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DNA Solves Million-Answer NP-Complete Problem

timothy posted more than 12 years ago | from the combinations dept.

Science 169

cybrpnk writes: "A 'DNA computer' has been used for the first time to find the only correct answer from over a million possible solutions to a computational problem. Leonard Adleman of the University of Southern California in the US and colleagues used different strands of DNA to represent the 20 variables in their problem, which could be the most complex task ever solved without a conventional computer. Details to be published in Science."

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169 comments

Trolls Must Go. (-1, Offtopic)

Anonymous Coward | more than 12 years ago | (#3172857)

Readers of Slashdot. I come before you today with a desire. A desire to rid Slashdot of the one thing that is driving me away: Trolls. As I have seen it put here before, the scum of Slashdot. Let me give you a quick explanation.

I know that this is offtopic and should be rated offtopic, but the statements I'm making here are true and must be addressed at once. I am posting this comment under a new account so as not to burn up the precious karma that allows me to post relavant articles and replies to meaningful stories. Did you read that last sentence? Relevant and meaningful. Two words that are all too often lost in the heightened "signal to noise" ratio that trolls are forcing on the intelligent readers and posters of Slashdot.

I'm no genius. I use windows at work because I have to. I use Linux (Mandrake)at home, but I'm a relative newbie and am still learning better ways to make Linux run. There are many stories on Slashdot that I do not understand. Most of these stories are about systems or technology that I will probably never use. Regardless, I have learned much about Linux from the postings and users of Slashdot. I also use Slashdot to keep me up to date on technology and current events/issues in the technology world. Things like napster, the DMCA, the hype of ginger, and many others.

Here's my point. I should be allowed to read Slashdot, regardless of who I am and what I'm reading it for, without having to worry about pictures of a man's anus being spread open, people telling me about some atm becoming a person, people talking about pouring hot grits down their pants, or people thinking about a petrified Natalie Portman! What's wrong with these people? Don't they have anything better to do with their lives/time than to bother others? I'm sick of people saying that Linux users are gay and communists. I'm neither of those things, and if even if I was, should that lessen my right to read Slashdot in peace?

I've said all that to say this: the trolls must go! I'm not saying that I have a solution. The moderation and meta-moderation systems are great tools. They have filtered out much of the garbage that people spread on Slashdot. Banning people's accounts and or ip addresses has also worked to a limited degree, but are not the answer. I'm also definitely not saying that we should impose some form of censorship, as I, like many other worthwhile Slashdot patrons, am against censorship in all its forms. But something must be done. At first I began thinking "trolls are on Slashdot and I don't like trolls, so I should just start reading a different techie news site," but thats not fair. Before you start the "life's not fair" flames, hear me out.

I certainly didn't start Slashdot. I haven't been around Slashdot for that long (only about 2 years). It would not be fair for me to say "our" website or "we" need to take back whats rightfully "ours". But in truth, thats what you old timers should be fighting for. I'm more than willing to "join the cause." I have been subjected to far too much worthless drivel while trying to enjoy Slashdot. Surely we, and I say we meaning the actual readers of Slashdot could come up with some sort of sure fire way to once and for all retake our beloved site from these people, these trolls. Come on there are a lot of smart people reading, posting, maintaining, and contributing to Slashdot. Surely among all these living clock cycles we could develop something to safeguard Slashdot from the trolls.

Sorry for the ranting and rambling, but I've said some things here I've needed to say for a while, and quite frankly are true. Shall we begin discussions of removing the troll element from Slashdot?

Re:Trolls Must Go. (0)

Anonymous Coward | more than 12 years ago | (#3172895)

Relevant and meaningful. Two words that are all too often lost in the heightened "signal to noise" ratio that trolls are forcing on the intelligent readers and posters of Slashdot.

A heightened signal to noise ratio is generally considered a good thing.

I'm no genius.

Quite so.

Slashdot doesn't care (0)

Anonymous Coward | more than 12 years ago | (#3172905)

If you really wanted to be troll-free, you'd read at +2.

However, the reason there are trolls is because slashdot doesn't give a rat's ass about the reader base. They have bugs they won't fix, and CmdrTaco won't even go back to school for grammar lessons. Then there is the moderation scandal they're involved in. The list goes on and on.

And they wonder why no one will give them money for subscriptions to slashcrap.

Sod off.

I DO IT WRONG!!! (-1)

Anonymous Coward | more than 12 years ago | (#3172945)

I do it wrong

Laying here in the shadows of my room, I squint up at my love. My Ms. Portman. I am sore and tired after fucking her for eight solid hours. My chapped and aching dick is soaking in grits to relieve the pain. She gets on her knees and starts lapping the grits up out of the bowl. She places her beautiful hands on my penis and starts to lick the grits off my achy piece.

Massaging my nutsack she....

WAIT, I DO IT WRONG!!!!

Yanking my dick out of her mouth I throw her to the ground and shove it in to her gaping freshly fisted ass. [goatse.cx]

"OH BIG ASS SPORK!! Fuck my ass, fuck my ass good. DEEPER, my stallion, deeper!! Make a Beowulf cluster of sperm on my back!!"

"Imagine a Beowulf cluster of this baby!"

I DO IT WRONG!!!!

I continue to hump her alabaster form. Glistening with beads of sweat, she bites her lip in delight as I tear her ass open with my engorged dick.

"Queen Amidala!!" I shreik as I near climax.

She looks up at me and screams, "You are so alive in me, unlike *BSD or VA Software!!! Fill me with seed!! Yes, Yes, Yess!!!!"

"For me you are calling, hhhmmm?"

"YODA?!? What the fuck, can't you see I am using the force here?"

He savagely kicks my Natalie aside, he pulls out his large green penis and impales me...

I DO IT WRONG!!

All your sporkz are belong to the dead homiez!!

This post has everything I hate, but... (0)

Anonymous Coward | more than 12 years ago | (#3173098)

Goddman. A natalie (not attractive) portman post, the goatcex crap (no pun intended), and worst of all, unforgiveable,a star wars reference.

I'm throwing up now.

However, I laughed. Something about "I DO IT WRONG" makes it all okay in the end. Again, no pun intended.

Not computing (-1)

October_30th (531777) | more than 12 years ago | (#3172859)

I wish guys like these would stop calling their pipe-dreams computing.

