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DNA For Information Processing and Data Storage
Haydn Fenton writes "Here is an article on using DNA for data storage and even information processing. From the article, "The DNA molecule - nature's premier data storage material - may hold the key for the information technology industry as it faces demands for more compact data processing and storage circuitry. A team led by Richard Kiehl, a professor of electrical engineering at the University of Minnesota, has used DNA's ability to assemble itself into predetermined patterns to construct a synthetic DNA scaffolding with regular, closely spaced docking sites that can direct the assembly of circuits for processing or storing data.""
Gives a new meaning to the term "Genetic Programming".
Ba-dum ching!
Online Starcraft RPG? At
Dietary fiber is like asynchronous IO-- Non-blocking!
i hope the feds don't find any copyrighted material stored in my DNA...
If you could really store info in your DNA, wouldn't it be impossible for proctors to stop cheating on exams? I mean seriously... when you register for university you will have to have a full blown DNA scan. Then they will have to force students to walk through metal-detector-type-DNA-scanners just to make sure that the DNA you come to the exam with is the same DNA you registered with. And then trolls could mess with you by resequencing your DNA when you pass out at parties. *sigh* More evidence of the complications of technology, although the future is always interesting to see unfold -- mostly like watching a car accident!
And another thing: chemically, DNA is almost heroically unchanging. It is among the most unreactive, inert molecules in the biological world. That means data integrity, a Good Thing.
-GillBates0.
An Indian-American Hindu committed to non-violent thought/speech/action alarmed by the global explosion of radical Islam
How long until Religious Nuts start claiming to see hidden messages encoded in our DNA telling us to love Jesus?
Or
How long until spies pass messages along in the form of biological matter by sneezing into a tissue?
Or
How long until we can buy books in readable vials full of liquid?
The possibilites are endless and cool but of course it will probably just be used to sell us Coca Cola... so much wasted potential.
Just a boy doing unproffesional IT work that's way above his head.
It varies from person to person.
I'll take a 5TB kidney and a 9TB heart please. Oh and while you are at it, staple my stomach and squeeze all of the storage you can from the excess. I'm sure you'll get a decent amount.
I remember hearing about this originally nearly 10 years ago now. I remember bringing it up in a discussion on Usenet, engendering many "It will never happen" trolls...still seems a few years off though from consumer product?
SJW: a person who perceives an injustice, and while correcting it, commits a greater injustice.
Just wait till SCO find infringing code in YOUR DNA..
DNA "tiles" that spontaneously assemble in a predetermined pattern to form a sheet of molecular fabric, much like corduroy.
This way to the egress...
Could people be *gasp* reading the article?
I read Slashdot for the articles
seems to me that this would be the big benefit, that rather than base 2 for data storage, you could use base 5, with each slot value as 0, 1, 2, 3, or 4 based on having no protien, a, g, t, or c in the "slot" - giving a larger number of values (and therefpre addresses) per slot
(base 5, would the 'slots' be called "quints" - not sure)
I would wonder - though, how quickly data transfer would really be....cell replication takes awhile because the DNA splicing takes a long time, right?
You gotta make something explode to really understand it...examine all those tiny particles while they're still on fire.
Unfortunately, when the tune "Jingle Bells" is coded in DNA for storage, it turns out to be a version of the flu...
I find this to be an extremely interesting and inventive process, but from the article I can't really decide if it has, or ever will have the ability to make something that isn't just a repeated pattern. Does anyone else know a little more about this technology?
Those who know, do not speak. Those who speak, do not know. ~Lao Tzu
It seems unlikely this week, but if Europe does the right thing and rejects software patents, will software vendors sneak in under the cloak of patented DNA?
OK, seriously, software-patents-as-dna-patents probably won't be a problem for the next few years, but as soon as "DNA data storage" its mainstream, it will be a big issue.
Can DNA be copyrighted? Can it be trademarked?
Damn, now where did I put that strand of DNA with all my pr0n.
Good point.
When DNA does go bad, typically what happens is that the telomeres wear out, leading to cell death.
-kgj
-kgj
I thought DNA was made out of M&M's?
While it is self-repairing, changes do occur from time to time during cell division, introducing errors.
A 100th-generation copy of your favorite MP3 may sound as bad as a 100th-generation analog copy. Maybe not quite that bad, but the md5's won't match.
