DNA Solves Million-Answer NP-Complete Problem 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."
is this breakthrough a threat to security? (Score:2, Interesting)
Which problem? (Score:3, Interesting)
I'm guessing 2-SAT; can anyone confirm/deny this?
Re:Travelling Salesman (Score:1, Interesting)
looks like 3SAT to me.
Re:Which problem? (Score:2, Interesting)
don't hold your breath (Score:3, Interesting)
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.
Re:is this breakthrough a threat to security? (Score:2, Interesting)
he would be the 'A' in RSA.
Re:don't hold your breath (Score:4, Interesting)
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
tip of the iceberg... (Score:3, Interesting)
this is not entirely true. nucleic acids are responsible for quite a few things in the cell. yes, DNA is not very reactive, designed to be a stable archival form of genetic material, but RNA (ribonucleic acid) is a different story. derived from DNA, it has a 2' hydroxyl (-OH) group on its sugar (hence the name ribo- instead of deoxyribo- which has a 2' hydryl (-H) group) and is much more reactive, causing cleavage, ligation, and other enzymatic modifications. there are programmed errors and very regular processes in the cells, things like SOS DNA repair, nonhomologous end-joining, and crossing over, that can result in modification. there is so much here to study it can make your head spin! so don't count any of it out =)
Re:Correct answer: maybe (Score:3, Interesting)
Actually, I disagree. Quantum computers are non-deterministic. These DNA computers, while being massively parallel, as you say, are still deterministic. If you can test a million solutions at once in parallel, that's great, but all it does is speed things up by a constant factor over trying them one at a time. It doesn't turn a super-polynomial time algorithm into a polynomial time one, because there's a limit to how many computations you can do in parallel.
On a quantum computer or some other non-deterministic machine, the idea is that you can essentially perform all computations (with no limitation on how many) in parallel.
Why DNA computing will never be practical (Score:2, Interesting)
Re:Correct answer: maybe (Score:3, Interesting)
Yes. To put it in perspective, though, the average DNA base pair has a molecular weight of 610. So one mole of the substance (ie. 610 g) contains 6.022 x 10 e+23 base pairs.
So, assuming that it takes you 10 days to set up a computation - approximately 10 e+6 seconds, you have 6 * 10 e+17 computational units per second. This assumes the computation time is trivial (which it is, compared to the set up time of 10 days do make all the DNA).
Lets say that again. 600 000 000 000 000 000 computations per second. In a large beaker containing a few litres of solute.
Of course, each unit only holds a quaternery bit of information (ie., one of four states for the four kinds of nucleotide).
At the moment we have computers that can run in the GHz range, ie., 2 * 10 e+9 computations per second.
A DNA computer will be able to operate at at least 8 orders of magnitude faster than any current conventional computer, and potentially at 10 e+12 times faster with increased amounts of DNA and faster setup times.
It may be deterministic, but it will take us another 25+ years to get to this point on the intel roadmap - which of course should derail before then. In other words, this technology is faster than anything that can be or is likely to be done on silicon.
My 2c worth.
Michael