It gives the public the impression that it is somehow comparable to real computing. Well, it's not. It's not really computing unless it's done on silicon.

Publishing stories like these in dubious pseudoscientific magazines like New Scientist or Science only serves to give serious research a bad name.

Re:Not computing (0)

Anonymous Coward | more than 12 years ago | (#3172928)

I thought that a process isn't really computing unless it's done with a read/write head on an infinitely long paper tape.

Grow an imagination, dude. Or buy a book on the theory of computation (Sipser wrote a very good one).

Re:Not computing (0)

Anonymous Coward | more than 12 years ago | (#3172936)

(replying to myself)
Also, note that Leonard Adleman (the researcher behind this DNA research) is one of the inventors of RSA encryption. You really sound like an asshole when you say that he doesn't know anything about real computation.

Re:Not computing (0)

Anonymous Coward | more than 12 years ago | (#3172949)

YHBT. YHL. HAND.

Press release here... (1)

56ker (566853) | more than 12 years ago | (#3172861)

Where is the promised press release here?

is this breakthrough a threat to security? (2, Interesting)

ardiri (245358) | more than 12 years ago | (#3172863)

now, one needs to ask - "can this same technology be used to break codes/algorithms used within security?" the article is a bit lacking in details of how they achieved this exactly, but, koas theory is in action here.

Short answer NO (2)

lars (72) | more than 12 years ago | (#3173063)

Well, any computer can be used to attack crypto algorithms, it's just a matter of whether the computer can do so in a reasonable amount of time (like, say, the lifetime of the universe :) ). With current technology, it is not possible to break these algorithms, because the problems they are based on are believed to be hard. You can view this DNA computer as simply just being a new architecture, like Intel or SPARC. It's cool, but it has no effect on the dificulty of problems. The computing models computational complexity theory is based on are mathematical, and do not depend on any physical implementation of a machine.

Quantum computers are a slightly different story. They are theoretically non-deterministic machines that can solve all problems in NP in polynomial time. In theory, with a big enough quantum computer you could break all currently used encryption schemes, but in practice, no one has really come close to building a quantum computer to actually do anything non-trivial let alone useful. I've heard it suggested (I don't really know anything about quantum mechanics, so maybe the physics geeks in the crowd could comment on this and let me know if I'm full of crap) that it may be the case that while a quantum computer may be able to solve NP-hard problems in polytime, the difficulty and complexity of building such a machine might be proportional to the difficulty of solving the problem in P.

If this is the case, then even if it's theoretically possible to build quantum machines to break known crypto algorithms, in practice it would be infeasible to do so. If the complexity of building the machine doubles when you add a qbit then you may as well just use a deterministic computer and wait a few billion years for your answer.

Re:is this breakthrough a threat to security? (2, Interesting)

r00tarded (553054) | more than 12 years ago | (#3173249)

well is guess Leonard Adleman is the guy to know.
he would be the 'A' in RSA.

questions, questions (1)

56ker (566853) | more than 12 years ago | (#3172865)

But with only a million different combinations - surely this is no match for today's computers yet! How long will it be before it can be used for more practical problems?

Re:questions, questions (1)

sketerpot (454020) | more than 12 years ago | (#3173039)

This is an important breakthrough. They have shown that DNA can solve their test problem, and that is a big and necessary step on the way to creating DNA computers more powerful than comventional computers for some special problems.

I look forward to when this will find a practical use. It is certainly possible. Hopefully this experiment generates some interest, not to mention good ideas for future DNA computers.

Which problem? (3, Interesting)

cperciva (102828) | more than 12 years ago | (#3172866)

The article is a bit garbled (exponential time != NP-complete!) so it's a bit hard to work out what problem they were looking at.

I'm guessing 2-SAT; can anyone confirm/deny this?

Re:Which problem? (1)

Rudie (141854) | more than 12 years ago | (#3172878)

But 2-SAT is not in NP-complete nor needs exponential time. Maybe you're thinking of 3-SAT or just plain SAT?

Re:Which problem? (1)

cperciva (102828) | more than 12 years ago | (#3172926)

Oops. It's been a while since I took those courses...

Re:Which problem? (2, Informative)

Permission Denied (551645) | more than 12 years ago | (#3172892)

2-SAT is in P. 3-SAT, 4-SAT and so on are all NPC. In fact, 3-SAT was the first problem which was proved to be NPC (and, AFAIK, the only problem proved to be in NPC without using a Karp reduction proof).

Re:Which problem? (2, Informative)

allanj (151784) | more than 12 years ago | (#3172898)

If memory serves me correctly, the problem described in the REAL article [usc.edu] is a 3-SAT, but algorithmics class was years back and beginning to fade from memory...

Re:Which problem? (2, Interesting)

Permission Denied (551645) | more than 12 years ago | (#3172937)

Yep, the article describes 3-SAT - so you're remembering your algorithms class just fine. Also, the article linked from the slashdot story describes 3-SAT in a nice, easy-to-understand but not too dumbed-down way (I posted before reading the article). I just looked it up and 3-SAT was proved to be NPC in 1974 by Cook and Levin.

Re:Which problem? (1)

johndv (147026) | more than 12 years ago | (#3172958)

The first problem proved to be NP-complete is SAT (that's Cook Theorem). 3-SAT is the first problem proved NP-complete by Karp in his seminal paper.

Re:Which problem? (1)

Permission Denied (551645) | more than 12 years ago | (#3172979)

Mea culpa, you're right. It's kind of embarassing that my comment was modded up for all to see and I was inexcusably WRONG.

Re:Which problem? (0)

Anonymous Coward | more than 12 years ago | (#3173184)

It's dumbasses like you that give slashdot a bad name.

Read the article (2)

lars (72) | more than 12 years ago | (#3172990)

Adleman and co-workers expressed their problem as a string of 24 'clauses', each of which specified a certain combination of 'true' and 'false' for three of the 20 variables. The team then assigned two short strands of specially encoded DNA to all 20 variables, representing 'true' and 'false' for each one.

Clearly the problem was 3-SAT.

Re:Which problem? (3, Informative)

Lictor (535015) | more than 12 years ago | (#3173093)

It was definitely 3-SAT; I just spoke with one of the experimenters yesterday.

Nice, but... (1, Informative)

Anonymous Coward | more than 12 years ago | (#3172871)

this doesn't make NP-complete problems polynomial ofcourse.

Still, impressive!

