DNA For Information Processing and Data Storage

ha by Anonymous Coward · 2004-12-20 08:17 · Score: 1, Funny

i hope the feds don't find any copyrighted material stored in my DNA...

Re:ha by bradkittenbrink · 2004-12-20 08:19 · Score: 1

Oh, they will... You can expect a letter from my lawyer.
Re:ha by hunterx11 · 2004-12-20 20:21 · Score: 1

I'm sorry, but clearly your DNA is the property of SCO. You'll have to buy a license if you wish to continue protein synthesis.

--
English is easier said than done.

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.

Re:It works on so many levels by tijnbraun · 2004-12-20 08:31 · Score: 1

On the otherhand the world is filled with enzymes called DNase that will willingly eat your TB DNA storage in no time.

Siliconase however does not exist.
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
Re:It works on so many levels by Anonymous Coward · 2004-12-20 08:37 · Score: 1, Interesting

See here. The data aren't being stored in the DNA, they're being stored in a magnetic layer on top of the DNA. The DNA sequence just drives the granularity of the magnetic layer. (To be precise, all this should be expressed in the future tense but I don't feel like backteracking...)
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.
Re:It works on so many levels by tijnbraun · 2004-12-20 08:52 · Score: 1

Well I quite certain they will not use 1 dna strand to store the data... they will use lots. See it as RAID but then with really cheap disks... and millions of them. As long there is no heavy selection on the replication (there is a bit of selection: AT bonds only have 2 H-bonds while CG has 3), it should be very accurate.

btw HIV is RNA (retro) virus
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.
Re:It works on so many levels by harvardian · 2004-12-20 09:13 · Score: 1

It is among the most unreactive, inert molecules in the biological world

The backbone of DNA is very stable, but the bases definitely do not fit your description (indeed, I smell troll). Bases can be oxidized (drink your anti-oxidants), thymines can be fused (UV light causes this), etc. The reason DNA retains such high fidelity over such a long time is because there are enzymes in the nucleus that are specifically designed to repair these unwanted changes (for example, 8-oxoguanine is repaired to guanine via a specially designed glycosylase). Somehow I doubt they're going to be including these in a chip, but you never know.
Re:It works on so many levels by BlueFashoo · 2004-12-20 11:44 · Score: 1

We in the real world have our own radiation resistant organisms. So we can't eat them and they are not exactly the most intelligent of organisms, but we have other animals for that. Deinococcus radiodurans, or "strange berry that withstands radiation," is the most radiation resistant organism known to science. A feisty little bug with some rather peculiar features. It's DNA is circular in structure, like all bacteria, but it also has many copies of the same molecule stacked on top of each other and special enzymes to repair it when damaged. Just thought you would be interested.

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Nice Marmot

640K DNA molecules... by GillBates0 · 2004-12-20 08:20 · Score: 2, Funny

ought to be good enough for anybody.

-GillBates0.

--
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.

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

--

Free XBox, PS2
Re:So how long... by JossiRossi · 2004-12-20 08:29 · Score: 1

9:32 Restate My Assumptions.

Been too long since I've seen Pi =) So the 3 word quote I gave is probably wrong.

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Just a boy doing unproffesional IT work that's way above his head.
Re:So how long... by roseblood · 2004-12-20 08:30 · Score: 1

Or
How long until someone injects this crap into themselves and brings about the end of the world?
[cough]Darwins Radio[/cough]

How do you use here w/o the damned site censoring out the funny fake HTML tags.

--
There are lies, damned lies, and statistics.
Re:So how long... by Flashbck · 2004-12-20 08:50 · Score: 1

If I had mod points you would be getting a few funny modifiers.

Oh and I watched Pi about a month ago and your quote is right on!
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
Re:So how long... by Khomar · 2004-12-20 09:44 · Score: 1

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?

Although I absolutely agree with you in regards to these crackpot code schemes, your reasoning here is flawed. The Christian God, as taught in the Bible, is omniscient (all-knowing) as well as sovereign (in control). He is outside of time and knows exactly what the future holds. Therefore, He certainly could think "far enough ahead" (especially if he thought "far enough ahead" to design the vastly complex yet strangely simple physical model on which our universe runs), and prophecy would be utterly worthless if He could not. However, every fulfilled prophecy is perfectly clear in the text when viewed from the future. There is not a single example of an encrypted message in the Old Testament quoted in the New Testament.

Therefore, while God certainly could have done it, there is no reason to believe that He has. Perhaps more focus should be placed on what is clearly stated in the Bible rather than looking for some "secret code" that probably doesn't even exist. I have found that most people who are looking for the codes do not even have basic understanding of the fundamental tenants of Christianity.

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I believe in de-evolution. God made the world perfect, man fell, and its been going downhill ever since!
Re:So how long... by leroybrown · 2004-12-20 10:01 · Score: 1

That's the difference between me and you... you believe that the Christian God is all-knowing, including the future and the outcome of our individual lives, therefore virtually anything can be argued and substantiated by saying "God and the bible say it, therefore it's true." I, on the other hand, do not believe in the Christian God, or his omniscient powers, or fatalism, so us arguing the point is pointless.

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Founder, Americans Allied Against Alliteration
Re:So how long... by Boronx · 2004-12-20 10:24 · Score: 1

So, do you believe in the omniscient God, or not? If so, why did he make man to fall?

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Play Command HQ online
Re:So how long... by Khomar · 2004-12-20 10:44 · Score: 1

Yes, I do believe in an omniscient God.

If so, why did he make man to fall?

