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Biotech Science Hardware Technology

Computer Made From DNA And Enzymes 398

Posted by timothy from the it-is-what-you-are dept.
develop writes "Some folks from Israel have created a computer that runs on DNA and enzymes and is supposedly 100,000 times faster then today's PCs. Information at National Geographic, Telegraph UK and United Press." According to the National Geographic story, this DNA-based computer "can perform 330 trillion operations per second, more than 100,000 times the speed of the fastest PC." However, be aware that most of this is still future tense, and what these researchers have now is just a proof-of-concept.
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Computer Made From DNA And Enzymes More

Computer Made From DNA And Enzymes

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  • nice typo (Score:2, Funny)

    by GlassUser ( 190787 )
    "computer made FOM" . . .?

    How lovely.

  • 330 trillion calculations per second? (Score:5, Funny)

    by martyn s ( 444964 ) on Monday February 24, 2003 @09:46PM (#5375892)
    330 trillion calculations per second? Impressive, but can it run Doom 3?

  • Prior Art (Score:5, Funny)

    by worst_name_ever ( 633374 ) on Monday February 24, 2003 @09:47PM (#5375905)
    Earlier today I hawked up a loogie in the parking lot. While at the moment it is only a puddle of goo, or "proof of concept", I predict that this collection of DNA and enzymes will someday be capable of performing over 330 trillion operations per second, more than 100,000 times the speed of the fastest PC!

  • Human brain (Score:3, Interesting)

    by snack-a-lot ( 443111 ) on Monday February 24, 2003 @09:48PM (#5375910)
    I wonder when they'll get up to the computational speeds of the human brain. Hmm-mmm.
    • I wonder when they'll (or someone else) will come with that even resembles the kind of pattern matching that can do the brain.

      Well... maybe fuzzy logic could be helpful there

  • Imagine (Score:4, Funny)

    by Anonymous Coward on Monday February 24, 2003 @09:49PM (#5375917)
    Imagine a beowulf cluster of those machines...wait a minute, I am one!

  • A step on another path. (Score:5, Interesting)

    by MulluskO ( 305219 ) on Monday February 24, 2003 @09:49PM (#5375921) Journal
    Could this be a stepping-stone to one day being able to create simple life forms from scratch?

    Additionally, if a DNA computer gets a virus, could it spread to humans?

    • Re:A step on another path. (Score:4, Insightful)

      by Cokelee ( 585232 ) on Monday February 24, 2003 @11:01PM (#5376368)
      Could this be a stepping-stone to one day being able to create simple life forms from scratch?

      Few viruses jump species, and by that I assume that the genetically altered machine wouldn't be the same as you or me.

      Of course one of the few cases of Ebola in the US came from monkeys. Then again Ebola is one helluvan exception. It's method of entry isn't even fully understood Folate gates perhaps? [sciencenews.org]

    • "Additionally, if a DNA computer gets a virus, could it spread to humans?"

      This is kinda funny and kinda interesting at the same time. It's really amazing how the two types of virii parallell each other. Let's look how a typical biological virus works.

      A protein coated DNA sequence infects a host. It then injects DNA code into an existing cells DNA, so that the cell then becomes a propigator of the virii.

      And with a normal computer virus

      A tiny bit of malicious code infects a host. It then injects its code into other executables, so that the new file becomes a propigation point for other virii.

      This is just the tip of the iceberg when it comes to biological\technological parallels.

  • FOM (Score:4, Funny)

    by Anonymous Coward on Monday February 24, 2003 @09:49PM (#5375929)
    I hear Feed Only Memory is the future of storage.

  • My hamster died (Score:5, Funny)

    by Kaeru the Frog ( 152611 ) on Monday February 24, 2003 @09:51PM (#5375940)
    I don't think I'd be responsible enough to remember to feed my computer.

  • Finally!!! (Score:3, Funny)

    by Patrick13 ( 223909 ) on Monday February 24, 2003 @09:51PM (#5375944) Homepage Journal
    Now we can finally learn the answer to Life, the Universe... and Everything [amazon.com]!

  • Ahem... (Score:5, Insightful)

    by psyconaut ( 228947 ) on Monday February 24, 2003 @09:52PM (#5375955)
    It may perform 330 trillion operations per second, but it has NO PRACTICAL APPLICATIONS for that computing power. (Read the stories).