Either Human DNA is programmed very well, or Office is programmed very poorly.
DNA is just a biologic/chemical process of storing info. The smallest bit of information you could reach has already been hypothesized to be an electron...polarize it one way and make it positive (one) and the opposite (zero). Last time I checked electrons are smaller than DNA. But could we go smaller? Quarks? Neutrinos? Photons?...as the smallest components of information?
...you'll just shoot your load into the floppy slot.
Wow, it looks all you need is some velcro and corduroy pants...
...Eddie, your super friendly shipboard computer.
So MySQL won't support it, then---but you can do it in the application layer.
I wonder if people are gonna start sequencing genomes to break security protocals now... Seriously, what would the encryption be like on this.
Go ahead and call me unreliable; reliable is just a synonym for predictable.
In the I, Jedi book, there was a reference to this type of technology, wherein someone would sequence flowers with DNA that contained encryption keys to a set of data stored elsewhere. Very useful for blackmail. Seriously, though, if we're approaching SW technology, I'm happy. When're the hyperdrives and usable ion drives coming?
no more electronic viruses. Now we can have the real thing.
Not only does your computer get infected....so do you!.
Performance Limits on Chemical Computation.
Hmm, Given that DNA is highly unreactive what do you tell your boss when it does react and mutate? And what kind of readers will you be useing to "read" the data? Bio-chemical? Mechanical? If its bio-chemical imagine the possibilities...
"hey boss the server is down with cancer right now..."
"Hey boss the server is trying to grow legs what do you want to do?..."
"Hey boss the server that we were having problems with just ate a rat... and is purring... George wants to take it home for the night. What say you?"
I think This technology wont take off too well... Way too small - "Oh, nuts..I dropped my Unreal 2008 DNA vial..There it goes spewing all over the floor" Or maybe..."Oh no..the cat, it ate my DNA processor!"
-- +
Can I get my brain to boot linux?
(another lame response)
Sex as a backup device!!!! That's way cooler than tape drives.
Well then, if all said is true, then I somehow must find a way to hook a USB 2.0 port into my body! Now, if I put the power wires here, and the data wires here...
Yeah, sounds great until you mix the DNA with human and make ComputerMan!
So the equivalent of a SQL, insert field command, will be a retro-virus? Will my database be down...with a cold?
Some drink at the fountain of knowledge. Others just gargle.
Heh heh heh. Richard Kiehl. DNA.
Am I the only one who thought of the MST3k episode where they did "The Human Duplicators?"
I will use RNA (Raided Nucleic Acid) instead.
-- Thou hast strayed far from the path of the Avatar.
Science hasn't discovered this and it still thinks that over 97% of DNA is 'junk'. Problem with DNA storage is that 10 out of the 12 layers (or 24, depending on how you look at it) are interdimensional and still unobservable to our consciousness (not to mention instruments).
The Digital Couture Collection
What will happen when the internet's vast archive of midget porn and snuff films gets stored on DNA strands? Reminds me of that movie with Will Wheaton - Mr. Stitch.
could it be?
[late 70s] that DNA was the only persistent data storage media nature had until we apes invented languages that we could symbolically preserve. All that has essentially progressed, and what has been changing rapidly with advances in biotech, is the speed of data access into DNA. 5 yeas ago, the best guess [and the big money of govt and industry] was that it would take us 10 years to transcribe the human genome...and now thats already done. We are getting faster even faster than we expected. [that technological acceleration could be partly attributed to the open exchange of techniques and discovered sequences that the consortium of biochemists had agreed upon at the outset of the project...kind of like developing products in open source]
When that data access speeds up another 8 or 10 orders of magnitude and is both R and W,[and not much sooner!] we can talk about DNA as if it were magnetic media and seriously talk about its applications...Makes you wonder if the lessons of open source are going to have to be rediscoverd as we further exploit what software engineering has to teach us about handling DNA.
SLASHDOT: news for people who can't concentrate on work or have no life at all and got tired of yelling back at the TV.
OK. Say this technology is applied to create a portable system injected into your body and kept functioning off your own metabolism. My guess is you implant a keyboard in your arm, but what oriface would they use to plug in the monitor~
There has been some discussion about using DNA as a massively parallel computer. Suppose you encode data in a DNA sequence (input), then somehow act on it (running a program), and then read the resulting altered DNA. You have a computer, albeit somewhat slow and not terribly practical. Now imagine you start with not one but *billions* of different DNA sequences.You "run" the program over all these inputs simultaneously, and obtain billions of possible outputs. You can then use some chemical tag that binds itself to the 'correct' answer. You now have a massively parallel computer with negligible power consumption in a test tube.