Quite honestely, I do not know. Why did He create the universe at all. It is not as if He needed it. I suspect the truth relies somewhere in the realm of creating a being that could choose to follow Him and so that He could communicate and relate with them -- somewhat like a RPG developer. It would be much more thrilling to be able to create a truly AI game character that you could talk to and relate with rather than a scripted character with no freedom of choice -- who will choose to interact with you simply because that was how they were programmed. The problem, of course, with creating something that has choice is that it can then choose to reject you. God had to accept the bad consequences by giving the ability to reject Him in order to gain the advantage of a closer relationship with those who would choose to accept Him.

I don't know if I will ever understand completely why God does what He does, but I hope to ask Him someday.

--
I believe in de-evolution. God made the world perfect, man fell, and its been going downhill ever since!
Re:So how long... by Artifakt · 2004-12-20 11:31 · Score: 1

Christianity went through a period very early (from about 150 AD to a time a little past Constantine's conversion, say 350 AD at the latest), when the biggest heresy was called Gnosticism. The Gnostics were big on hidden messages, secret meanings only the elect could know, codes and symbols, and so on.
The basic reason for rejecting their ideas was when those ideas were reduced to simplest common assumptions, the Gnostics believed in a God who would damn all the stupid people just for not being smart enough to follow the Gnostic arguements. Their model assumed a coldly intellectual God, who wanted only the companionship of a few equally cold intellectual types. Everyone else was a throw away. At its best, Gnosticism incorporated some interesting and novel (for the time) ideas about the nature of creation and the origins of evil, pain and death. Some of these ideas were accepted by the mainstream in time, and there is still some interest on the part of Christian scholars in studying the whole movement. At its worst, however, it was a flurry of arguments each designed to exclude some person or group so someone else could feel superior for being a 'real' Christian. (Yes we still have a tendency to fall into this error, sorry!).
My own take on this point is: God doesn't want to hide anything. As Einstein said, He may be subtle, but not malicious. IF there's any hidden code in the Bible, it isn't needed for salvation, or even for anything else even half-way as important as that. Love that which created you, and love your neighbor - the rest is, (by comparison) commentary.

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Who is John Cabal?
Re:So how long... by Boronx · 2004-12-20 11:54 · Score: 1

I don't see how God could be omniscient and still think the choices we make are interesting, since he to him they appear scripted just like bad RPG NPCs. But the moment he makes the script interesting, with some fuzzy or random or chaotic function, then the devoloper loses his omniscience, since he can't possibly know what his own creation will do next.

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Play Command HQ online
Re:So how long... by anethema · 2004-12-20 12:41 · Score: 1

Exactly, omniscience and free will cannot exist in the same universe.

--

It's easier to fight for one's principles than to live up to them.
Re:So how long... by drgonzo59 · 2004-12-20 18:13 · Score: 1

For a comment on a geek playground (read "Slashdot") that is a pretty good description of the God's purpose for the Bible. You are the first person, I've seen on Slashdot that seems to have any knowledge of church history. I would agree with you and I don't think the Bible was meant to be a history, math, cryptography, astrology or sociology manual. It pertains only to God's relationship to humanity, faith and salvation. It discusses and mentions specific places and names but overall that is not the purpose.
Anyway back to discussing Linux and how we don't like Microsoft.

Convert me now! by Byzandula · 2004-12-20 08:21 · Score: 1

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.

Re:Convert me now! by Byzandula · 2004-12-20 10:34 · Score: 2, Informative

And you sir, are an Anonymous Coward!

The things people doubt by Marxist+Hacker+42 · 2004-12-20 08:21 · Score: 1, Interesting

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?

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SJW: a person who perceives an injustice, and while correcting it, commits a greater injustice.

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.
Re:The things people doubt by Marxist+Hacker+42 · 2004-12-20 08:39 · Score: 1

Oh, ok- so more like nanotechnology than actual biomatter data storage. The only data being stored in the DNA itself is the PATTERN of the storage material- which in turn stores the data AFTER the DNA has been wiped away.

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SJW: a person who perceives an injustice, and while correcting it, commits a greater injustice.
Re:The things people doubt by myowntrueself · 2004-12-20 12:13 · Score: 1

I studied this at uni as part of my (*abortive) MSc degree;

I was looking into genetic algorithms at first, then decided that to really understand genetic algorithms I should look at nature and went and studied cell bio and genetics. For a comp-sci guy that was a humbling experience... we think that we are so smart with our computers but they have nothing on the simplest of organisms. Anyway, where was I oh yeah

Leonard Adelman (sp?) did some really interesting work with DNA computing (about 10 years ago, probably what you are referring to) like a solution to the Travelling Salesman Problem in O(1). Well... O(1) in time but still a bit exponential in space.

Still, an olympic size swimmingpool of DNA solution would solve most of the TSP's that you'd want

:)

Then theres the work I read about involving hijacking the RNA editing mechanisms of trypanosomes (the protist that causes sleeping sickness). Their RNA editing mechanisms (which they use to change coat proteins to evade immune response) was demonstrated to be Turing complete.

Protists are awesome; our trick, as multicellular organisms, is that we build houses out of lots of bricks. But protists build an entire house out of just *one* brick. I think thats impressive.

--
In the free world the media isn't government run; the government is media run.
Re:The things people doubt by Marxist+Hacker+42 · 2004-12-20 12:55 · Score: 1

As I remember- it was the RNA stuff that I read about, basically switching from base-2 to base 4 (GATC) encoding to get extremely dense storage.

Protists are awesome; our trick, as multicellular organisms, is that we build houses out of lots of bricks. But protists build an entire house out of just *one* brick. I think thats impressive.

I agree- it's amazing how much is packed into a single cell organism.

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SJW: a person who perceives an injustice, and while correcting it, commits a greater injustice.
Re:The things people doubt by myowntrueself · 2004-12-20 13:19 · Score: 1

"I agree- it's amazing how much is packed into a single cell organism."

they are so sophisticated; one of the things I always wanted to try was putting protists through the kind of cognitive psych tests that they use on rats and pigeons to guage their intelligence and ability to learn from experience. I have a suspicion that there would be some surprises..