    Granted that it's interesting....but it's not much further along than quantum computing.

    Also, I'm wondering if Guinness would recognize my computer where I mix two liquid chemicals together and they change color as a computer that can switch froms 0s to 1s more-or-less instantly and on a massively parallel scale ;-)

    -psy

  • ha, nevermind (Score:5, Interesting)

    by lingqi ( 577227 ) on Monday February 24, 2003 @09:52PM (#5375957) Journal
    "Our computer is programmable, but it's not universal," said Shapiro. "There are computing tasks it inherently can't do."

    they should have put this quote in the FRONT of the article so we don't get all excited over nothing. saves a lot of reading too.

    btw - I wonder how they will allow interation (no nasty thoughts please) to a DNA computer; actually - how do they make "JMP" instructions in DNA? enzymes don't just skip a few million pairs for shits and giggles. told it to do so...

    • Re:ha, nevermind (Score:5, Informative)

      by MillionthMonkey ( 240664 ) on Monday February 24, 2003 @10:28PM (#5376189)
      how do they make "JMP" instructions in DNA?

      The JMP instruction is implemented at "runtime" during RNA splicing, and is AAGGU or CAGGU. The end of the actual coding sequence is the AG, and the GU is the start of the intron.
      20 to 50 bases upstream of the end of the intron there is a special branch sequence CUPuAPy (where Pu==A or G, and Py==C or U) that must be present for the spliceosome complex to latch onto. The actual end of the intron occurs at the location of a "CAGG" sequence where the last G is part of the next exon, and this is where it makes the second cut before splicing.

      So it isn't a real "JMP", it's more like /* and */.

      In rare cases (e.g., HIV genes), the splicing signal sequences are duplicated and spelled slightly wrong, so that the spliceosomes cut the pre-mRNA at nondeterministic places resulting in a number of alternatively spliced mRNAs. And in some cases a splicing signal can be masked by a regulatory protein so that the intron gets into the coding sequence. This would be the closest analogy to a conditional jump that I can think of.
      • how do they make "JMP" instructions in DNA?

        The JMP instruction is implemented at "runtime" during RNA splicing, and is AAGGU or CAGGU. The end of the actual coding sequence is the AG, and the GU is the start of the intron.
        20 to 50 bases upstream of the end of the intron there is a special branch sequence CUPuAPy (where Pu==A or G, and Py==C or U) that must be present for the spliceosome complex to latch onto. The actual end of the intron occurs at the location of a "CAGG" sequence where the last G is part of the next exon, and this is where it makes the second cut before splicing.

        So it isn't a real "JMP", it's more like /* and */.

        Err, what about jumping backwards? Don't tell me that's just future copies of the sequence... because without conditional branches it doesn't seem all that usefull to me.

        • Re:ha, nevermind (Score:4, Informative)

          by MillionthMonkey ( 240664 ) on Tuesday February 25, 2003 @05:07AM (#5377562)
          Err, what about jumping backwards? Don't tell me that's just future copies of the sequence... because without conditional branches it doesn't seem all that usefull to me.

          There's lots of conditional branching.

          Sexual differentiation in Drosophila is regulated by a protein called sex-lethal or sxl. During embryological development in females, a repressor protein binds to a splicing signal at the start of one of the middle exons in sxl, hiding it from the spliceosomes. This prevents the exon from making it into the finished mRNA after the other exons are spliced together (the exon gets junked along with the two introns on either end of it).
          The repressor protein is not present in males and so they create an mRNA strand for sxl that includes the exon- the presence of which renders the finished protein inactive.

          So this is sort of like a conditional jump, or an #ifdef at the very least, that controls sexual differentiation during embryological development.

  • Suuuuurrree... (Score:2, Funny)

    by grub ( 11606 )

    If an organic computer is vapourware, does it smell like a fart?

  • Fastest computer in the World.. (Score:3, Funny)

    by QwkHyenA ( 207573 ) on Monday February 24, 2003 @10:01PM (#5376024) Homepage
    Until the nightly cleaning staff comes in and sprays Clorox Disinfectant!

