DNA For Information Processing and Data Storage

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DNA For Information Processing and Data Storage

Posted by CmdrTaco on Monday December 20, 2004 @08:14AM from the but-how-many-mp3s-can-it-store dept.

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.""

26 of 234 comments (clear)

It works on so many levels by antimatt · 2004-12-20 08:19 · Score: 5, Informative

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.
1. Re:It works on so many levels by LSD-OBS · 2004-12-20 08:36 · Score: 2, Funny
  
  Mayonnaise, however, does. And it goes great with chips!
  
  --
  Today's weirdness is tomorrow's reason why. -- Hunter S. Thompson
2. Re:It works on so many levels by cafn8ed · 2004-12-20 08:41 · Score: 2, Interesting
  
  Disclaimer: IANA[Molecular Biochemist/Geneticist]
  
  I'm not so certain that's something to brag about in this case. DNA may be stable, but DNA replication is not always reliable and accurate. Genetic mutations are common - they are the result of random errors in the replication process. Some organisms have turned really rotten replication accuracy into an advantage (e.g. HIV, which mutates so fast that it has demonstrated an amazing ability to survive everything science has thrown at it). Other organisms do a better job, but never perfectly, as far as I know.
  
  I'm utterly certain the scientists involved know more about DNA than I ever will, so surely they've considered this. I merely wanted to point out that, there are many really cool things that DNA can do, 100% copy accuracy is not one of them.
  
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  Coffee is my drug of choice.
3. Re:It works on so many levels by jhoger · 2004-12-20 09:00 · Score: 3, Interesting
  
  The solution to such problems is redundancy. One efficient form is padding with extra bits to add error correcting codes.
  
  Science fiction may have an answer too. I believe the Slavers [Niven, Known Space series] engineered giant food animals (with intelligence just because the Slavers were really mean) that had specially engineered DNA so that they would not be impacted by radiation. As you say, mutation is necessary in evolving systems, but if one were engineering a system, you'd want to take that out of the equation.
640K DNA molecules... by GillBates0 · 2004-12-20 08:20 · Score: 2, Funny

ought to be good enough for anybody.
-GillBates0.

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An Indian-American Hindu committed to non-violent thought/speech/action alarmed by the global explosion of radical Islam
So how long... by JossiRossi · 2004-12-20 08:20 · Score: 5, Interesting

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.
1. Re:So how long... by savagedome · 2004-12-20 08:27 · Score: 5, Funny
  
  How long until Religious Nuts start claiming to see hidden messages encoded in our DNA telling us to love Jesus?
  
  Each DNA strand is a number. Like the Hebrew A, Alef is 1. B, Bet is 2. You understand? But look at this. The strands are inter-related. Like take the Hebrew word for father, 'Ab' - Alef Bet... 1, 2 equals 3. Alright? Hebrew word for mother, 'em' - Alef Mem... 1, 40 equals 41. Sum of 3 and 41... 44. Alright? Now, Hebrew word for child, alright, mother... father... child, 'Yeled' - that's 10, 30, and 4... 44
  
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2. Re:So how long... by leroybrown · 2004-12-20 09:17 · Score: 4, Insightful
  
  For the love of god, who in the hell thought this was anything but funny? Look people, the universe does not give a rat's ass that we count to ten. That is, the fact that we have ten digits in our numbering system is COMPLETELY arbitrary. So is the fact that we have 26 letters in our alphabet. I guarantee you all that if we had four fingers on each hand like the Simpsons characters, we'd be counting in octal. Anyone that manages to apply any sort of relation between letters and numbers to come up with some sort of code which bears any sort of relevance is deluding themselves.
  
  Think about it this way... the Bible was originally written in Hebrew. The Hebrew alphabet has 22 letters. Do you really think that the Christian God (should he exist) thought far enough ahead to include people in the bible who numerological name conversions would apply in English? No, that's absolutely absurd.
  