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In the free world the media isn't government run; the government is media run.
Re:The things people doubt by Marxist+Hacker+42 · 2004-12-21 04:26 · Score: 1

I wouldn't doubt it- there's got to be some instincts in there somewhere. I seem to remember a theory about mitochondrial memory some time back- wouldn't surprise me a bit if a protist had enough mitochondrial DNA to form some sort of a memory structure to carry that form of information.

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SJW: a person who perceives an injustice, and while correcting it, commits a greater injustice.

SCO and DNA by lordsilence · 2004-12-20 08:22 · Score: 4, Funny

Just wait till SCO find infringing code in YOUR DNA..

Re:SCO and DNA by peragrin · 2004-12-20 09:15 · Score: 1

Well you have two arms, two legs, ten fingers(counting thumbs) and ten toes.

Yep you must be of your protected IP.

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i thought once I was found, but it was only a dream.

Hi-Tech & Stylish... by YodaToo · 2004-12-20 08:23 · Score: 1

DNA "tiles" that spontaneously assemble in a predetermined pattern to form a sheet of molecular fabric, much like corduroy.

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This way to the egress...

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

Re:Slow Posting by cflorio · 2004-12-20 08:33 · Score: 1

No, my guess they are all Christmas Shopping... Probably at a website, there's no way the average /. reader is going to go to a mall.
Re:Slow Posting by grahamsz · 2004-12-20 08:40 · Score: 1

You must be new here...

base 5 computing? by Chillybott · 2004-12-20 08:24 · Score: 1, Insightful

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.

Re:base 5 computing? by Mr.+McGibby · 2004-12-20 08:30 · Score: 1

Your post shows a complete lack of understanding of DNA completely. Please don't post about this again.

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Mad Software: Rantings on Developing So
Re:base 5 computing? by lubricated · 2004-12-20 08:54 · Score: 1

wow this makes me shiver when I read it.

1. it's spelled protein.
2. It can only be a, c, g, t in dna
3. those aren't proteins they are bases
4. Proteins are coded by dna, they do not comprise dna in any way.
5. Dna doesn't get spliced during cell replication. It gets copied.
6. therefpre isn't a word.

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It has been statistically shown that helmets increase the risk of head injury.
Re:base 5 computing? by jacksonj04 · 2004-12-20 09:05 · Score: 1

no, he was right first time. base 5 - NULL, A, C, G, T.

Except I can't think of an easy way to have a NULL in place of a base... hmm.

--
How many people can read hex if only you and dead people can read hex?
Re:base 5 computing? by Chillybott · 2004-12-20 09:15 · Score: 1

Yeah - that WAS what I was thinking re: the fifth value....but the more I think of it, the more I think it can't be done. It'd have to be base 4....the peptides (yeah yeah, not protiens) need a partner with which to bind, so a NULL would not really work it seems to me.

Now - if I recall correctly, each base can only pair with one other base - so that the quaternary digits would be foreced to come in specific pairs, limiting somewhat the gain of a base 4 system I would guess.

Anyway - thanks for the clarification...it's nice to see it done in a constructive manner (and you didn't karma yourself up to do it either ;p )

--
You gotta make something explode to really understand it...examine all those tiny particles while they're still on fire.
Re:base 5 computing? by Tsiangkun · 2004-12-20 09:18 · Score: 1

1 A 00
2 T 01
3 G 10
4 C 11

How does this lend itself nicely to base 5 ?
Re:base 5 computing? by jacksonj04 · 2004-12-20 09:23 · Score: 1

Actually you're right - it wouldn't even be base for because you can only have CT and AG pairs (I think, any molecular biologist want to correct)? So effectively you get base 2.

Unless, I suppose, you have a way of only reading one half of the helix, in which case you can use all 4 bases independantly. Euch...

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How many people can read hex if only you and dead people can read hex?
Re:base 5 computing? by lubricated · 2004-12-20 09:39 · Score: 1

> .the peptides (yeah yeah, not protiens)

No they are not peptides either. They are simply bases. You are right though NULL doesn't work. The fact that they come in pairs doesn't limit this in any way. You always get 2 strands of dna they pair with each other. So long as you only look at one strand there are four possibilities in each position.

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It has been statistically shown that helmets increase the risk of head injury.
Re:base 5 computing? by lubricated · 2004-12-20 09:44 · Score: 1

> any molecular biologist want to correct

Well a biochemist of sorts would be better. As a genetecist I'll respond. A pairs with T and C pairs with G. Dna is a double helix and one is an exact inverse copy of the other. Where one has an A the other has a T and vice versa. Since generally only one strand is read you have base 4 at each site.

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It has been statistically shown that helmets increase the risk of head injury.
Re:base 5 computing? by izomiac · 2004-12-20 13:02 · Score: 1

Or nucleotides... Peptides are what genes code for (after RNA splicing and everything). Although, it might be possible to have base-5. Perhaps Uracil could be used in artificial DNA (it's already in RNA). Of course, that'd probably make replication harder, since the DNA replication process would probably need to be modified to accommodate the extra base.
Re:base 5 computing? by lubricated · 2004-12-21 04:08 · Score: 1

> Perhaps Uracil could be used in artificial DNA (it's already in RNA).

This would be very difficult, Since each strand is a template for the other during replication. If adding uracil as a seprate base you would also loose the nice RAID(mirroring) feature.

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It has been statistically shown that helmets increase the risk of head injury.

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...

Re:Nasty unforeseen consequence by SsShane · 2004-12-20 08:42 · Score: 1

insert into dna_Widgets values (*COUGH....AHHCHOOOBLEHHHH!!!);

>>BLESS YOU
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:Nasty unforeseen consequence by Tablizer · 2004-12-20 10:45 · Score: 1

Unfortunately, when the tune "Jingle Bells" is coded in DNA for storage, it turns out to be a version of the flu...