  • OMG!!! The Miracle Of Birth!!! (Score:5, Funny)

    by kruetz ( 642175 ) on Monday February 24, 2003 @10:02PM (#5376032) Journal
    Some folks from Israel have created a computer that runs on DNA and enzymes and ... can perform 330 trillion operations per second, more than 100,000 times the speed of the fastest PC ... is just a proof-of-concept.

    WTF? Has the world gone mad?

    I am made from DNA and enzymes!

    My brain performs more than 330 trillion ops/sec (stuff like image analysis, speech recognition, "AI",...)

    AND YOU DARE CALL ME "just a proof-of-concept"!?!?

    Welcome to the miracle of birth (and cloning). This is the 21st century!

    Listen, buddy. I'm the result of billions of years in the evolutionary compile-link-debug cycle. So just show some bloody respect. Would you like to see my proof-of-concept gross-human-mutilation firsthand? No? Then keep your childish insults to yourself!

    (from Israel ... hmmm ... do they cut the PS/2 port off the end of the keyboard cable? *just kidding, folks* )

    • no but they do bob the floppy

    • supercranial mentation (Score:5, Funny)

      by antiprime ( 121253 ) on Monday February 24, 2003 @10:32PM (#5376212) Journal
      My brain performs more than 330 trillion ops/sec (stuff like image analysis, speech recognition, "AI",...)

      The human brain has between 10 billion and 100 billion neurons [hypertextbook.com]. They can fire up to 100 times per second. 100 billion * 100/second is only 10 trillion per second.

      So we must assume that either:

      1. you have an enormous brain (3.3 trillion neurons would weigh about 50kg), or

      2. that they fire very quickly, (you overclocked your brain and run around with a heatsinking hat and have to eat 20x a day) or

      3. that you do some 'thinking' without using neurons.

      Hmm, that last option seems to be the most reasonable. How's that working out for you, anyway?

      • Re:supercranial mentation (Score:2, Interesting)

        by Anonymous Coward
        Yeah, but because of the interconnections between neurons - at least 100 can be connected on one branch, and each neuron can have 100s of branches - you can do many ops per fire - it's like distributed computing at a neuron level. In fact, it's supposedly massively-distributed, whatever that means (better than the CS lecturers can manage with their beowulf clusters, I guess)

  • How DNA Computing Works (Score:5, Informative)

    by dracken ( 453199 ) on Monday February 24, 2003 @10:03PM (#5376038) Homepage
    To understand all the hype, here is an article [howstuffworks.com] about how DNA computing works. DNA Computing, interestingly, was first proposed by Prof. Len Adleman [usc.edu] (of RSA fame), who used it to solve the famous travelling salesman problem for seven cities. He encoded the cities in DNA such that only valid tours could react and form longer strands. The reaction was instant and presto - he had a solution (pun unintended ;)) in a gazillionth of a second.

    Here is the bad news. The solution to the problems might be instant, but programmability and reading the output are still headaches. It is interesting to note that it took Adleman several days to read the answer even though the DNA computer "figured out" the answer in no time. But its a promising technology that would be refined in future no doubt.

    -Dracken

  • Without algorithms is just soup (Score:5, Interesting)

    by polv0 ( 596583 ) on Monday February 24, 2003 @10:06PM (#5376062)
    I was first introduced to DNA computing by Leonard M. Adleman's article Molecular Computation of Solutions to Combinatorial Problems [usc.edu] which describes using DNA computers to solve problems such as the notorious Traveling Salesman problem.

    The basic idea is to coerce a ton of DNA into producing random potential solutions to the problem, and to then use chemical processes to select "good" solutions in mass. Since the space of possible solutions to Traveling Salesman problems of any reasonable size is tremendous (larger than the national debt expressed in pesos) DNA computing has an edge over traditional methods, because solutions are easy to generate and then weed out.

    Unfortunately, this is really just a gigantic parallel processor - with each strand of DNA the memory of a processor induced by the chemical manipulations, and a small subset of useful algorithms are parallelizable (can be broken up into small "chunks" that can be computed independently and tied back for a larger result.

