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Science

Getting Closer To DNA Computing 131

Posted by timothy from the and-one-day-they'll-be-bipedal dept.
jwambach writes: "This brief article over at Yahoo! describes how scientists are attempting to create molecular electronic circuits using DNA. They say that they could potentially create circuits 10,000 times smaller than with current technology." The article says that "[r]esearchers have already created molecular wires, logic gates (a building block of computers) and switches, which could be hooked up to make a working computer a fraction of the size of ones based on silicon chips." The coolest part is that assembling the tiny components could be done with DNA-tagged components, shaken (or stirred) in a test tube.
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Getting Closer To DNA Computing More

Getting Closer To DNA Computing

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  • Well DriveCar could probably use some alteration for a lot of people (random alteration's probably going to be an improvement for many), and who in their right mind even has TalkToManager installed?
  • Ewwww....I don't think I like the idea of a sweaty bio-computer burping and farting on my desk.
  • Six times 10^23, not 1023. 6 * 10^23 , number of molecules in 1 mol, Avogaddro's constant.
  • We all consider cooling to be of vital importance in our silicon based machines, don't we? What kind of new cooling device are they going to create/use that will keep the DNA from degrading or just plain denaturing?

    Plasma baby! :-)

    "Humanoid detected.....
    slashdot.org needs plasma badly...
    Come here fat boy, time to feed me."

  • Damnit!

    You *CAN NOT* make stuff 10000 times smaller than something else. Why? Let me explain.

    1. You have 1 dollar and your uncle Bob has none. You feel sorry for him and you decide to give 1 time that amount to your uncle. So, how much do you give your uncle? 1 dollar, leaving you with nothing left.

    2. You have 10 dollars and your uncle Bob has none (he's a gambling addict, you know). Once again you feel sorry for him (damnit you're soft!) and decide to give him 1 time that amount. How much do you give him? 10 dollars, once again leaving you with empty pockets, except for the gum you accidentally stuck there and get off the garment.

    3. You have 10 dollars and your uncle Bob once again has nothing (he's an alcoholic, too) and you decide to give him two times that. In this case you'll give your 10 bucks to your dear, beloved uncle and - after that - still owe him another 10 bucks. In other words, you gave it all away and ended up with negative total.

    Get it?

    1 time smaller/slower/less leaves you with ZERO.

    Thus, making something 10,000 times smaller than something else makes the end result's size 9,999 times the original size, ON A NEGATIVE SIZE-SCALE!

  • The head of the pin is the end with the angels dancing on it......

  • I've build for myself an organic computer long time ago, it's called "brain" and I tend to use it everyday..... well mostly every day.
  • What are using for food? If it replicates, it's a living form of DNA, if it's alive, it can die, which means I've got to feed it at least enough to replace what dies off...
  • I would actually think there would be less cooling needed, not more. The gates would work at an atomic to subatomic level, so changes in "voltage" with the registers would be extremely small.

    You're unto something about that "denaturing" process, however. How would we keep DNA-based electronics from being torn apart by bacteria?

    • The ability to control your blood flow and other various bodily functions
    • A possible /kill function that would cause the instanteous death of the host
    • Possible mind control
    • Electronical tracking and control of the gene pool
    • Making people think Bob Saget is funny


    We're already there:
    • Your body already does all of this, or should. It can also be done with drugs and/or machines. Or exercise, or crossing your legs and humming. I have to do this last bit because I'm controlling (i.e. increasing) my urine output at the moment via a nonprescription substance known as Beck's.
    • Any different from a .44? How? Potassium cyanide? Radiation? Stroke? We can all be discreetly zapped from a distance; it's nothing new and hasn't been since the advent of archery (or rock-tossing, if you want to go back that far.)
    • This has been perfected in the form of TV. 'Nuff said there.
    • GPS. Timecards. Tollbooth receipts. Credit card bills. Fingerprints. Biometrics in general. As for control of the gene pool, issues 2 and 3 address that if nothing else does.
    • Without A-C-G-T, Bob Saget is Bob Set. How funny is that? ;)


    I don't think it's wrong to be a paranoid android, though, but you have to choose your phobias and aversions wisely.
  • This is really exciting. I wish I could get involved, but I don't have a degree in molecular stuff.

    I wonder what kind of equipment you need to do this stuff. Not too long, I perused through an article that talked about how to do dna something or other in your kitchen.

    When will we be at the point when we can start hacking this stuff, be it in the kitchen, bathroom, bedroom, or office?

    --fred

  • Missile Command? I don't think I'd yield control of our nukes to an old Atari cartridge, but that's just me...