Virus? So that's why I can't get that damned Brady Bunch theme song out of my head dispite a reboot (good night's sleep).

--
Table-ized A.I.
Re:Nasty unforeseen consequence by Tablizer · 2004-12-20 10:55 · Score: 1

Unfortunately, when the tune "Jingle Bells" is coded in DNA for storage, it turns out to be a version of the flu...

It would even be more ironic of the Goatse image encodes the cure for cancer.

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Table-ized A.I.
Re:Nasty unforeseen consequence by izomiac · 2004-12-20 13:07 · Score: 1

I can see it now... some bacteria mistakes a computer virus for a plasmid and you have a bacterial version of AIDS. Of course, if it's an STD then it probably won't spread given the people exposed to it.

Re:Cheaters Paradise? by bradkittenbrink · 2004-12-20 08:25 · Score: 1

Just because the information is in my body somewhere doesn't mean I can access it during an exam. Otherwise I'd have gotten perfect scores on every exam. My point is that you just need to prohibit DNA reader devices, then all the DNA cheat sheets in the world won't help you any more than all the Spanish I've learned helped me during the exams...

What are the possibilities? by jessecurry · 2004-12-20 08:25 · Score: 1

The article states that this technology could be used to allow for faster recognition technologies, but can this be used to create a computer in the more typical sense?

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?

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Those who know, do not speak. Those who speak, do not know. ~Lao Tzu

Already see problems. by RedA$$edMonkey · 2004-12-20 08:27 · Score: 1, Funny

Damn, now where did I put that strand of DNA with all my pr0n.

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:Already see problems. by c.emmertfoster · 2004-12-20 15:47 · Score: 1

It's probably on a dirty sock, with the rest of your genetic material.

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We can neither love nor pity nor forgive. If you make a slip in handling us you die!

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

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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----- One learns to itch where one can scratch.
Re:DNA heroically unchanging by handy_vandal · 2004-12-20 08:52 · Score: 1

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.

Thanks for the clarification.

-kgj

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-kgj
Re:DNA heroically unchanging by CupBeEmpty · 2004-12-20 20:07 · Score: 1

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.

Hrmmm.... as a cellular biologist I must protest. Some DNA is "heroically unchanging". Some is actually incredibly variable. What is truly impressive is the ability of biological systems to squelch DNA mutations (ie change/damage) by killing damaged cells before they can copy themselves and repairing DNA damage. Without these repair mechanisms cell lines that would normally live literally forever if allowed to grow in sufficeint media (immortal cancer cell lines) die because of DNA damage by UV light in a matter of hours. So under the right conditions, the right DNA can be "heroically unchangeable" but it is not nearly that simple. The number of DNA samples that I have lost in lab due to degredation can attest to that.

I am not yet ready to lay all my trust in DNA for data storage, although I am sure that there are more short-term memory needs on the nano scale that DNA is perfect for.

DNA does not clone perfectly by Anonymous Coward · 2004-12-20 08:29 · Score: 1, Interesting

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.

Re:DNA does not clone perfectly by stratjakt · 2004-12-20 08:58 · Score: 1

Umm, it would be exact because the algorithm to copy would be:

copy(file1, file2)
while (md5 of file1 != md5 of file2) { try again }

You should be verifying your backups no matter what the storage medium is.

DNA is AFAIK, much more "stable" than photoreactive dyes or magnetic films. Crocodiles have had the same DNA for billions of years, how long will your CD-R last?

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I don't need no instructions to know how to rock!!!!

But Office is bigger than your DNA. by Anonymous Coward · 2004-12-20 08:31 · Score: 1, Funny

I doubt Gates said this, considering that Microsoft Office is bigger than your entire genome

Either Human DNA is programmed very well, or Office is programmed very poorly.

Re:But Office is bigger than your DNA. by Bnonn · 2004-12-20 14:42 · Score: 1

Or both.

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?

Re:DNA versus the Elecron by liangzai · 2004-12-20 08:51 · Score: 1

Can't go smaller. Quarks are bound in pairs or triplets, unless a tremendous amount of energy is released to overcome the strong force that glue quarks together. It is meaningless trying to communicate with a single quark.

Neutrinos interact extremely weakly with other matter particles, and only rarely is there a "collision" that causes a reaction. This is why it takes a year to detect a neutrino hit in tons of water buried deep underground. Furthermore, neutrions can't be contained like an electron.

Photons carry information, but they need a trigger, like electrons. Photons have the awkward feature of traveling at the speed of light, and so cannot be contained for more than a few picoseconds.

Now there is of course the possibility of entangled photon pairs http://www.sciencedaily.com/releases/2000/09/00092 6071220.htm, but this is still mostly theoretical stuff.
Re:DNA versus the Elecron by AtillaTheKilla · 2004-12-20 09:13 · Score: 1

DNA might be more efficient yet, because each slot can contain 1 of 4 states, so we'd be working in base 4 instead of binary.
Re:DNA versus the Elecron by Jerf · 2004-12-20 11:15 · Score: 1

*mouth drops*

*eyes boggle*

Pop quiz, a DNA molecule (I'll be sporting and add "the smallest one possible") contains how many electrons?

How does your universe work, where the fundamental information element of the universe is the "slot"?

Make your own at home by ksaylor · 2004-12-20 08:31 · Score: 1

Wow, it looks all you need is some velcro and corduroy pants...

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

...Eddie, your super friendly shipboard computer.

D'oh by Anonymous Coward · 2004-12-20 08:33 · Score: 1, Funny

That means data integrity, a Good Thing.

So MySQL won't support it, then---but you can do it in the application layer.