This sort of DNA computer could be useful for a number of problems that involve a lot of trial and error, such as protein folding. In a paper some years ago some scientist managed to solve a traveling salesman problem using one such computer. They generated different strands corresponding to each city, and let them mix in a tube randomly to produce different candidate 'paths'. Then, they used some chemical selector (the tricky part) to eliminate the strands corresponding to invalid paths. Left in the tube were all valid paths, which could then be easily replicated using PCR.
I couldn't find the original paper, but a pretty good explanation can be found here
"In Breaking news, a minor short circuit has caused a freak mutation at Genetic Information Inc. causing all the chips to asexually reproduce and take over the coffe machines"
This is such bullshit people.
The comments going on around here with "+5 informatives" are just amazing.
WTF, people!
Everyone will have to have DNA replicators in order to copy files. This means the cheap production of in home laboratories capable of producing, modifying, and duplicating DNA strands...
I find it... disconcerting.
Go ahead and call me unreliable; reliable is just a synonym for predictable.
As America's original "Melting Pot", NYC has always been a hotbed of cutting-edge DNA research. Dr. Seeman's NYU lab leads the world in the other kind of DNA chemistry, that doesn't rely on COOH in the bars and clubs of Greenwich Village. Ever since Dr. Seeman taught me in college to see stereoscopic molecular images by going crosseyed, his work has been messing with my mind, and making my longest molecules even more interesting. If you want a part of the info revolution of the millennium, forget California and Germany - NYC is the future, where it all comes together.
--
make install -not war
Well, it may not work in a typical computer type situation - we'll probably not be playing Doom9 on a DNA computer but there are other applications where it could come in handy.
The researchers spending their time on this are looking at the challenges and possibilities. Think beyond the confines of typical computing. For one, DNA based computing and storage would allow for base4 computing. This could be interesting. How about creating DNA based "computers" that could actually be administered as pharmaceuticals.
Another, albeit very far reaching possibility is that you could create computers that actually increase or decrease their processor power as necessary through coordinated regulation of duplication of the DNA. Realistically, I think we can look at DNA computers as the first step to artificial cells which could be of considerable benefit.
See. All you talk about is bullshit.
DNA would allow for bas4 computer
We can already do it in silicon.
Administering computers as pharmecutical
(rolls eyes) WTF? What are you smoking?
first step in artificial cells
They've already created "artificial cells" and the computer data storage potential of DNA has nothing to do with it.
Art imitating life: In ST:TNG a Klingon was found to be stealing secrets by reading information off some chips. The raw data was encoded into inert DNA chains and eventually injected into a person. In effect anyone could become a roaming hard drive and not even know it.
You say things that offend me and I can deal with it. Can you?
Having said all that, if you've massive archives where you're less interested in immediate access as you are in bulk storage, DNA would be perfect. For example, you could dump the entire contents of every movie ever made into a DNA-based database. You'd then "cache" in a higher-level form the movies people regularly requested, only pulling out of the DNA storage those which are very infrequently required - but nonetheless required at some point.
Movies would be great for this kind of storage, as they're basically linear. You don't have to build up the search from multiple queries, which would swmp a DNA system rapidly.
For those familiar with older memory storage techniques, DNA is not much different from a Bubble Memory.
However, such "strings" are not necessarily the best form of storage. X-Ray fluorescence offers other possibilities, but it would likely be a write-once medium. Basically, if you fire an electron at the nucleus of an atom, at the right speed, the electron is absorbed and X-Rays are emitted, where the frequency of the X-Rays is determined solely by the type of atom struck.
That gives you a "read" mechanism. Simply have an electron gun, and an X-Ray detector for the right frequency. If the number of X-Rays falls below a certain level, that bit is zero, otherwise it is one. How about writing?
Let's say you use calcium as your medium. Calcium has the property that if you fire an electron at some other specific frequency, the atom turns into Aluminium. (Calcium/Aluminium ratios are one way of finding out how long certain rocks have been exposed to the surface.)