Re:Nice, but... (2)

s20451 (410424) | more than 12 years ago | (#3172985)

Indeed. The advantage of DNA computing is massive parallelism, but consider the 3-Satisfiability problem (the classic NP-complete problem) with n predicates. Regardless of the number of parallel processors (be they silicon or DNA), the only known algorithm has complexity O(2^n), which means:

  • For n=10, a few thousand operations are required.
  • For n=30, a few billion operations are required.
  • For n=250, somewhere around 1e+80 operations are required, which is roughly the same number as the number of atoms in the universe.

So imagine a DNA computer consisting of every atom in the universe -- even for this computer, a solution to 3-Satisfiability for n>250 would be basically hopeless.

Re:Nice, but... (2, Informative)

gkatsi (39855) | more than 12 years ago | (#3173100)

These numbers are nice, but ignore the fact that the current algorithms for solving SAT can routinely solve random 250-variable problems in subsecond times and even larger structured problems. zChaff, the fastest solver currently has even solved some 1-million variable problems (of course it probably took a few days, but it's still better than the multiple-universe-lifetimes prediction of 2^n).

Re:Nice, but... (0)

Anonymous Coward | more than 12 years ago | (#3173164)

almost there, but the machine consisting of every atom in the universe would do that in a few clockcycles. (which is probably around 10^-30 s or so)
if it was capable of utilizing all of its atoms for such a short time that is. more realistic vision would be to use a smaller portion of it and for a longer time. (say, 1000 ly space for 1000 years)

This is the future... (1)

Sunda666 (146299) | more than 12 years ago | (#3172875)

Our old binary digit computers have been around for AGES (50+ years in tech time ;-)

It is really the time for searching new and more complex computer architechtures if we ever want to have true IA (a la HAL 9000). I always wondered why ppl insist on building neural nets based on ordinary computers rather than building them on dedicated neural hardware (expeeeensive, but needs to be tried more often).

Of course, today's computers do a good job resolving them, but there are too many architechtural limitations. Brains are a hella lot older than computers, and a hella lot more advanced (but very fragile).

Way to go dudes.

Re:This is the future... (1)

tomstdenis (446163) | more than 12 years ago | (#3172934)

This isn't new research. In fact Adleman has published materials on his results before.

The big setbacks of DNA computing are

1. Slow to setup
2. Takes a while to get results
3. Has a high rate of error [compared to a typical computer]

What people mistake is that while a DNA computer could test 2^n cases simultaneously it still takes a while to get the results back. During that time errors can creep in (this is real life...)

Tom

Real article (5, Informative)

mnordstr (472213) | more than 12 years ago | (#3172881)

Here is the article [usc.edu] at USC which covers the subject, including an interesting picture!

Re:Real article (5, Informative)

bcrowell (177657) | more than 12 years ago | (#3173150)

And here's the group's web page [usc.edu] , including their preprints and FAQ. No preprint of the present paper, though.

Haiku (0)

Anonymous Coward | more than 12 years ago | (#3172883)

Digital is old;
Genetic algorithms
Are quite new, again.

I AM NOT A TROLL! (-1, Offtopic)

Anonymous Coward | more than 12 years ago | (#3172884)

I am constantly finding that i'm being moderated as 'troll'! Most of my comments are NOT INTENDED TO BE TROLL! But moderators have seem to of forgotten what a 'troll post' is!

A 'troll' usually tries to get the first post in a article

Trolls talk about discusting topics such as gay nerds and sex with animals such as goats!

Trolls posts links to vile websites, the most well known one is http://www.goatse.cx. Sometimes they try and discuise it through another website such as AOL.com.

Trolls post anti linux material, trying to prove how windows is superior. which often is moderated as 'flamebait'

Trolls post useless information known as 'crapfloods'.

I AM NOT A TROLL, STOP MODERATING ME AS A TROLL!

If it happens again, you will be SORRY!

Is this a troll? No I don't think so! [troll.com]

Re:I AM NOT A TROLL! (0)

Anonymous Coward | more than 12 years ago | (#3172901)

ahhh shaddup ya troll!

Re:I AM NOT A TROLL! (0)

Anonymous Coward | more than 12 years ago | (#3172997)

Trolls post useless information known as 'crapfloods'.

Useless information? Gee... You mean like this post [slashdot.org] ? -1 Offtopic, please.

Whining accomplishes nothing. If you don't like being moderated down, then start writing ontopic, anti-inflammatory, appropriate, legal, non-offensive posts, and deal with the real cracksmokers in metamod.

P.S. First-posters are not trolls, they're just offtopic.

Re:I AM NOT A TROLL! (0)

Anonymous Coward | more than 12 years ago | (#3173356)

best trolls get +5. i'm almost serious.
when you tell people what they wish to hear, you dont need to be accurate and even less imaginative.

be first and be obvious. rant.

i'm waiting for something like "standard counterargument library" where a bot could paste a backfire before anyone else on the most common crap so that people could think with their own brains instead of trying to become the collective mind of slashdot group x or whatever.
this probably wouldn't help a bit though.

Here's a Thought (0)

Anonymous Coward | more than 12 years ago | (#3172885)

Can't we somehow sue Microsoft with this new knowledge?

And in 5 years Microsoft will say... (5, Funny)

Ozan (176854) | more than 12 years ago | (#3172887)

...it's not a bug it's a mutation.

Re:And in 5 years Microsoft will say... (0)

Anonymous Coward | more than 12 years ago | (#3173024)

How the hell does this get modded up this high? What is the relevance?

Re:And in 5 years Microsoft will say... (0)

Anonymous Coward | more than 12 years ago | (#3173072)

It got modded up because it's making a joke at Microsoft's expense. And, as we all know, to slag opff Microsoft is a sure-fire way to get modded up.

Re:And in 5 years Microsoft will say... (0)

Anonymous Coward | more than 12 years ago | (#3173172)

Fucking Micro$oft fucking suck rocks. Their shitty software crashes all the time and costs a pissing fortune.

Re:And in 5 years Microsoft will say... (0)

Anonymous Coward | more than 12 years ago | (#3173134)

If you were a registered user, you could set your comment options to downgrade "Funny" comments to 0 so you wouldn't see them.