I, Jedi by silvergoose · 2004-12-20 08:34 · Score: 1

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?

Just Imagine.... by Bucky_the_AV_Guy · 2004-12-20 08:34 · Score: 1

no more electronic viruses. Now we can have the real thing.

Not only does your computer get infected....so do you!.

Re:Just Imagine.... by izomiac · 2004-12-20 13:10 · Score: 1

So your computer helps in a DDOS attack against www.whitehouse.gov while you drive there and start pounding on the doors?

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.

Re:Performance Limits on Chemical Computation by Jerf · 2004-12-20 09:27 · Score: 1

Wow, excellent link.

The Slashdot-relevant portion of the abstract:
I compare the maximum possible performance of proposed DNA computers from the literature with current commodity electronic computers, and conclude that diffusion-driven, DNA hybridization based computers cannot exceed the performance of current electronic computers by more than a factor of 40,000, and probably by much less.
This doesn't speak to using DNA as a construction scaffolding, which I am not skeptical of, but DNA computing has never impressed me, and this gives rigorous arguments backing up my intuition, and based on my reading, I think he's not even discussing the setup time necessary for complicated chemical computing, just the processing time. Check out pages 70ish-77ish.

Using the discussion on page 76 in section 4.2 as a jumpoff, my problem with DNA computing is that it can never beat properly-designed electronic or optical computing, because DNA can never match the speed of the "molecules" used for information transport in such systems, electrical impulses or photons respectively, with that last one being rather firmly unbeatable. It isn't that DNA computing is impossible, it is that it can't be better than current or certainly feasible future systems (not even counting optical) for any computational problem. (It has, on the other hand, proven a certain utility for storing data in an organic system, but DNA doesn't so much compute in the body, as have computation done on it...)
Re:Performance Limits on Chemical Computation by espressojim · 2004-12-20 10:06 · Score: 1

Unless of course you consider that the only problems that are worth solving on DNA computers are ones that are massively parallelizable.

On the other hand, synthesising all those oligonucleotides is still pretty expensive. Ordering 20 oligos in the order you want them might cost you $.50 or a $1 (if I remember my numbers right...) Or is it about $1 a base? I haven't looked at the lab side of things for prices in a while.

Needless to say, if you want to order a TON of different oligos to to some massive operation, it's going to cost you time and lots of money to synthesise what you want to run. And what if you screw up your 'code', and you have to run it again with a different set of oligos? Ouch. I guess you'd have to 'debug' pretty heavily with simulations before you do the real thing, which um...might be as good as just doing it on a computer.

Ouch.

-Jim
Re:Performance Limits on Chemical Computation by JDevers · 2004-12-20 10:37 · Score: 1

$1 per base with ~$15 per oligo up front fee (at least that is what I pay MWG, but we order small quantities and only a few at a time...)
Re:Performance Limits on Chemical Computation by Jerf · 2004-12-20 11:03 · Score: 1

Unless of course you consider that the only problems that are worth solving on DNA computers are ones that are massively parallelizable.

You're wrong.

Specifically, you're wrong in the assumption that I haven't considered it.

Read the paper. If you don't understand it (I basically did, I have the background for it), well, you feel free to believe whatever you like, but have you got the science?

Amoung the other points made in that paper, parallelism isn't free; consult the paper for details. A well-designed, real world super-computer of today, and a commodity computer of tommorow, will beat any feasible DNA computer, no matter how perfect the problem is for DNA computing... and the paper even grants DNA computing its theoretical max capabilities given that the "soup" is already set up which is exceedingly unrealistic.
Re:Performance Limits on Chemical Computation by brettper · 2004-12-20 15:14 · Score: 1

So is there a discount for all your base?
Re:Performance Limits on Chemical Computation by espressojim · 2004-12-22 18:37 · Score: 1

I don't much doubt you on the infesability of DNA computers. As a former molecular biologist (turned informatics guy), I have an idea of what primers cost, and how much effort it would take a lab to run any sort of analysis.

Even if it took a cluster a week to solve a problem, that would still be "free", as the cluster is running, and we don't really count electricity bills in our lab costs. Primers cost money, money takes PO's, and PO's have to be explained to the boss.

I can solve any problem using the lab clusters (and hey, MIT has a fairly nice set of machines for me to use any time I want...:) On top of that, after I write the code, there's no additional effort - what if the person running the lab work screws it up? After working in a lab for 5 years, I can say - it does happen, and you'd hate to waste the time and effort repeating the process (and if you get results you wouldn't assume are right, you'll repeat the process anyway, just to make sure...)

Wont take off by wizardNinja · 2004-12-20 08:36 · Score: 1

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!"

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-- +

And it's really fun to make backups.... by Anonymous Coward · 2004-12-20 08:38 · Score: 1, Funny

Sex as a backup device!!!! That's way cooler than tape drives.

Re:And it's really fun to make backups.... by Tackhead · 2004-12-20 09:12 · Score: 1

> Sex as a backup device!!!! That's way cooler than tape drives.
"Only wimps use tape backup: real men just wank over their ftp server, and let the rest of the world mirror it."
- Definitely Not Linus Torvalds
Re:And it's really fun to make backups.... by chadjg · 2004-12-20 11:08 · Score: 1

Does mean, somehow, that condoms are now illegal under the no-circumvention provisions of the DMCA? Maybe Senator Hatch and friends really were forward thinking folks.

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Why do I have this? I don't smoke.

USB Time by jedkiwi · 2004-12-20 08:39 · Score: 1

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...

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?

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Some drink at the fountain of knowledge. Others just gargle.

An extra "h"? by carcass · 2004-12-20 08:41 · Score: 1

Heh heh heh. Richard Kiehl. DNA.

Am I the only one who thought of the MST3k episode where they did "The Human Duplicators?"