  • It sounds like this is more like they are trying to put a virus on every computer out there! Don't let them infest your computer with a virus. Save your computer.

    I mean virii are just usually just DNA or RNA and some protective coating, right?

  • DNA is the fundamental molecule of Life, it is capable of self-replication. Creating computers with DNA can lead to self-replicating computers !

    So what happens when it mutates? It turns into Windows ME.
  • maybe DNA computers wouldn't hook up to wires. what about the brain? perhaps you could install a math coprocessor in your head.
  • ehm ... nope, when you make it 10,000 times smaller, it's the same as multiplying with 1/10,000, or 0.0001.
    What you do is remove 10,000 times the original, not reduce the original 10,000 times.

    1 time smaller is a "nop", it leaves you with exactly what you had from the beginning

  • hrmmm (Score:1)

    by aswan ( 24269 )
    And as we approach the dawning of the age of aquarious computers get smaller, and ludicrously faster. I want my 8088 back... long live text adventure games... oh well... at least monitors are getting bigger.....
  • And what would petrifying the device accomplish? All you'd end up with was a lump of rock shaped like a computer, incapable of processing anything.

  • Artificial Intelligence. (Score:4)

    by onyxruby ( 118189 ) <onyxruby&comcast,net> on Wednesday August 09, 2000 @06:57PM (#866103)
    New form of artificial intelligence. DNA evolves with useage. Computer refuses to run Windows and won't take input from user attached to keyboard.

  • Wrong.

    Like I said, it's semantics.
    The correct way to put the phrase would be something along the lines:

    "They say that they could potentially create circuits 1/10000th of the size of the circuits created with current technology."

    1 time smaller means the size is 100% smaller than the original size, which doesn't means the darn thing ceases to exist (1 - 100% = 0).
    Okay, I was wrong in that when you take 100% out of the original size once, you have nothing left, which means that taking the rest 9,999 times that 100% out of the original size (of which nothing is left anymore), we still have nothing. In other words, the size would not go to negative scale.

  • The next question is.. (Score:4)

    by PopeAlien ( 164869 ) on Wednesday August 09, 2000 @06:57PM (#866105) Homepage Journal
    So can I take these DNA circuits and introduce them to my body.. Can I overclock my brain? Can I change my mind? Johnny Mnemonic here we come!

  • Ack, remove the word "doesn't" where it doesn't belong in the previous posting.

  • So now we have a computer sweating. This means it needs water (or something) to sweat out. And if it needs water, I'm sure it needs food too. So now I have a smelly organic lump that I have to feed and water constantly.

    Modern science has developed a pet that can check email.



    "Hey, what kinda software you running on your dog?"

  • You can put regular silicon gates into your body, and they'd do you just as much good.

    --
  • There's a researcher in Saskatchewan (whose name I unfortunately forget) that's done some pretty nifty work in making DNA "wires". He's able to reliably use metal ions in DNA chains, as the "backbone" of the chain. The base-pairs are still the same, and he doesn't have to trap particles in the chain itself.

    Apparently he's having a hard time getting funding for his research, since nobody A) believes that it works and B) he's stuck in a dinky university in the middle of nowhere.

    . . . a scientist I know is on one of this guy's grant committees, which is how I heard of him . . .

  • DNA, as they're using it in these experiments, is nothing more than an organic molecular structure. Organic in the CHEMICAL sense, not in the casual non-scientist parlance.

    It's not alive. It couldn't even BE alive -- life requires WAY more support infrastructure (yes, even viruses need more than these things have).

  • Re:A few other issues. (Score:1)

    by Anonymous Coward
    One word Bluetooth
  • given that we have bio-pcs.. will they sweat to disspiate heat??? and could you overclock them with caffeine?
  • Completely agree with the DriveCar()... TalkToManager() was installed and enabled by default on my RH system, but on my OpenBSD system they had performed an audit on it a year and a half ago and corrected the buffer overflow exploit, but it's not installed as a default. {:-)

    ----
  • But then again, why believe in DNA when you can have Jerry Falwell tell you it doesn't exist?

    Larry told me he fucked his momma in th' outhouse.
  • I went into this thinking of how what are today hackers may tomorrow be browsing our brains, but that's not really what this could be used for; programming and such would be the same sort of thing as before, the genetic engineers would just take over hardware.

    It does add a whole new dimension to computers, though, just to think about what technology you'd be using, particularly if/when it started talking to you...