So, with an electron gun and X-Ray detector, you can both "read" and "write". Allowing for reasonable design tolerences, you should be able to get comparable storage densities to those achievable with DNA, only it would have much shorter access times and would be "random access" rather than sequential.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Evolution has worked for billions of years. I'd say it's worked out quite a few of its bugs. So why don't we copy it when doing computing? I think the book stated (VERY generally, I assume), that there are 4 bits that get used to build with DNA - A, T, C, and G... obviously this has advantages, so why are we using binary computers?
I don't get why we don't copy this in as many of our simulations as possible. It's obviously prevailed for a reason...
Berto
Man, always thought my computer had no trouble winning against my brain in terms of speed.
I'm not sure why there is a lot of interest in attempting to use DNA as part of a storage medium other than the potential data density it offers. While current computing components don't operate at temperatures that will denature DNA, they aren't out of the realm of possibility (96-100 degrees celsius). In addition, it is hard to imagine DNA staying stable long term under even normal operating temperatures. There is also the issue of ubiqitous enzymes present on any biological organism that will chop it to pieces. DNA works well as a template in living organisms because there is an entire living support system to correct errors and ensure data integrity. There is also a homeostatic environment as far as temperature, pH, etc. I would think there are much less problematic solutions to increasing data storage density for the forseeable future. The work is interesting, but doesn't seem very practical.
Sounds like prior art to me.
We've gone from "heroicly unmodifiable" to "has modifiable sidechains" with two +5 informatives.
Someone's right.
What people often don't realize when they read popular articles about quantum experiments is that they are usually performed in extremely low temperatures.
In Solviet Russia, the DNA computes YOU!
you look fat in that SW costume
Show me two crocodiles with the exact same DNA in all of their non-gamete cells.
For that matter, show me a single crocodile in which every cell has identical DNA, without any mutations whatsoever.
Your point is well taken - DNA is largely unchanged over long periods of time.
My point is that over short periods of time, uncorrected 1-bit errors DO occur, rendering it an imperfect storage medium.
Perhaps with error-correction protocols a la CDs and DVDs and only-the-fly verification-on-copy, it can be workable.
1: Theorize alternative data storage means with total disregard for reality and submit a story on it to /.
2: ???
3: Profit!
Just what I want, my application mutating on me!
I read an article on this around five years ago where a scientist used DNA to solve a traveling salesman problem. An NP complete problem that was solved in a chemical reaction that took less than a second. However, it took the scientist about 3 months to set things up.
This would be scary... what if some ingenious sabateur were to walk into the server room with a small item.. like a UV light or a small can of an intercalating agent... You could even pump a retrovirus into the computer with little effort.. imagine The next generation of hackers are going to be molecular biologists who spend their free time coding.
By the way, if you want some good info on home hacking of DNA, proteins, etc. check out DNAhack.com.
hm... just imagine a Beowulf cluster of these things!
but wait will it come out before DNF?
wow... two jokes in one post! If this isn't +5 Funny I'll stop quoting http://en.wikipedia.org/wiki/Slashdot_subculture
See pictures of tits
You can put all your pr0n on DNA instead of putting your DNA on your pr0n!
Disconnect your television. Do your own research. Draw your own conclusions. They're probably lying. Don't be a sheep.
C'mon. It's not hard. They're talking about using DNA for templates for PHYSICAL design. More like tracing DNA than anything else.
Just ONE application happens to be data storage [any not quite in the way you think]. We're talking absurdly small chip design. Which is pretty damn cool, but something NO-ONE has commented on yet!
for the love of god, RTFA.
[karma-burn off]
'If you're flammable and have legs, you are never blocking a fire exit.'
mod the parent up!! This site is great!
See pictures of tits
What about ECC and Cosmic Rays?
It's well known that cosmic rays can cause nth in a billion chance to cause a genetic mutation in DNA.
So have they thought about this yet?
Imagine yourself: a beowulf cluster of these things.
So, when my DNA hard drive goes South I get to call the Oncologist and schedule Chemotherapy? That would be a Gene-uine pain! Then when my repair shows up I'll have to listen to a whole new litany of excuses, such as: Sorry, your nitrogenous bases all got mixed up! Or: Sorry, I left my spliceosome and DNA polymerase back at the office...
does this mean all our porn will start evolving, resulting in a big porno ring run by skynet?