Which OS? (3, Funny)

Gangis (310282) | more than 12 years ago | (#3172888)

Which OS did they use? Microsoft DNA? [extropia.com]

*rimshot*

Travelling Salesman (0, Redundant)

Rudie (141854) | more than 12 years ago | (#3172889)

After reading the article at USC it seems to me that they have solved an instance of the Travelling Salsesman Problem of size 20 encoded in SAT, can anyone confirm or deny this?

Very interesting in any case, well done.

Re:Travelling Salesman (1, Interesting)

Anonymous Coward | more than 12 years ago | (#3172914)

Adleman and co-workers expressed their problem as a string of 24 'clauses', each of which specified a certain combination of 'true' and 'false' for three of the 20 variables.

looks like 3SAT to me.

I must resist.... (1)

Rhinobird (151521) | more than 12 years ago | (#3172896)

I must resist my urge for an inane beowulf cluster comment here....so instead...can you imagine a beowulf cloned with one of these?

Re:I must resist.... (2, Funny)

Mr Teddy Bear (540142) | more than 12 years ago | (#3172920)

Actually, the beowulf comment MIGHT actually be applicable this time. Because that is what clustering is all about. So really... a beowulf cluster of digital machines is an attempt at making one huge DNA machine.

Now if only they could stop making the damn DNA computer morph into Bill Gates. And I thought sheep were baaaad.

Re:I must resist.... (1)

Rhinobird (151521) | more than 12 years ago | (#3172925)

please forgive me, for i know not what i do...plus i'm really sleepy...

Re:I must resist.... (1)

sketerpot (454020) | more than 12 years ago | (#3173075)

If you won't make an inane beowulf comment, I will.
Imagine a beowulf cluster of these!
It's easy to imagine, since that is basically what DNA computers are: clusters of DNA molecules.

They can put a lot of DNA molecules together and have them compute in parallel, which is why this has so much potential.

Re:I must resist.... (1)

Cowculator (513725) | more than 12 years ago | (#3173236)

A Beowulf cluster of DNA?

I think it's called the human body...

before it get's slashdotted (0)

Anonymous Coward | more than 12 years ago | (#3172899)

'DNA computer' cracks code
15 March 2002

A 'DNA computer' has been used for the first time to find the only correct answer from over a million possible solutions to a computational problem. Leonard Adleman of the University of Southern California in the US and colleagues used different strands of DNA to represent the 20 variables in their problem, which could be the most complex task ever solved without a conventional computer. The researchers believe that the complexity of the structure of biological molecules could allow DNA computers to outperform their electronic counterparts in future (R Braich et al 2002 Science to appear).

Scientists have previously used DNA computers to crack computational problems with up to nine variables, which involves selecting the correct answer from 512 possible solutions. But now Adleman's team has shown that a similar technique can solve a problem with 20 variables, which has 220 - or 1 048 576 - possible solutions.

Adleman and colleagues chose an 'exponential time' problem, in which each extra variable doubles the amount of computation needed. This is known as an NP-complete problem, and is notoriously difficult to solve for a large number of variables. Other NP-complete problems include the 'travelling salesman' problem - in which a salesman has to find the shortest route between a number of cities - and the calculation of interactions between many atoms or molecules.

Adleman and co-workers expressed their problem as a string of 24 'clauses', each of which specified a certain combination of 'true' and 'false' for three of the 20 variables. The team then assigned two short strands of specially encoded DNA to all 20 variables, representing 'true' and 'false' for each one.

In the experiment, each of the 24 clauses is represented by a gel-filled glass cell. The strands of DNA corresponding to the variables - and their 'true' or 'false' state - in each clause were then placed in the cells.

Each of the possible 1 048 576 solutions were then represented by much longer strands of specially encoded DNA, which Adleman's team added to the first cell. If a long strand had a 'subsequence' that complemented all three short strands, it bound to them. But otherwise it passed through the cell.

To move on to the second clause of the formula, a fresh set of long strands was sent into the second cell, which trapped any long strand with a 'subsequence' complementary to all three of its short strands. This process was repeated until a complete set of long strands had been added to all 24 cells, corresponding to the 24 clauses. The long strands captured in the cells were collected at the end of the experiment, and these represented the solution to the problem.

According to Adleman and co-workers, their demonstration represents a watershed in DNA computation comparable with the first time that electronic computers solved a complex problem in the 1960s. They are optimistic that such 'molecular computing' could ultimately allow scientists to control biological and chemical systems in the way that electronic computers control mechanical and electrical systems now.

Author
Katie Pennicott is Editor of PhysicsWeb

for comparison sake (3, Funny)

Alien54 (180860) | more than 12 years ago | (#3172911)

It would be interesting to find out what the comparitive time for finding an answer would be for common conventional computers. vs this process.

at least we would have a benchmark of sorts.

I imagine that the problems of creating a truly AI computer will be solved using a DNA based computer.

;-)

Re:for comparison sake (1)

dollargonzo (519030) | more than 12 years ago | (#3172965)

that is the biggest illusion people have themselves running under. everyone seems to think the only problem with as you call it "truly AI computer", which doesnt even make much sense in itself, but ill give u the benefit of the doubt...

is computing power and parallel processing vs the inherently serial nature of todays conventional computing solutions. the benchmark idea is nice, but the BIGGEST problem with AI is trying to create a model that can handle every kind of input (and even one to start with would be nice) and be able to generalize concepts as well as learn independantly (without predefined associations between internal structure and external input).

computing power is nice, but we can't even create the correct models yet. even if its slow, at least it'll work. sure, DNA sounds nice...cause its biological ala humans, but beyond that, its just another computing method.

QED

I see now. (1)

Alien54 (180860) | more than 12 years ago | (#3172987)

ah, I see.

You took it very seriously because it hit a hot button.

There is a technical term for the comment I made about a DNA based AI computer.

It is called a "joke".

This is because of the cognitive dissonance between the usual attempts at AI using wires and cirsuits and such, the DNA from living creatures, where some form of awareness and intelligence can occasionally be found.

go have yer morning cup of coffee, and relax. perhaps you didn't see the smiley face in the original post.

Re:I see now. (1)

dollargonzo (519030) | more than 12 years ago | (#3173284)

oh, i took it as a joke, just the joke seems to also sum up what EVERYONE thinks...that's all!

QED

Re:for comparison sake (1)

gkatsi (39855) | more than 12 years ago | (#3173131)

On, say, a P3 1Ghz.... I guess it would talk around 0.000000 sec, if you use some of the older algorithms. That is, times() is not accurate enough to measure how long it would take.