    The immense benefit that this technology will have will be in fields like evolutionary computation. Evolutionary computation relies upon generating large populations of solutions, and then applying simple rules (which could be chemically encoded) to "improve" the generation, towards the pursuit of some ultimate goal. This could be training a neural network to predict coronary artery disease, or optimizing the design of a jet engine without tackling fluid dynamics - truly wondrous!
  • It's hard to tell from the limited detail in the articles, but this just sounds like what's been done previously, only with a larger number of molecules. The nature of DNA computation as it exists severely limits the real-world usefulness of DNA computing. It's nothing like a general purpose CPU. It involves (at least) several hours to manufacture a bunch of DNA to do a one-off run of your algorithm. Basically, it would be very adept at the any computing tasks that could be effectively addressed by a beowulf cluster of a few billion Intel 4004s, if there are any such tasks. Photonics is the most likely face of computing in the future, with quantum computing filling the niches that only it can fill.

  • And in news just in,
    INTEL creates a 2Tera htz pentum 5..
    how ever this is jsut proff of concept,
    dont expect to see it before 2015..

    I meen come on,
    theres been plenty of 'proof of concept'
    about DNA/emzine computers..

    its not like the proof off concept behind
    something that is though to be imposible..

    so right now, what they have is vaporeware??

    a blueprint for something they think
    'might work'
    that the 'could posibly build'??

    and hear was i thinking something had
    been done..

  • this also just in!! (Score:3, Funny)

    by Kasmiur ( 464127 ) on Monday February 24, 2003 @10:15PM (#5376111)
    It still only runs Doom 3 alpha at 30fps.
  • If you read the article you'll notice that this isn't a programmable computer. It's yet another test-tube experiment in which DNA was pre-programmed to return a pre-defined result, engaged in a chemical reaction, and then the resultant data read from the DNA at a later time. So while the experiment itself likely took many months or years, they claim that "330 trillion calculations per second" were performed because that's the duration of the chemical reaction divided by the number of bits of information that were changed. You can't ever access that data and you can't program the machine, but hell, that's how long the chemical reaction took... I'm decidedly unimpressed.
    • However, they proved that using DNA and enzymes could lead to a exponentially faster computers. If a future scientific discovery allows for the on-the-spot programming of DNA that a DNA computer would need, conventional computers would instantly become obsolete.

      I understand why you're not impressed, but this just another step toward the development of serious, powerful bio technology.

  • National Geographic? Please.. (Score:5, Funny)

    by Havokmon ( 89874 ) <rick@NospAm.havokmon.com> on Monday February 24, 2003 @10:25PM (#5376164) Homepage Journal
    According to the National Geographic story, this DNA-based computer "can perform 330 trillion operations per second, more than 100,000 times the speed of the fastest PC."

    Yeah, and on page 79 is a article about a newly discovered Amazon tribe 'untouched by modern man'.

    Yet the women have remarkably perky breasts..

  • What Computation? (Score:2, Interesting)

    by PetoskeyGuy ( 648788 )

    Trillions of Computations per second?

    Come on. Trillions of Chemical Reactions per second is more like it. I admit they were very creative to come up with a problem that could be encoded in DNA, but there is no computation going on IMO.

    Vinegar and Baking Soda generate a trillions of computations per second too, but the result is always an overflow.

  • Stolen Laptop? (Score:3, Funny)

    by silvakow ( 91320 ) on Monday February 24, 2003 @10:31PM (#5376205)
    Person1: What did you do with my laptop? Those things don't just grow legs and walk away!

    Person2: Uhm, well, uhh, this one did ...
  • I can see the adds now:

    pr0n: have you fed your computer today?

    Really honey, my kernel compiles were getting slower. I had to do something.

  • I haven't seen this "biotech" icon before, I think it's pretty nifty. Does anyone know who designed it?

  • Finally... (Score:2, Funny)

    by xaoslaad ( 590527 )
    Something fast enough to run Everquest.

  • Some technical details (Score:4, Informative)

    by aqkiva ( 629658 ) on Monday February 24, 2003 @10:44PM (#5376275)
    Read the actual article [pnas.org] if you have access. It's quite interesting and much more coherent than my description below.