  • Um, excuse me Scully (or Marvin, gotta give you credit for the Hitchhiker's Guide reference), but where did the article say anything about chips in your bloodstream or knowing your DNA sequence or the NSA locking on to you and knowing where you are at all times???

    This is about nanotech, something that is coming and will change everything. Just because this specific application uses DNA doesnt mean the DNA is yours or mine or Bob Sagets, its just how the technology works..

    With that said, your point could be valid about nanotech and the possibility of nano-probes (star trek: voyager, anyone?) floating around in your blood, but please save your conspiracy theory possibilities for when those things actually exists!

  • I tend to replace it with NodAndGruntAtManager(). If they happen to be saying anything important, you can notice the facial expression shifting, and explain that you were considering a possible solution to the latest code problem that just came to you.
  • Could a circuit based on DNA tech create something random? Or will we have to rely on other types of components to do this? Think about it.
  • Like all things nano, we can laboriously put together a working subunit as a proof of concept--create a biochemical logic gate, write "IBM" on a pinhead--but mass production is still pie in the sky. We can all talk about shaking up a bottle and out comes a computer, but that's all day dreaming. The nano industry will probably have to be bootstrapped the hard way: build the first nano-factories laboriously by hand, atom by atom, molecule by molecule. Then have this factory build other factories, which build others, etc etc. Only once you have a critical mass of cooperating nano-factories in place can you actually build real things in finite amounts of time. Mass producing something like a full nano-scale computer will take shitloads of factory units and lots of production infrastructure that probably hasn't even been given much thought yet, like how to supply raw materials to the factories, how to mount all this stuff--you can't just bolt a nano-factory to the floor, etc, etc.

    I think I'll be lucky to see nano-tech mature to industrial levels within my lifetime, and I'm 30. Still, along the way it can produce very interesting and useful evolutionary products, especially in the "near-nano" fields, such as the TI DLP chip, or the new accelerometers in airbags.

    Uwe Wolfgang Radu

  • Imagine a beowulf cluster of these things... (Score:3)

    by laborit ( 90558 ) on Thursday August 10, 2000 @04:09AM (#866120) Homepage
    ... it could actually be Beowulf!
  • Consider an intentionally designed and created virus. And biologically active viruses do go from species to species - most influenza in china comes from birds, particularly chickens.
  • Does this mean we are closer to quantum computers too? That would open up a whole other can of worms the government will fall behind in their knowledge of. I can see it now. Company A patents DNA sequence A and Company B patents the building blocks of DNA sequences. Think that won't happen? Look at the current patents granted. Doesn't somebody have patent on the . in .com?
  • I know! I just about cried myself. But I dried myself up and found the will power to watch Full House and the comedy stylings of Bob Saget and John Stamos. And all was better. =)
  • "Modern science has developed a pet that can check email"

    Why not just train your cat to check your e-mail? They seem to enjoy walking on keyboards :)
  • You are standing on pathway that runs through a densly wooded forest, to the north you see a castle, to the south you see a cave. >look down on the ground you see a 2 inch by 2 inch purple imac. >squish it like a bug. on the ground you see a 1 millimeter by 2 inch purple thing.
  • We already have a computer that does that.. it's called a Macintosh, and courtesy of Jobs, some programs /do/ ignore user input...
  • According to Britannica [britannica.com], DNA is simply "organic chemical of complex molecular structure".
    Therefore what is interesting are the implication of having a biological, that is alive, component in our computer.

    The greatest risk is that of degradation overtime from simple aging of the DNA-based tissue, not to mention being able to become victim of biological diseases since it's alive, after all.
    I personnaly would shake in horror at the thought of my computer developping AIDS ;)
    This said, I doubt such an implementation would actually happen over time, there are just too many risks involving 'live' components in mechanized objects.

    --
    Kiro

  • I have something growing in this old carton of king tao's chicken that may be able to help. It's a sentient slime mold, but it also has a slight attit#$*_$ NO DON'T PUSH THAT BUTTO
  • Christ, I can just see it - overclocked DNA-based computers with piped antibiotics instead of liguid nitrogen... :-)

  • Wouldn't this give a new meaning to the concept of computer virus?

  • I've never really gotten this about molecular computing either. It seems like the capabilities of these technologies are fundamentally different from the standard math/memory model that underlies current computing. You could create a traditional computer using these technologies, of course, but they seem capable of so much more.

    The brain, for instance, is massively parallel and has processing on numerous levels, with no separation between data and processing -- this simply can't be done on a conventional computer except in the most painstaking and roundabout way (even with Lisp!). Presumably these new technologies would be more suited to such a problem.