That would be even faster for newer and better algorithms.

I REPEAT IM NOT A TROLL! (-1, Offtopic)

Anonymous Coward | more than 12 years ago | (#3172913)

I am constantly finding that i'm being moderated as 'troll'! Most of my comments are NOT INTENDED TO BE TROLL! But moderators have seem to of forgotten what a 'troll post' is!

A 'troll' usually tries to get the first post in a article

Trolls talk about discusting topics such as gay nerds and sex with animals such as goats!

Trolls posts links to vile websites, the most well known one is http://www.goatse.cx. Sometimes they try and discuise it through another website such as AOL.com.

Trolls post anti linux material, trying to prove how windows is superior. which often is moderated as 'flamebait'

Trolls post useless information known as 'crapfloods'.

I AM NOT A TROLL, STOP MODERATING ME AS A TROLL!

If it happens again, you will be SORRY!

Is this a troll? No I don't think so! [trolltech.com]

Need to know all the answers? (1)

glasslemur (238045) | more than 12 years ago | (#3172915)

Each of the possible 1 048 576 solutions were then represented by much longer strands of specially encoded DNA, which Adleman's team added to the first cell

So they had to go through and find all the possible answers and put them in the mix? I don't think this will every be a viable solution when to find the correct answer you have to know all the wrong ones as well. Part of problem solving is starting out with 0 answers. I bet they couldn't use the DNA computer to figure out all those 1048576 wrong solutions. Although I think it would be an interesting concept, until they can figure out a way to solve problems without knowing all the answers, I do not see how it could be used for serious calculations. I think it could possibly be the next great search engine, or maybe an RC5 engine. But how long would it take to encode 18,446,744,073,709,551,616 strands of DNA?

Re:Need to know all the answers? (1)

tomstdenis (446163) | more than 12 years ago | (#3172942)

Actually the correct answer should stand out like a beacon.

In early Adleman experiments the correct solution is one where the opposing strands completely bind together. Then they use a comb+gel+electrode+glow_in_dark_radioactive_die. The shorter strands will make it further through the gel towards the electrodes. the longer [complete answer] strand will not move far.

Obviously new DNA computers use different filtering techniques...

Another thing you should read up on is PCR or Polymeraese Chain Reaction [and I know I can't spell]. Its a technique that won a Nobel prize. I don't recall the technique but it involves making each strand duplicate themselves. So to get the 2^64 strands you alluded to you apply the PCR technique 64 times.

[no mention of errors...]

Tom

Re:Need to know all the answers? (0)

Anonymous Coward | more than 12 years ago | (#3173216)

Er, they simply get all possible solutions to a problem first. For instance, in a factorisation problem, we know that certain numbers are not possible solutions (ex:- even numbers), so they use some sort of preliminary criteria to get a possible solutions.

Cool, but... (1)

allanj (151784) | more than 12 years ago | (#3172923)

The REAL article [usc.edu] states that

"It would take a breakthrough in the technology of working with large biomolecules like DNA for molecular computers to beat their electronic counterparts".
So while the article also mentions code-breaking as an obvious application for this ... device ..., electrons will be our computing friends for the foreseeable future.


LSD (2, Insightful)

GigsVT (208848) | more than 12 years ago | (#3172924)

And to think, LSD made this all possible [thegooddrugsguide.com]

"Would I have invented PCR if I hadn't taken LSD? I seriously doubt it,"

-- Dr Kary Mullis, Nobel Prize Winning inventor of the Polymerase Chain Reaction that allows pretty much all the modern research in DNA technology.

And to think on the same Google search that I found that, there was a sponsered link to "How drugs support terrorism" from the government.

Re:LSD (0)

Anonymous Coward | more than 12 years ago | (#3173132)

This is nothing but the opinion of one person, and even he won't stand behind it with 100% conviction. Unless you can prove 100% that LSD 'enlightened' him to create PCR, you have nothing to stand on.

Is this new? (1)

tomstdenis (446163) | more than 12 years ago | (#3172927)

Two years ago I bought

ISBN 3-540-64196-3

which discussed Adlemans experiements.

How could this article describe it as the "first" dna computer used to solve a problem?

Re:Is this new? (3, Insightful)

Lictor (535015) | more than 12 years ago | (#3173105)

Well it certianly isn't the "first" DNA computer to solve a problem. However, it *is* the first one to solve a problem that would be seriously non-trivial for a human to do by hand.

Re:Is this new? (1)

mofolotopo (458966) | more than 12 years ago | (#3173291)

Precisely my question. I would swear that I saw an article about this exact experiment using eight variables in SciAm three or four years ago. My first reaction when I saw this piece on Slashdot was actually "this is news?".

Keep trolln' trollin' trollin' trollin' trollin' (-1, Offtopic)

Anonymous Coward | more than 12 years ago | (#3172930)

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Great (0, Offtopic)

Chayce (199487) | more than 12 years ago | (#3172931)

Now how many months before they come out with a USB version?

It's only a matter of time... (4, Funny)

guttentag (313541) | more than 12 years ago | (#3172935)

before we hear:

It looks like you're attempting mitosis. Now would be a great time to sign up for a Passport account. WARNING: Are you sure you want to attempt mitosis without a Passport account? Your ancestors may regret it!

And on the other side of the coin, the Open Source DNA advocates will be saying:
You don't need a Passport account to have kids, honey. Yes, it's perfectly safe. Support? Who the hell told you Microsoft was going to support our child?! A free PC?!

don't hold your breath (3, Interesting)

hyrdra (260687) | more than 12 years ago | (#3172964)

According to Adleman and co-workers, their demonstration represents a watershed in DNA computation comparable with the first time that electronic computers solved a complex problem in the 1960s. They are optimistic that such 'molecular computing' could ultimately allow scientists to control biological and chemical systems in the way that electronic computers control mechanical and electrical systems now.

Huh? What they did here is use the self-construction property of DNA whereby only the respective nucleotides A, T, C, and G only form a bond with their compliment.

That means you can have millions of solutions and the whole thing will solve itself because only the correct solutions 'fit' into the problem which you have represented in the ATCG language. You can do the same thing when you add more variables, and it's just as easy. That is something very hard to do with electronic computers, because they deal with information on the quantity level whereas DNA is able to solve a problem on the problem "abstraction" level itself.