Re:An extra "h"? by BeaverCleaver · 2004-12-23 17:57 · Score: 1

Yes.

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sustainable living

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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-- Thou hast strayed far from the path of the Avatar.

Re:I would prefer to use RNA by espressojim · 2004-12-20 10:09 · Score: 1

You mean the stuff that degrades naturally, and is hard-as-hell to work with without totally screwing up? :)

After doing DNA-RNA extractions and experiments for a while, I know which one I'd rather work with.

-Jim

Live Sex on DNA spirals by bennyp · 2004-12-20 08:45 · Score: 1

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.

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could it be?

Re:Live Sex on DNA spirals by xyeeyx · 2004-12-20 09:04 · Score: 1

What will happen when the internet's vast archive of midget porn and snuff films gets stored on DNA strands?
george w. bush

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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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.

Re:Carl Sagan pointed out in Dragons of Eden by Tablizer · 2004-12-20 10:51 · Score: 1

[late 70s] that DNA was the only persistent data storage media nature had until we apes invented languages that we could symbolically preserve.

Persistence is relative. We and our language might be wiped out by a comet or nukes one of these days. I think you mean inter-generational persistence. However, most mammals pass at least some knowledge to their children, who in turn pass it on to their own. For example, if a mother teachers her cub that it is okay for the cub to eat barries and fish, then the cub will probably teach that to her children also. They may not otherwise learn this on their own.

Incedently, it makes for interesting debates to think about programming if there is no (visible) difference between RAM and disk.

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Table-ized A.I.

Human Computer by Dash'n'SlashDot · 2004-12-20 08:46 · Score: 1

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~

Re:Human Computer by Dash'n'SlashDot · 2004-12-20 08:51 · Score: 1

As a side thought, the keyboard implant in the arm would work, since most of us are surely adept at typing one-handed *cough*

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

Re:DNA computers by pragone · 2004-12-20 09:14 · Score: 1

Very interesting stuff because The Travelling Salesman Problem is NP-Hard. Perhaps, you were looking for http://physicsweb.org/articles/news/6/3/11/
Re:DNA computers by wronski · 2004-12-20 09:33 · Score: 1

Thanks for the link. The DNA sorts out this NP-Hard problem by doing massively parallel classical computing in a test tube (putting Google to shame). The other cool way of solving NP stuff (like factoring large numbers) effectively is quantum computing, which is different in a pretty fundamental way (but also off-topic).
Re:DNA computers by Boronx · 2004-12-20 10:28 · Score: 1

Heck, if you want to use DNA to study protein folding, why not just code the protein in DNA, mixit up with some transcriptase, some ribosomes, some RNA and some amino acids and fold the darn thing?

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Play Command HQ online
Re:DNA computers by espressojim · 2004-12-20 10:28 · Score: 1

How much does it cost to generate those billions of oligo combinations?

I forget what the current cost of an oligo for an order is, but it might be on the order of $1 per 20bp. Or maybe I have that an order of magnitude too cheap.

Why 20bp? That's a normal standard for 'unique in the human genome' length for a primer. I'd guess when you're in the 'billions' of sequences, you'd probably go at least that specific. Good luck checking them all to make sure they aren't cross-reactive, btw.

So, you're talking about massive amounts of money to get a 'real' computer up and off the ground. The one advantage is that you can solve the same problem over and over - or, if you can reuse subsets of a massive oligo order, you might be better off.

But, between price, time, and design issues, I can't imagine someone doing this in the near future. It's just not a feasable from the reagent side of things.
Re:DNA computers by wronski · 2004-12-20 11:27 · Score: 1

For another NP-complete problem Adleman et al. generated a small (40) number of sequences (equivalent to one for each city in the TS problem), and let them self-assemble randomly into a much larger number (1 048 576) of candidate answers (equivalent to paths in TS). See the link in Pragones post above for details.

I suppose this can be scaled up in a a working computer so as to have some 1000 seed sequences generating all those billions and billions of sequences I so Carl Sagan-ly mentioned.

IANA Molecular Biologist, so correct me if I am wrong, but it seems to me these prices apply only to specific sequences of base pairs. You can stay in the black by generating semi-random sequences. I have no idea how to solve the cross-reactive problem you mentioned, but this apparently was sorted out as well.

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:This is such bullshit. by Bucky_the_AV_Guy · 2004-12-20 08:51 · Score: 1

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.

Re:TROLL !!! by jacksonj04 · 2004-12-20 08:54 · Score: 1

a. It's not trolling, possibly misinformed and:
b. It's actually right. If you wish to be a molecular biologist, post with a name so you have some actual respect.

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How many people can read hex if only you and dead people can read hex?

Re:interdimensionall by NarrMaster · 2004-12-20 08:55 · Score: 1

What the hell are you talking about? If this is an elaborate joke that I don't get, please, fill me in.

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That's right. All your base.

Been done in Star Trek by randomErr · 2004-12-20 08:58 · Score: 1

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.

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You say things that offend me and I can deal with it. Can you?

Re:Been done in Star Trek by Raistlin77 · 2004-12-20 09:50 · Score: 1

If ST:TNG already did this, then wouldn't it be life imitating art?

DNA is problematic. by jd · 2004-12-20 08:59 · Score: 1

First of all, it is super-twisted. That means that you've massive latency in accessing it. Secondly, it is linear, which means that finding the Nth "word" is going to be HORRIBLY slow. Thirdly, the existing duplication system is "good enough" only on a large scale. Finally, the protein generator has no exception handler, so if the raw materials aren't available, there is no means of handling the exception.

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.