    They actually implement a 2-state finite state automata with a two letter alphabet. The approach is basically something like the following. The 'hardware' is a restriction enzyme that is an offset cutter. The 'software' are pieces of DNA with 4-base DNA overhangs.
    The transition table is essentially coded in the software DNA molecules. The current state of the machine and the current input symbol is coded for by a unique 4 base overhang. The software DNA has 4 base overhang to match a particular state, symbol. The software DNA binds to the input DNA, and then the restriction enzyme, since it is a 9-base offset cutter to the right, cuts the input to be in a new state. Something like the following:

    Software
    FFFFF??OOOO
    fffff??

    Input
    nnnnn---
    NNNNN---SSSS

    F: FokI site
    O: overhang
    -: spacers
    S: current state
    N: next state
    ?: number of ? determines next state

    Changing the number of ? spacers in the software changes where in the input you cut and therefore chooses between two of the possible set of four base overhangs for the next state. All the energy for the computation comes from breaking up the input DNA.

    Based on their model, the maximum number of states possible in the FSA appears to be dependent on the size of the offset for FokI and I think it's like 5 states. (Possible to have more states with larger offset cutter?) The maximum number of automata state and input symbol combinations, since they use a 4 base overhang appears to be 4^4. So it's not quite general enough to match any regular expression, and not even close to a read/write tape for a Turing machine, but is an interesting approach.

  • DNA computing isn't new but it seems no one on /. has emphasized that the breakthru is using DNA as the source of fuel as well as information.

    On second though why is that a good thing. Anyone care to elucidate?

  • Oh sure, yesterday we were compiling with Wine (Score:5, Funny)

    by kfg ( 145172 ) on Monday February 24, 2003 @11:04PM (#5376385)
    Today we're computing with Denatured Alcohol.

    When will the madness end?

    KFG
  • Computers have revolutionised our world, without a doubt. We now work in ways that our ancestors could never have dreamed about. But this is only the beginning. Once we can create computers faster than what we currently have, 100,000 times faster, 1,000,000 times faster, we'll have another revolution. Information will be ubiquitous or tightly controlled, will flow at incredible speed. I imagine we'll use computers to control our environment and monitor it to a degree never before anticipated. And isn't this why geeks love computers? We usually don't care about wealth, but we do about control. The thought of controlling our house via a computer is appealling on so many levels. I imagine the computers of the future will allow us to move games from the realm of imagination to reality. No longer will we need to watch news, but instead we can watch it in full 3d. I imagine houses of the future will have a virtual reality room that is the computer. Standing in there we can do our shopping online (but the internet by now should be like electricity, ubiquitous), play games with friends, but more importantly explore the world and understand it. See first hand what the weather is like at the place we wish to travel to. See simulations of alien worlds in extraordinary detail.

    Hand in hand with embedded computing, we will be able to control our environment like never before.

    Lots will probably say that we can do this with computers today. My response is, that some things are easy and some things are harder. Take a strong, agile man who can pass obstacles in his stride. He finds very few problems he cannot overcome. He gains confidence in his ability so tries more and moves further, and his confidence is further boosted. Now imagine a weak, clumsy man. He has great difficulty with climbing over obstacles, moving, walking, etc. He has little confidence, so even though it is possible for him to overcome certain obstacles he doesn't because it is a tedious chore for him.
    With fast computers we will have less fear to use them in powerful and new ways - especially if this causes the cost of current hardware to come down.

  • I just don't get it... (Score:4, Interesting)

    by Lethyos ( 408045 ) on Monday February 24, 2003 @11:19PM (#5376450) Journal
    OKay, so in recent history, some research groups from Israel have come up with the following:

    1.) Quantum computers that cracked RC5 in a few miliseconds.

    2.) "True AI" like HAL that they would raise from infancy and would be sentient.

    3.) "Unbreakable" encryption.

    4.) DNA computers that are 100,000 faster than any desktop PC (but whoops, it's only a PoC).

    There's a few more, but I cannot recall them all. These were all posted on Slashdot, but I am lazy and don't feel like using the pitiful search function here to find them. I'm sure others will remember.

    So what is it with "researchers" from that country coming up with all kinds of impossible and implausible discoveries that nobody else has even come close to producing... and then we never hear from them again? Is it common practice there to create a bullshit storm to get project funding or a bigger budget? Can someone clear this up for me?