However, conventional *serial* problems are something very hard to do with DNA, because it involves the manipulation of a single strand whereas you would be working in parallel with millions, even billions of strands for NP complete problems. A DNA strand is infismal compared to today's current Si processes, where we measure things in micrometers. DNA is in the single nanometer range. That's several 100 times smaller than a single wavelength of light.

I don't think DNA will be viable for most standard computational tasks, or for a practial turing machine. Biological systems don't use DNA to do logical operations (that I know of), and the only thing they use it for is for data storage (instructions for building proteins). The only operations (under normal circumstances) an organism does with DNA is copy. Mutations (reversals, transpositions, etc.) occur because of chemical errors. That is the only operation it does really.

This all seems very interesting albeit limited to the lab.

Bizzare order (2)

nusuth (520833) | more than 12 years ago | (#3173036)

That means you can have millions of solutions and the whole thing will solve itself because only the correct solutions 'fit' into the problem which you have represented in the ATCG language.

Well, the way you stated the problem, all problems are solvable (on a digital computer) in linear time wrt problem representation The most amazing order I've seen so far.

Hint: char alphabet[]="AGCT";

Re:don't hold your breath (2, Insightful)

isenguard (14308) | more than 12 years ago | (#3173043)

However, conventional *serial* problems are something very hard to do with DNA, because it involves the manipulation of a single strand whereas you would be working in parallel with millions, even billions of strands for NP complete problems.

You are missing the point: NP complete problems (like 3-SAT, which is what they are solving with this DNA computer) are incredibly difficult for serial computers to solve. Nobody seems to be suggesting that DNA computers should be used for serial problems that we can already solve with conventional computers. However, being able to solve SAT (and hence other NP-hard) problems more efficiently is incredibly useful, because SAT problems exist that we can't (and might never be able to) solve using existing techniques.

Re:don't hold your breath (3, Informative)

MarkusQ (450076) | more than 12 years ago | (#3173156)

You are missing the point: NP complete problems (like 3-SAT, which is what they are solving with this DNA computer) are incredibly difficult for serial computers to solve.

Not quite. If you have a class of problems, characterized by some parameter n, then for large enough n, the problems in a class that is NP will get harder with increasing n faster than they would if the class was P.

But for any particular instance of a class of problems, it doesn't really matter what the class is--in fact, you can construct example problems that would be NP if generalized in one way, P if generalized another, or even constant time if you choose a perverse "generalization" (e.g., n=date on which the question is posed).

Saying that the problem was NPC is a red herring; what they are actually doing is making a time/space tradeoff which would be hard of conventional computers, and then solving a particular example problem (not the class of problems).

-- MarkusQ

Re:don't hold your breath (3, Informative)

isenguard (14308) | more than 12 years ago | (#3173209)

Not quite. If you have a class of problems, characterized by some parameter n, then for large enough n, the problems in a class that is NP will get harder with increasing n faster than they would if the class was P.
True as far as it goes. That's the whole point of complexity: to talk about the growth in the difficulty of solving a problem as the problem size grows. The reason we spend so much time studying NP hard problems is because all known general methods for solving them grow exponentially in the worst case.
Saying that the problem was NPC is a red herring; what they are actually doing is making a time/space tradeoff which would be hard of conventional computers, and then solving a particular example problem (not the class of problems).

The reason I replied to your original comment was that you implied that the work wasn't useful, or wasn't as much of a breakthrough as Adleman claims. Saying that they only solved a single instance isn't relevant: they have a method that works on any 3-SAT problem for which they can construct a long enough DNA chain to represent an assignment, and they have an implementation that actually finds the solution.

Don't forget that the first practical computer algorithm for SAT (Davis and Putnam, A Computing Procedure for Quantification Theory, Journal of the ACM, 1960) didn't even have a computer implementation: they demonstrated its usefulness by working an example out by hand!

Re:don't hold your breath (1)

the_2nd_coming (444906) | more than 12 years ago | (#3173060)

the only thing they use it for is for data storage (instructions for building proteins). The only operations (under normal circumstances) an organism does with DNA is copy. Mutations (reversals, transpositions, etc.) occur because of chemical errors. That is the only operation it does really.

oh god......Microsoft is going to use this for their next generation Office File format!!!!!

now we will have to pay royalties to reproduce!!!!

Re:don't hold your breath (1)

xenotrope (86854) | more than 12 years ago | (#3173231)

"Limited to the lab" is right. The title of this article is rather misleading, since it indicates that the answer had one million components, instead of one million choices. It's far less impressive for a DNA computer to pick one right answer out of a million when you consider that's the only advantage that DNA computers are really said to have.

When I first started reading the article, I thought this was a big breakthrough for security and encryption (knee-jerk reaction, I know). When I saw "million-answer" and "Adleman", I thought he'd found a way to factor an enormous composite number into a million factors. Correct me if I'm wrong, but he is the "A" in RSA, right? I was very quickly disappointed.

This article is a total letdown and, dare I say it, neither news for nerds, nor stuff that matters. The sheer theoretical limitations of this project demands that this sort of thing will never, ever make it into common and public use until every Joe on the street has at least a BS in biogenetical engineering.

There are so many constraints to this kind of work that it will only ever be useful to academics with too much free time. Is it interesting? Sure, for some. Is it useful? I don't see how. When every Linux-loving 14-year-old out there has his own little genetics lab in his bedroom next to his homebrew Apache server, maybe this article will start to stir real interest on this site. This subject is so far removed from "real" computing, by which I mean conventional transistors and whatnot, that it's virutally useless to the computing community. Bravo, Dr. Adleman.

Re:don't hold your breath (0)

Anonymous Coward | more than 12 years ago | (#3173394)

> Biological systems don't use DNA to do logical operations

Perhaps in the strictest sense, but there are boolean logic machines throughout biology, many involving DNA and DNA-binding proteins.

The classic example is the LAC operon in bacteria. The switch controls an enzyme for digesting lactose (a type of sugar). The bacteria prefers glucose because it takes less work to digest. But if there's only lactose for dinner, it eats lactose. The switch definition:

if (lactose present && ! glucose present)
generate beta-galactosidase mRNA // enzyme for digesting lactose
else
don't do anything.

For a short and very readable introduction to this area, see the classic book A Genetic Switch by Ptashne. Only a basic biology background is needed.