    But I've never heard anyone describe how, even in the most general terms, a science of such a thing would look. What's the molecular/genetic equivalent of binary math?
  • I wouldn't be holding my breath for this to replace silicon in your laptop. While it is a wonderful concept, and a scientific tour-de-force, the reliability of these things will probably be miserable. I'm sure someone will eventually put together a molecular computer. But what happens when it gets too hot? What happens when a single chemical bond gets screwed up? The only ways I see to address this reliability issue is with either redundancy or self-repair. The first is easier, but the second is probably an long way off.

    This may have shorter term applicability in composite/injectible medical devices. Imagine a million mini-machines injected into your bloodstream to remove the Sirloin-Steak-Cholesterol from your arteries. Hopefully no problems with overheating here, and who cares if 90% fail. That's what your kidneys are for.

    So far so good, but imagine even later when one of these mini-machines somehow mutates and takes off to do its own thing. Bacteria commonly exchange DNA, so it it possible that these things will combine themselves with bacteria. Maybe this won't happen with the first generation of devices, but once these things are have self-repair chemistry (presumably using RNA) it becomes more likely. It is both awe inspiring and scary to realize that we are entering the era where human induced evolution will greatly outpace and overwelm natural evolution.
  • Huh? I don't see at all how DNA Computing "literally removes every advantage the human brain presently enjoys over silicon CPU's in the way of problem solving." All DNA computing introduces is massive parallelism. The human brain doesn't have much parallelism at all. Just try and add 2+2 and 3+3 at the same time in your head... The advantage of the human mind is intuition, a "feel" for problems. Knowing instinctively what solution just might work. And that's something that won't be able to be emulated for a long time (if ever).
  • Adds a whole new meaning to "my computer died" now doesn't it? Since resurrection is unheard of recently, I suppose if your computer catches a cold and dies, you're just out of luck and have to buy a new one.

    And those computer viruses could now become *really* nasty. People might be more careful about hanging around in IRC and Usenet for fear of catching something. Worse yet, you might catch something from your computer!

    You have to laugh at the futurists that push views like this - they're right up there with autopiloted atomic-powered flying cars. Seriously, folks, it would take a LOT of work to build an immune system to keep this thing running. We'll need them to guide the antigravity cars, though.

    Oh, and make sure it's got plenty of antioxidants and all the complex machinery required to repair DNA, whih we are only barely starting to understand...
  • Researchers today admitted that they're swimming upstream in their attempt to build a computer based on salmon sperm DNA, but vowed to spawn a working computer or die trying.
  • DNA based computers might be much more sensitive to the effects of radiation, or other mutagenic factors. I can just see the label on the computer, " Caution, the hacker general has determined that smoking causes crashes ".

    Hmm, I don't know but I'm pretty sure this is only a problem during self-replication of DNA. People grow new cells a lot (and that's why we're so mutation/carcinogen prone) but your computer shouldn't be making any new DNA structures; any that are going to exist are going to be made at the factory, which is the only place they need to really worry about radiation/carcinogens/etc.

    I would be concerned about the possibility of your computer infecting you with a biologically active virus....

    There is /no/ way this could happen. As one other person who responded to you pointed out, who ironically had score 1 even tho' he raised better (more insightful?) points than yours, viruses can't even cross-infect from one /species/ to another. However, the danger of viruses spreading from computer to computer of this design would be heightened because they would operate on the molecular level rather than the code level. Of course because the computing components are just structures and not cells with any way of replicating the virus would rely on the code level for replication but could infect on the molecular level. Yeah, something like that; wait till the stuff actually comes out, then I'll design one, work this stuff out. For educational purposes only, of course.

    Ever get the impression that your life would make a good sitcom?
    Ever follow this to its logical conclusion: that your life is a sitcom?
  • Yes, but how many people are going to sit through an explaination of how the bit analogy only works if the DNA is of a certain type, in the presensce of certain enzyme, in certain heat and pressure etc... What I said was a generality, thus true in most cases.
    I saw an update on CNN. What they have done is take strands of DNA, bend then back on themselves (like a clothespin), then use a partial complementary strand and an enzyme to close the 'pin'. They can then use a different enzyme to open it. This discovery is the rough equivalent (in computer terms) to get the first few registars of the first processor to fire up.
  • After reading the other comments I have a few questions.

    If DNA computers become fact, will we have to change how one would plea in our legal system?

    Let's say I commit a murder. Could I then blame the deed on a "software" or "wetware" problem?

    Would it be harder to prove intellectual property, when someone could "download" your mind while you sleep?