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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)

Re:DNA is problematic. by myukew · 2004-12-20 09:33 · Score: 1

"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.)" Are you really sure you can do this with an electron? IANAP, but I think this is quite impossible. You'd need to split the 20-Ca in 13-Al and 7-N... show me an electron with enough energy to do that and you get a buck

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See pictures of tits
Re:DNA is problematic. by jd · 2004-12-20 10:28 · Score: 1

High-energy cosmic rays travel awfully fast, so don't blink...

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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)
Re:DNA is problematic. by izomiac · 2004-12-20 13:18 · Score: 1

Finding the Nth word wouldn't have to be slow. Just label each data value with it's position in terms of N and have a protein find it (or several thousand identical protieins with markers scattered across the length of the molecule). It's not like RNA Transcriptase has to travel down the entire DNA strand before it can transcribe a gene.
Re:DNA is problematic. by myukew · 2004-12-20 20:12 · Score: 1

Yeah ok, but those aren't electrons (ok, some are but...), an electron has a mass of 9.11 × 10^-31 kg [wikipedia] it's max. energy can thus be m*c^2=8,199*10^-14 J.

I doubt this is enough

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See pictures of tits

Re:If Euro rejects software patents by xyeeyx · 2004-12-20 09:01 · Score: 1

i call the DNA of halle berry

The Selfish Gene... by MicroBerto · 2004-12-20 09:03 · Score: 1

I just finished reading Richard Dawkins' The Selfish Gene, and was thinking about some stuff like this. Note that I'm a computer engineer and don't know much about this stuff:

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...

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Berto

Re:The Selfish Gene... by Dachannien · 2004-12-20 09:46 · Score: 1

The reason we use binary computers is because computers are based on transistors operating in saturation mode, and long-term storage is based on alignment of magnetic materials or optically reflective pits. I suppose we could have computers whose basic unit of data had more than two levels, but it would be a lot less reliable than our current technology until some significant problems could be solved (such as getting these non-saturation-mode transistors to work well at very, very high speeds).

On the other hand, it's hard to say why evolution originally resulted in organisms all of which use the same four bases in their DNA. But it's pretty easy to say that, once transfer RNA was encoded in the genome and proteins started to be built based upon those tRNA sequences, the scheme of using those four bases became essentially carved in stone, since even the smallest change to the scheme makes every single protein produced by an organism no longer function properly. There's just no evolutionary path out, and so the fact that life on Earth has used these four bases for many hundreds of millions of years doesn't really reflect on the efficiency or insight of the system, just that it worked well enough originally to bootstrap itself into a place where it's irreplaceable.
Re:The Selfish Gene... by Anonymous Coward · 2004-12-20 14:12 · Score: 1

So why don't we copy it when doing computing?

The main reason is that even Evolution finally dropped this idea. DNA was way to much overhyped back than: DNA this, DNA that. But Evolution kept cool and finally came up with something called Brain. Brain was even cooler and came up with Computer. Now that is something for computing.
Re:The Selfish Gene... by gibson_81 · 2004-12-20 17:40 · Score: 1

Well, technically, I think DNA is binary too =) what matters isn't what base you have, but what base pair. Each of those four bases match with only one of the others (don't remember which ones though). It might be a bit weird to talk about "reasons" for why DNA is the way it is, but if I do it, then the reason for using base pairs instead of bases is that it's a lot easier to detect errors in copying - if one of the bases on the copy is wrong, the DNA will not match up.

Speed of the Brain by Omniscientist · 2004-12-20 09:03 · Score: 1

The technology could help computers identify objects in images with something approaching the speed of the human eye and brain

Man, always thought my computer had no trouble winning against my brain in terms of speed.

Re:Speed of the Brain by rzebram · 2004-12-21 12:57 · Score: 1

Perhaps in your case, yes, but for everybody else, the brain is the most powerful computer around. Millions of "transistors" with millions of paths between them combine to form a computer on your shoulders far faster than anything you can possibly have on your desk.
Re:Speed of the Brain by Omniscientist · 2004-12-28 22:06 · Score: 1

I totally agree with you. Why wasn't this modded up?

Re:Proof !!! by Bucky_the_AV_Guy · 2004-12-20 09:17 · Score: 1

See. All you talk about is bullshit.

Well with a carefully crafted argument like that, it is hard to respond but I'll do my best....

First - base4 computing: yes I realise it could/can be done in silicon, and possibly this is something we may see come into reality before DNA computing but as of yet it is not something that has really come into practical use. The advantages of base4 computing would be very large compared to binary systems. Computing times would decrease, storage capacities would increase etc... There is nothing wrong with taking a few different approaches however.

Administering computers as a pharmaceutical: No need to roll your eyes. If one were to create a specific "virus" that can target certain cells, such as malignent cancers and respond based on what it "finds" this would be an example of a simple computer. Most diseases are a) multifactoral and b) expressed/caused differently in different people (and even in different cells of the same person). As such, it is very hard to find a "one size fits all" solution. If we were able to create a virus encoding several different siRNAs for example but only express the ones necessary for the particular cell being infected it would be of tremendous benefit and potentially reduce side-effects that are so common with traditional pharmaecuticals. Yes this is out there but not beyond the scope of what some people are hoping to do.

Artificial Cells: Sure artificial cells have been created in some basic ways, however, we can make it more efficient and able to respond specifically to certain stimulii and provide output signals by using "DNA computing". If you were to read the title of the topic, it talks about processing AND data storage. Granted data storage is not necessary for this application (although I am sure someone with a bit of imagination can see how it would come in handy - a cell for example that gathers information about its environment and stores that information), but the processor potential would be interesting.

Simply dismissing the potential of this work is short sighted. The people working on this have many peers inside and outside their fields that obviously think there is potential or they would never get any funding from the granting agencies. I assume however from your very witty retorts that you are more highly educated than these people.

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.