Re:don't hold your breath (4, Interesting)

Nagash (6945) | more than 12 years ago | (#3173472)

I don't think DNA will be viable for most standard computational tasks, or for a practial turing machine.

No (respected) person in the field of DNA computing thinks that DNA computing will be practical for everyday tasks. It's just too slow. (For that matter, no turing machine is practical. Every try to program one?)

For the record, I (Geoff Wozniak) am a graduate student of Dr. Lila Kari [csd.uwo.ca] , a well known member of the field of DNA computing. Incidently, Lila was involved in the project talked about in the article.

However, what DNA computing could be useful for in the future is solving problems that can take electronic computers far too long to figure out. Consider the SAT problem that was solved in this article. Suppose we are able to get DNA to solve SAT problems with hundreds of variables. Sure, it might take a week to do it, (maybe even a month), but it sure beats waiting for millions of years.

Quantum computers, however, could change the whole spectrum. However, they are not as evolved as "DNA computers" are right now and I suspect they may take a longer time to be viable.

Biological systems don't use DNA to do logical operations (that I know of), and the only thing they use it for is for data storage (instructions for building proteins). The only operations (under normal circumstances) an organism does with DNA is copy. Mutations (reversals, transpositions, etc.) occur because of chemical errors. That is the only operation it does really.

Biological systems do a lot more than just copy. Look up work by Landweber and Kari on ciliates and gene rearrangement, for starters. In addition to copy, biological systems also to extracting/cutting, filtering, and pasting/annealing.

You mentioned data storage. Here is where the real benefit of DNA could come into use. The way genes are expressed using only A, C, G, T is quite remarkable. The real advantage of DNA computation lies, imo, in the encoding proerties of DNA. The language of DNA has incredible error-detecting/correcting capabilities. Our work is focusing on learning more about this language and using it for the computational process in some way. I/O would be slow to DNA, but if it can store huge quantities of information, it's worth the effort, especially if better ways for long term storage can be found (of which there is a good chance).

You have to think outside of the conventional computing process to see why DNA computation is so interesting. The problem is that "computers" and "electronic" seem to be synonymous, which they are most certainly not.

Woz

What is P vs. NP and why should I care? (5, Informative)

rtos (179649) | more than 12 years ago | (#3172972)

Perhaps you are wondering what an NP-complete problem is or what this P vs. NP stuff is all about. You might want to check out the comp.theory FAQ [cs.unb.ca] and scroll down to 7. P vs NP. It gives a bit of history and a decent description.

Or check out The P versus NP Problem [claymath.org] at Clay [claymath.org] for a really good description (unfortunately too long to quote here). And lastly, you might want to check out Tutorial: Does P = NP? [vb-helper.com] at VB Helper for a little more info.

Ok, but what is it good for? The Compendium of NP Optimization Problems [nada.kth.se] is a great place to look for real world examples of NP problems. Including everything from flower shop scheduling [nada.kth.se] to multiprocessor scheduling [nada.kth.se] .

Hopefully that helps. I was very clueless when it came to P vs. NP stuff that always seems to be mentioned on Slashdot. So I took the time to look it up. Now I'm clueless but I have links to share. :)

Good links! (1)

rueba (19806) | more than 12 years ago | (#3173029)

I already knew something about P vs NP but some of these links have really non-technical easy explanations.
I am particularly enjoying the one on the link between Microsoft Minesweeper and NP complete problems
(Yes I remember when it was reported here, but it only linked to the guys academic paper which was too deep for me)

DNA computers (1)

FrostedWheat (172733) | more than 12 years ago | (#3172983)

It's amazing the things possible with DNA computers, little tiny ones implanted in the human brain.

Of course, it won't be long until people are over clocking. Or worse, adding transparent case mods. *shudders*

Errata: First Complex Electronic Solutions (3, Informative)

Baldrson (78598) | more than 12 years ago | (#3173018)

the first time that electronic computers solved a complex problem in the 1960s.

Although the author may be responding to Seymour Cray's first supercomputers circa 1960 [digitalcentury.com] it is untrue that complex computations weren't being performed electronically until the 1960s.

The History of Unisys [unisys.com] shows the earliest milestones with the following one almost certainly qualifying as "complex computation":

1952 UNIVAC makes history by predicting the election of Dwight D. Eisenhower as U.S. president before polls close.

Re:Errata: First Complex Electronic Solutions (1)

Ed Avis (5917) | more than 12 years ago | (#3173262)

That history is quite amusing to read from bottom to top. It shows how highly the Unisys marketroids rate their own importance.

So we have in 1946 'ENIAC developed', and in 1997, with about the same amount of emphasis: 'Lawrence A. Weinbach named chairman, president, and CEO. Unisys Windows NT servers lead industry in price/performance.'.

Comparable to 1960s computers (3, Informative)

isenguard (14308) | more than 12 years ago | (#3173022)

According to Adleman and co-workers, their demonstration represents a watershed in DNA computation comparable with the first time that electronic computers solved a complex problem in the 1960s.

The description of the problem they are solving corresponds to a 3-SAT (propositional satisfiability with clauses of length 3) instance. In 1962 Davis, Logemann and Loveland published a paper entitled "A Machine Program for Theorem-Proving", in which they described a computer program which could solve SAT problems of a similar size, extending earlier work by Davis and others published in 1960. (You can read the paper in Communications of the ACM if you have a library that goes back that far.) So it looks like their comparison is correct.

The method they are using for the DNA computer is rather crude compared to that proposed by Davis et al, whose procedure is still in use today for solving SAT problems. We can now solve problems with thousands of variables, and actually do useful things in the process (e.g. verify hardware specifications).

The A in RSA (1, Informative)

Anonymous Coward | more than 12 years ago | (#3173076)

This is Leonard Adleman .. the A in RSA, difficult to tell from his homepage .. unless u dig. i guess he keeps in low key.

Ironic, by showing how to do 0computation with DNA he may be undemining RSA!

It needs to be said... (0)

Anonymous Coward | more than 12 years ago | (#3173081)

...imagine a beowolf cluster of these babies...

Obligatory (2)

lars (72) | more than 12 years ago | (#3173088)

Imagine a Beowulf cluster of these!

