thinking standard 512 byte sectors, complete with sector header, data section, and ECC section, but rectilinear rather than arcs.
Possible, but utterly meaningless.
Well sure, meaningless to you. But not to my family.
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Hey, in that scope it is a cool idea!
And now we know (Score:1)
how Jor-El implanted the codex in Kal-El.
Not that I need a reason to rewatch a movie with Diane Lane and Ayelet Zurer in it.
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...seems like the most obvious use. This is a Bond film waiting to be made.
Exactly. The implications for data security could be high. The NSA can tap any wire or wireless transmission but how do you stop DNA? How can you detect DNA data? Pedophiles with kiddy porn stored in a fleck of skin under their fingernails beside Cheetos residue?
Bit Rot (Score:2)
Ask anyone who has cancer.