  This is why I swerve to hit these wacky numerologists out there. They're so blissfully ignorant of the arbitrariness of our numbering system and number of letters in our English alphabet that they try to apply some grandiose scheme to letters in order to convince people that they're some kind of mystic.
  
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  Founder, Americans Allied Against Alliteration
SCO and DNA by lordsilence · 2004-12-20 08:22 · Score: 4, Funny

Just wait till SCO find infringing code in YOUR DNA..
Slow Posting by ClownsScareMe · 2004-12-20 08:24 · Score: 5, Funny

Could people be *gasp* reading the article?

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I read Slashdot for the articles
Nasty unforeseen consequence by borroff · 2004-12-20 08:24 · Score: 4, Funny

Unfortunately, when the tune "Jingle Bells" is coded in DNA for storage, it turns out to be a version of the flu...
1. Re:Nasty unforeseen consequence by HarveyBirdman · 2004-12-20 08:48 · Score: 2, Funny
  
  You think that's bad? Encoding a Britney Spears album produced Ebola, Rift Valley fever, four Marburg variants and the freakin Andromeda Strain.
  
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  --- Ban humanity.
Re:The things people doubt by Anonymous Coward · 2004-12-20 08:27 · Score: 2, Informative

This has (essentially) nothing to do with older ideas of storing data in DNA sequences. The DNA is being used here as a scaffold to lay down a particularly dense array of unformatted storage material.
DNA heroically unchanging by handy_vandal · 2004-12-20 08:27 · Score: 2, Informative

... 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.

Good point.

When DNA does go bad, typically what happens is that the telomeres wear out, leading to cell death.

-kgj

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-kgj
1. Re:DNA heroically unchanging by InternationalCow · 2004-12-20 08:34 · Score: 4, Informative
  
  Good point indeed but you misunderstood. DNA inside the cell IS changing all of the time although changes to its chemistry are being repaired all the time. Telomere change is something else, that happens at cell division. Higher-order structure, like folding, also changes. What the parent meant is that DNA, when taken out of the cell, is very very stable with most of its primary and secondary structure remaining intact over a long long time (see extraction from Neanderthal bones). However, the point of using DNA as a scaffold for the assembly of information is not in its stability per se. It's in its ability, per its repetitive structure with lots of nice modifiable side chains available, to direct assembly of other molecules. This is what is meant, methinks.
  
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DNA versus the Elecron by Piewalker · 2004-12-20 08:31 · Score: 2, Interesting

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?
DNA plus Information Processing equals... by amstrad · 2004-12-20 08:32 · Score: 2, Funny

...Eddie, your super friendly shipboard computer.
Performance Limits on Chemical Computation by tjic · 2004-12-20 08:34 · Score: 5, Informative

For those interested in such things, a friend wrote his PhD thesis on defining the limits of achievable DNA computation:
Performance Limits on Chemical Computation.
Viruses by goombah99 · 2004-12-20 08:41 · Score: 4, Funny

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.
I would prefer to use RNA by dfn5 · 2004-12-20 08:43 · Score: 3, Funny

Sure, go ahead and use DNA, if you want your data to mutate.
I will use RNA (Raided Nucleic Acid) instead.

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Carl Sagan pointed out in Dragons of Eden by museumpeace · 2004-12-20 08:45 · Score: 4, Interesting

[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.

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DNA computers by wronski · 2004-12-20 08:46 · Score: 4, Interesting

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
I can just hear it now... by Bhasin_N · 2004-12-20 08:47 · Score: 3, Funny

"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"
Re:Already see problems. by ClownsScareMe · 2004-12-20 09:07 · Score: 3, Funny

Take a wild guess.

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I read Slashdot for the articles
Re:So ... by lucabrasi999 · 2004-12-20 09:20 · Score: 2, Funny

We've gone from "heroicly unmodifiable" to "has modifiable sidechains" with two +5 informatives. Someone's right.
You have forgotten Slashdot Rule #6: Don't let the facts get in the way of the moderation.
Re:Convert me now! by Byzandula · 2004-12-20 10:34 · Score: 2, Informative

And you sir, are an Anonymous Coward!