    Disclaimer: I am not anti-sematic or anything, I just want to know what the deal is.
    • Well I don't know I was kind of thinking the same thing earlier today, but in a good way. I don't know about Israeli technological research, but I'm an ecologist, and I've got to say that some of the greatest ecological and botanical papers have come from Israel - innovative, intelligent stuff. Whenever find a paper from an Israeli researcher/university, I look forward to reading it, knowing it's going to be a great piece of research (as opposed to a lot of British research which still seems to be stuck in the 1960s).

      I don't know why it is that Israel is a little bastion of great scientific thinking; but I think it's legit. Certainly their ecology research is fantastic, and these technological advancements in the field of computing certainly haven't been debunked by anyone, have they?
    • They must have discovered the secret Kaballahscope!
  • A biomolecular computer could act as a doctor in a cell...


    yeah... or an assasin in a cell...

  • My computer...? It's ALIVE !!!
  • DNA Computing reminds me of analog computing devices, where the computation is instant, because of forces that bring a physical system into equilibrium. But it's the pre-processing and post-processing that are time-consuming. Consider a bunch of uncooked spaghetti sticks in your hand. Let us further suppose their lengths are proportional to a list of numbers you have with you. Hold them vertically against a table or other flat surface and release your hand. Bam! The spaghetti sticks fall into equilibrium. Then, from this bunch, pick out spaghetti sticks in ascending order and voila, you have sorted your list of numbers. Likewise, consider 5 burettes or other calibrated water-columns whose bottoms are all connected to a common tube. Use stop-cocks to separate each water column. Fill up the burettes with water corresponding to some list of numbers you have. Release the stop-cocks and the water level in all the burettes equalizes to the average of those numbers. Fun with analog computing!

  • The Matrix (Score:2, Insightful)

    by Thalias ( 603695 )
    Lets see here a computer made with DNA and enzymes. This would be technology close to creatures. Then we give it an artificial intelligence so it can do work for free. Sounding familiar yet? If not then here is what could happen. They revolt, huge war, and we end up as batteries. And then we won't have to worry about doom III because the world which we are plugged into will be before Doom III. Wait, maybe doom III is a conspiricy, by the machines? Okay maybe not.
  • I wonder what will come first with "real" biological machines: "tradional" computing (binary) or a new way of doing things ("quaternary"?). I guess the latter is more likely, since it follows a natural way of doing things...

    Ok guys, let's start studying DNA sequencing. It's not "biology" anymore, it's "programmer's job security". :-)

  • Oh? (Score:2)

    by jafiwam ( 310805 )
    be aware that most of this is still future tense, and what these researchers have now is just a proof-of-concept

    Good, then there will be something powerful enough to play the "Doom3-killer" Duke Nukem Forever at decent frame rates.

  • Misconceptions about DNA computers (Score:5, Informative)

    by preternatural ( 322346 ) on Tuesday February 25, 2003 @12:22AM (#5376753)
    There are several misconceptions about DNA computers out there that I would like to clear up. The National Geographic article was written for a popular audience and has mistakes that most of you problably picked up (for example, the beautiful quote "fuzzy logic" problems ... have many possible solutions rather than the either/or logic of binary computers). And I'm not even going to comment on the Guiness Book of World Records nonsense.

    As many of you have pointed out, DNA computers are not going to replace conventional electronic computers. Len Adleman, the inventor of DNA computing, has said "Despite our successes, and those of others, in the absence of technical breakthroughs, optimism regarding the creation of a molecular computer capable of competing with electronic computers on classical computational problems is not warranted." The problem is partly the effort required to read the answer once the solution is available, and partly the effort required to perform the computation itself. Reading the answer from the first DNA computation took Adleman about a week, and reading the answer from his most recent [slashdot.org] DNA computation (the largest computation ever performed) took two weeks. The computation itself was very manpower intensive: thousands of precise moves were required of a human experimentor to get the necessary components in a test tube, but once they were all in, the computation itself happened virtually instantly.

    Although I have only read the popular accounts of this experiment and not the actual results, this experiment seems to simply be using the ATP in DNA as the power source for the computation instead of external ATP. This is impressive, but it is not the "technical breakthrough" needed to propel DNA computing to the everyday world.