The problem is the energy by mangu · 2004-12-20 09:20 · Score: 1

You can store information on anything, as long as you keep the temperature low enough or the energy high enough. The minimum energy per bit you need is kT/6, where k is Boltzmann's constant and T is the absolute temperature of the medium where your information is stored. Sure, you can store a bit of information as the polarization of a free electron. But unless the temperature is low enough, your information will be quickly randomized by thermal noise. Or else you can have your electron in an atom, inside a molecule in a crystal, and then the total mass of your setup will be much larger than an electron.

What people often don't realize when they read popular articles about quantum experiments is that they are usually performed in extremely low temperatures.

Re:Nasty unforeseen consequence - Hijacking by Supero100 · 2004-12-20 09:24 · Score: 1

In Solviet Russia, the DNA computes YOU!

The plan by Jason+Mitcheson · 2004-12-20 09:33 · Score: 1

1: Theorize alternative data storage means with total disregard for reality and submit a story on it to /. 2: ??? 3: Profit!

Re:This is such bullshit. by Massamune · 2004-12-20 09:34 · Score: 1

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.

Hacking DNA by TheSync · 2004-12-20 09:43 · Score: 1

By the way, if you want some good info on home hacking of DNA, proteins, etc. check out DNAhack.com.

A DNA Computer? by myukew · 2004-12-20 09:54 · Score: 1

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

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So now... by infinite9 · 2004-12-20 09:55 · Score: 1

You can put all your pr0n on DNA instead of putting your DNA on your pr0n!

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Dear GOD people! RTFA! by flynns · 2004-12-20 09:56 · Score: 1

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]

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mod the parent up! by myukew · 2004-12-20 09:56 · Score: 1

mod the parent up!! This site is great!

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Had to be said. by pragma_x · 2004-12-20 10:05 · Score: 1

Imagine yourself: a beowulf cluster of these things.

Re:Had to be said. by Legato895 · 2004-12-20 10:30 · Score: 1

i was just waiting for it....

Oncology for Data Recovery Operations? by 0311 · 2004-12-20 10:15 · Score: 1

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...

evolution. by blackomegax · 2004-12-20 10:32 · Score: 1

does this mean all our porn will start evolving, resulting in a big porno ring run by skynet?

Zombie by Tablizer · 2004-12-20 10:41 · Score: 1

So *that's* why I am so forgetful. Some hacker is stealing cycles from my brain.

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Table-ized A.I.

Safeguards In Mind? by buckhead_buddy · 2004-12-20 10:56 · Score: 1

To think that when I was born, the idea of using DNA to identify suspects at a crime scene was unheard of, but now criminals have to be mindful of hair loss, dandruff flakes, and any sort of DNA they might accidentally leave lying around that could incriminate them.

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:

GNU authors working on widely avaiable, open-source drugs that undermine lucrative drug markets.
Macro virus writers authoring new strains of Ebola or SARS to kill some time between classes.
Militant vegans creating a mad-pig virus to introduce into the Hormel Spam plants.
BitTorrent being sued by the NBA for supplying athletes with performance enhancing viral strains.
Every person with a Napoleon complex engineering yet another weapon or drug to further their goals.
Religious evangelicals engineering their mythological creatures and monsters into reality.
Anti-abortionists engineering a prenatal drug that makes it impossible for a mother to abort a fetus without taking her own life.

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

Broken data mends itself? by phorm · 2004-12-20 11:36 · Score: 1

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?

Forget the spies by phorm · 2004-12-20 11:39 · Score: 1

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.

Thanks for the link by Catullus · 2004-12-20 11:52 · Score: 1

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... by freedom_india · 2004-12-20 12:13 · Score: 1

infinitely indexed memory bank...Somehow the Movie seems to come true...

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"Doing what i can, with what i have." ~ Burt Gummer

Woah there... by commieboyredux · 2004-12-20 12:19 · Score: 1

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!

Oh no - here it comes... by Linker3000 · 2004-12-20 13:10 · Score: 1

Will applications released for free use with DNA RAM be known as 'Open Wound'? [makes hurried exit]

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Re:With a name like "Seeman" by Doc+Ruby · 2004-12-20 14:40 · Score: 1

Moderation -1
100% Troll

What is remotely "Troll" about that post? This TrollMod crisis is getting ridiculous.

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Re:Cheaters Paradise? by Nefarious+Wheel · 2004-12-20 17:09 · Score: 1

Geez .. maybe they could just add the information to your DNA as you walk through the door. Save the hangovers.

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DNA for Data Storage Just Another Worm by fedrive · 2004-12-20 17:16 · Score: 1

This technology will never have " REWRITABLE " potential, but will be a great back up, distribution disk, or write once read many times disk.

Me too, please by multatuli · 2004-12-20 20:45 · Score: 1

Gosh! DNA s awesome! I want it, too. Tons of it.

Re:This just doesn't seem like a good idea... by Viol8 · 2004-12-20 22:39 · Score: 1

Indeed. They seem to forget that DNA in cells require a HUGE amount of supporting biochemical infrastructure to make it work and keep it together. Without that it would , like any other complex biological molecule break down and/or be eaten by bacteria. And as you mention , the temperature problem is not a small one. Unless they come up with some sort of "life support" system for these DNA computers they'll be useless in all but the most benign enviroments. DNA is found in nature because thats one of the few ways you can get SELF REPLICATION chemically. If you simply want pure COMPUTATION or storage then you're probably better off looking elsewhere.

hmm... by Siva · 2004-12-21 05:23 · Score: 1

"Solylent RAM is people! It's people!!!"

hmm...maybe not...

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Re:interdimensionall by MindStalker · 2004-12-28 05:35 · Score: 1

Na, I don't think he is joking, take a look at
http://slashdot.org/comments.pl?sid=134182&cid =111 99775

Slashdot Mirror

DNA For Information Processing and Data Storage

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