But seriously, I imagine these things must be pretty slow, since they are powered by chemical reactions. I don't forsee one of these babies supplanting my desktop any time soon. Of course, the whole point is that this shows the power of genetics, and it is amazing in that sense, to think that life is basically created by computer programs. Fortunately Microsoft hasn't gotten into the DNA software market yet, I'd hate to have bugs growing out of my skin and stuff. :)

Re:Obligatory (1)

Fiver-rah (564801) | more than 12 years ago | (#3173167)

I imagine these things must be pretty slow, since they are powered by chemical reactions.

DNA base pairs are not held together by chemical bonding. That would be a really, really difficult. They're held together by hydrogen bonds. The breaking and formation of hydrogen bonds takes on the order of picoseconds (it's the same timescale as rotations in the medium, since that's the basic mechanism for their breaking). Furthermore, they can break and form in parallel.

You can read more about the mechanism for base pairing here [utexas.edu] or if you want to see google render the pdf here [google.com] .

Re:Obligatory (2)

SpinyNorman (33776) | more than 12 years ago | (#3173193)

That's like saying that the brain is slow because it's based on chemical reactions...

The whole point of this "DNA computer" is that it's massively parallel - it evaluates all possible solutions in parallel. Increase the size of your problem .. no biggie - just add another pint of "computer".

Re:Obligatory (2)

lars (72) | more than 12 years ago | (#3173267)

That's like saying the brain is slow because it's based on chemical reactions...

Yes, exactly -- what would you use if you wanted to factor a 256-bit prime, your brain, or a computer? Similarly, this technology isn't going to be useful for solving general computational problems. I imagine it would be very useful for controlling biological systems, but it's not something I'm going to pull out when I want to do some number crunching! That's my point.

it evaluates all possible solutions in parallel.

Which means it's limited by the number of solutions you can represent in parallel. You're not going to be able to use this to evaluate 2^1024 possible solutions in parallel, unless there's funky quantum mechanics stuff involved. There probably aren't that many particles in the universe.

Increase the size of your problem .. no biggie - just add another pint of "computer".

Not exactly. For a problem like 3-SAT (the problem they solved here), a linear increase in the size of the problem input = an exponential increase in the number of solutions they need to evaluate. If they doubled the input size from 20 variables to 40, they'd need to evaluate 1 TRILLION solutions in parallel instead of 1 million. So they'd need the equivalent of 1 million of these DNA computers running in parallel. I'd consider that more than "just another pint".

Imagine... (1)

WetCat (558132) | more than 12 years ago | (#3173096)

if a byproduct of that solutions of problems
becomes a monster (some cells actually incorporated problem DNA-s).
WoW!

Re:Imagine... (1)

mofolotopo (458966) | more than 12 years ago | (#3173301)

Odds are it would do nothing. Without an intron, a strand of DNA isn't translated into protein and therefore does nothing. The odds of it being inserted into a coding sequence are less than one in ten, and even if it was the odds of it producing some sort of constructive mutation that would do anything interesting are vanishingly small.

Preparation is extensive (2)

Jobe_br (27348) | more than 12 years ago | (#3173207)

It seems to me that the amount of preparation that went into constructing the long strands and each of the truth sets is extensive. For this type of computing to become useful, it would appear to me that this construction of the parts necessary to carry out the computation would need significant work. I am very, very hopeful that DNA based computing as well as quantum molecular based computing will begin to make rapid gains in the very near future. The potential to astronomically increase the available computing power is there, I've read all the theories. It just needs to be made to happen :)

Just imagine ... quantum computing devices become common, as do DNA based computing devices - each in their own niche, possibly (neither device may be promising as a 'general computing' device, but used in conjunction they may complement each other) and the article previously posted about table-top fusion from the collapse of bubbles provides us with practically limitless and clean energy to drive the energy needs of all our computing devices. I can't wait :)

Add to that the possibilities for human augmentation by cybernetic implants and I feel that the day of Gibson's Neuromancer may be soon approaching. As the geek I am, I can't wait :)

Re:Preparation is extensive (2)

Jerf (17166) | more than 12 years ago | (#3173374)

Each of the possible 1 048 576 solutions were then represented by much longer strands of specially encoded DNA, which Adleman's team added to the first cell.

Granted I'm not a bio-engineer, but it's very difficult for me to believe that DNA will ever solve a problem faster then the computer can.

For this problem, millions of DNA strands were generated. I guarentee you the researchers didn't do it by hand. In the time the computer was instructing the hardware on how to make any given solution, it could have checked a thousand solutions. And the speed is accelerating.

Maybe, just maybe, if the strands could be generated automatically by a gene-gen'ed life form, except for the query strand, this could keep up with conventional silicon. But that's a tough nut itself.

I'm more intrigued by the QM computers... and I don't really believe in them, either.

(Biological computing may someday take off. But I don't think it's going to involve DNA. DNA is not meant for computing in the sense most of us find interesting. The gymnastics necessary to answer this simple question demonstrates that, and unlike conventional computers, where there has always been a clear path of progress, exactly what part of this computation is going to be streamlined? Millions upon millions of unique strands must be generated; what's the equivalent of shrinking the transistor by a factor of 2? I'm not holding my breath.)

A few questions (2)

sean23007 (143364) | more than 12 years ago | (#3173260)

This is interesting, but would it have worked at all if the scientists did not know the answer already? I mean, they set up all the variables, and then they set up all the possible answers, and the DNA just matched up with the one that they already knew to be correct. What if they didn't know which one was correct? What if there were a billion possible answers? Would they have to program them all in? At what point is it actually faster to use a computationally inefficient conventional PC instead because the compiler does the brunt work for you? Is this DNA method ever faster?

Obviously, there are a lot of questions to be asked about this, but it will be very interesting to see what happens when somebody develops some kind of compiler for the DNA computer, and you can just input an equation and some parameters and in several minutes you have the answer... But until then, this doesn't seem all that useful. On the other hand, it is fascinating research, and by all means, they should continue research on it.

only 1048576 solutions to check? (0)

Anonymous Coward | more than 12 years ago | (#3173261)

My computer could do that in under a second. This is news WHY?

truely useful (0)

negativekarmanow tm (518080) | more than 12 years ago | (#3173506)

the calculation of interactions between many atoms or molecules.

So their going to use the interactions between many atoms and molecules (DNA) to calculate the interactions between many atoms or molecules? Sounds like writing a PS2 emulator for the PS2

Anyway, I'm not going to use this until it comes with a decent GUI and a .NET backend.

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