So *that's* why I am so forgetful. Some hacker is stealing cycles from my brain.
Table-ized A.I.
Computers used to cost the government and corporations huge amounts of money. The desktop computer competition brought these fees down tremendously and even when governments, companies, and universities find a need for something different, they can often meet their own needs by modifying off-the-shelf technology or having their custom needs met with technologies that are signifcantly cheaper.
Now if DNA manipulation becomes the next technology to be driven down in price by mass competition, it's an idea that makes me very nervous. I'm not sure that we have in place the moral safeguards on our current, expensive DNA engineering laboratories, and we're talking about making a price pressure that will put DNA manipulation affordable to millions?
Isn't manually manipulating DNA just creating viruses on a grander scale? Admittedly there's no intent to make data that can self-replicate, but there seems to be no intent to make sure that this stuff can't do so. If our computers become an infinite number of monkeys typing randomly, we very well could come up with something amazing or something horrible.
I certainly hope that technology designers will do something to make natural exposure of this computer DNA architecture incompatible with natural DNA, but my bigger frights are on the moral front.
Technology safeguards will only make it safe for you to work on repairing your hard drive if you happen to have an open cut. I fully expect the more brilliant tech geeks to figure out ways to circumvent these limitations for their own experimentation (whether in this country or another) just as the case-modder will circumvent electrical or FCC standards to feed their own experimental lusts. That leads to some absurd possibilities:
Warning: Mildly Off Topic Tin Foil Hat Theory Below:
In the early eighties, public awareness of GRID (gay related immune deficiency) began to awaken judgemental choruses of "God's punishment for sinners" and ideas of concentration camps for homosexuals. There were also people saying that the US government had engineered this new "human immunodeficiency virus" from other rare cancers or simply found a naturally occurring virus and found a way to introduce it into a population that would be extremely destructive. When "innocent" people started dying of GRID and the name changed to AIDS, the theories of it's engineering or opportunistic cultivation became theories of attack from the USSR.
Today, the origin of HIV is irrelevant whether it was natural, cultivated, or engineered. My thought at the time was that these were crackpot theories. These are governments that had trouble feeding their own people, tallying census figures, and managing money. They certainly weren't smart enough to engineer a virus. Without going into a big debate of communist versus capitalist or democrat versus republican, I have to say that the possibility of such theories is more realistic today in my mind. We're talking about governments (US and USSR) that engineered and used nucl
How about right now?
That doesn't directly tell us to 'Love Jesus', but realizing the existance of a supreme super-intelligent creator certainly will take you down that road.
although changes to its chemistry are being repaired all the time
How about this for redundancy/error correction? DNA could yield almost inconceivably high storage values. Replication and repair could form a futuristic form of data integrity protection and duplication abilities. Want to copy your dish (petri, that is), have the DNA "replicate" itself - no hardware needed.
Petri-dish is a joke of course, but one wonders what the optimal instrument for storing such data would be?
When the DNA could be carried as data in ones body, I'd be be super-paranoid about viruses. If you were captured, it could carry the 2900AD version of "this message will self destruct" causing you to crap your pants, go blind, mute, and then expire...
Integration of technology and biology has scary possiblities... especially in nanotech.
I knew there was some reason I still read Slashdot. I've barely skimmed the thesis, but assuming the analysis is correct, that factor of 40,000 is quite depressing - guess we're stuck with quantum computers if we want to achieve some serious speed-ups!
infinitely indexed memory bank...Somehow the Movie seems to come true...
"Doing what i can, with what i have." ~ Burt Gummer
some of you were talking about storing this DNA in your bodies, but you gotta be careful to keep it out the reperductive cycle! Imagine if a man and a woman implanted with half-life had a child... Baby Headcrab zombie!
Will applications released for free use with DNA RAM be known as 'Open Wound'? [makes hurried exit]
AT&ROFLMAO
This technology will never have " REWRITABLE " potential, but will be a great back up, distribution disk, or write once read many times disk.
Gosh! DNA s awesome! I want it, too. Tons of it.
I think ist possible to 'program' DNA in such away that when under the right conditions, a complex set of inter-functioning modules can be produced. These modules could form a network on which information can be processed and thus computation can be done.. It can even be made selfsupporting, when it assembles devices to use energy and resources from its environement..
"Solylent RAM is people! It's people!!!"
hmm...maybe not...
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