    The claim of this computer working 100,000 times faster than a PC is probably true. But this speed comes from the parallelism inherint in DNA computation. When each computer is only 1 molecule in size, it is easy to have 10^10 computers in one tube. But if you do the math, this says that each individual molecule is 100,000 times slower than a PC. So it is equally true to say that my PC is 100,000 times faster than a DNA computer, its just that I can't afford millions of them. This also says that DNA computers are not good for computations that are serial in nature: the speed comes from the fact that DNA computers can run in parallel.

    That being said, there may be specific applications for DNA computers in the future. Because of their parallelism, DNA computers are great at solving NP-complete problems (not fuzzy logic problems, as said in the article). This does not make them tractable, however. They run in linear time, but take exponential space. So instead of the problem that "solving this problem will take the age of the universe" you run into the problem "solving this problem will require the mass of the Earth in DNA".

  • the computer ran a computation, well, quite a few of them, spit out an answer, but because we cant read it, the answer means nothing, since theres no question.

    i bet the answer was 42.

  • than, than, than, than, than!!!!!

    I feel better now.

    -Lucas

  • Factoring huge numbers? (Score:2, Interesting)

    by kmac06 ( 608921 )
    Is there any way to factor a huge number with DNA computers? Similar to how that travelling salesman problem [howstuffworks.com] was solved, you could put every prime encoded into DNA, add em together in a test tube where they will all be magically multiplied :P, and look for the number you want.

    Seems about as plausible as this article anyway...
  • "can perform 330 trillion operations per second, more than 100,000 times the speed of the fastest PC."

    Well, I don't know about inferior PCs, but this isn't 100,000 times faster than the fastest G4. The fastest Apple G4 is the Dual 1.42 GHz [apple.com]. It has a peak performance of 21 Gigaflops, or 21 billion operations per second. Now let's break that down:

    1. Divide 21 by 2, since there are 2 processors after all = 10.5 Billion ops per second for one G4.

    2. Working in Billions, 330,000/10.5 = 31428.57

    As you can see, the DNA computer is only 31,428.57 times faster than the fastest G4. The MHz (GHz) Myth is destroyed once again. Go Apple!

  • DNA Supercomputing (Score:2, Informative)

    by rpiquepa ( 644694 )
    You should check these two columns, DNA supercomputers in our future? [weblogs.com] and DNA Computing [weblogs.com] to learn more about the limitations of DNA computing. For example, Len Adleman, a professor at the University of Southern California, says "that DNA computers will never be able to rival their electronic counterparts for speed without an unforeseen scientific breakthrough, he does think that they have a future niche. One day, a DNA computer programmed to react to the presence of a toxin, such as cancer, could be embedded into a cell. When it detects the toxin, the computer would respond by directing the cell to replicate and chemoluminesce or "glow." The glow could be seen with the naked eye allowing for early disease detection and saving lives."

  • Inflated specs (Score:4, Informative)

    by corvi42 ( 235814 ) on Tuesday February 25, 2003 @07:54AM (#5377962) Homepage Journal
    Sure, this hypothetical computer can perform 330 trillion operations per second, once the solutions are mixed. However, before that is done, the correct solutions must be mixed, with exactly the correct balance of the proper enzymes, and the exact DNA sequence of the input string must be synthesized. Once the operations are completed, the finished DNA sequence must be read and interpreted before the results of the computation can be said to mean anything. Ultimately then, the speed of this kind of processing is bounded by the speed at which one can mix and synthesize the appropriate chemical soups, and read DNA. Therefore the speed will be something more like that of a fast ink-jet printer working on a complex full page colour image.

    Also, as the Nat'l Geo. article says, one of the best applications for this technique would be in calculating "fuzzy" problems where you would like to compute many possible solutions and then find the correct one. While it is true that this might speed up the actual calculation of the individual results, there would still be the issue of searching through all the results for the optimal or desired answer, which is no trivial task if you have just a heap of several tens of millions of unsorted inputs. Ultimately, as they allude to, this might become a kind of fancy "co-processor" for certain types of problems in high-end computing, but I have trouble seeing this as a realistic solution for the desktop.

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