    Also with the advent of Carnivore from the FBI, will they also demand access to what people are thinking or "computing"?
    I know I don't want that to happen, I don't even tell my wife what I'm thinking!
    And do we stop with people?
    If my dog gets "wired", what then?
    Do I really want to know that the reason he jumps up on the bed in the morning, stands on my balls, and breathes in my face is because I had him fixed?
    Could he then SPAM me while I'm at work?
    I for one think that this should be stopped NOW!!!

  • I can live with that rating. Some mod's seem to favour -1 for effort as well as -1 for effect though...
  • I don't know if this would work, but IIRC, there are modified base-pairs for both purines and pyramidines that are more stable than the ones that normal organisms use?

    Someone more up-to-date with this stuff help me out here?

  • If you think about it, both silicon computers and DNA record data in the same manner, binary. Computers use 0s and 1s, where as DNA uses 4 acids that can only be combined in two possibilities per 'space'. For this reason, DNA computing is very sutable for problems involving calculating a path between two points, if certain routes can only be chosen from certain starting places. I think I read an article in an old wired where they used it to solve a complex traveling salesman problem (go through all cities, but never repeat a city, you can only get to certain cities from certain other cities).The acids would align if you could travel from one city to another,thus creating one step solution. ex.
    *LA**Atlanta
    GT-CA*CT-AG*
    ***TG-TC****
    **Phoenix***

    It prolly won't show well, but that's just html for you.
  • Now we'll have moody computers: "I'm sorry, I just don't feel like playing Unreal Tournament today, sorry!"

    Grr.
  • One interesting tool used in DNA research is called PCR, which is a way of multiplying the amount of DNA in a sample. 24 cycles of PCR amplification would yield a 2 ^ 24 increase in the quantity of a DNA based circuit, and takes less than a day to do. For once, memory could grow faster than data!

    Yes, but there are practical issues that must be resolved with mutations that slip through the cracks in the PCR process, and how they might affect the data being processed by the DNA circuits ...

  • towards the BOFH!

  • This is true in an organism, but in a laboratory setting things get close to that simple--part of the point to the "DNA tweezer" article was to show that the researchers could control the 3D structure of the molecules. Also, the researcher controls what enzymes (nucleases, methylases...) are included in the reaction.

  • Nanotech is still far away (Score:5)

    by GMOL ( 122258 ) on Wednesday August 09, 2000 @08:24PM (#866146)

    The article suggests that we have all the molecular tools and that it is a straightforward matter of hooking them together to make molecular scale computers/robots....this is misleading. There have been a number of published papers that describe molecular logic gates (based on 'inputs' of ions, or particular DNA strands) and the 'output' is often flouresence...which doens't allow you to hook these components up into large arrays. I have tones of ref's if anyone cares to look them up. Even things like Adleman's approach, while actually quite brilliant in design, fail to provide either faster more efficient computers or application to control (bio) chemical systems. Winfree's stuff with Seaman's DNA cubes is again quite interesting, but it's difficult to see where it will go or what insight it will provide. Anyone remember bacteria rhodopsin based memories? I think work continues on them, but no one sees practical application. The stuff coming from UCLA and HP (rotaxanes) is actually quite interesting; and given the population of things that has to do with molecular computing; it probably has the greatest chance of actualy realization.

    Most real nanotech you see today is just some real nice bio/organic/supramolecular chemistry that has been moving along since the inception of chemistry (a-hemolysin stuff, self replicating peptides, nanotubes etc.). Not to say that it isn't wonderful work or un-useful...but it is just renamed chemistry.

    The other thing I have a problem with people like drexler is that suppose one does actually succeed in producing one of the molecular machines he describes through synthesis or AFM techniques...we don't have the technology to characterize such beasts. Ask an enzymoligst how many molecules of enzyme he needs and the things he neeeds to know before he can say what an enzyme is doing (or what it looks like). Enzymes are in many ways much simpler than the kinds of things Drexler proposes. In other words even if you could build a nano-bot; I don't know how you could know it was actually there or convince other scientists given the trouble we have with the molecules that nature has given us.

    What is frusturating out the whole molecular computing field is that when you actually try to sit down and do it, it seems impossible to try to figure out a way to do computation on a molecular level....yet natural things like remarkably organized biological cell and the human brain show us that there is a way, but is it the only one?

  • It was not put there to save you from embarassment.

    ---
    Despite rumors to the contrary, I am not a turnip.
  • Another interesting possibility for this is to make self-reassembling chips (ala Transmeta "code-morphing"). If the chips could be made malleable enough internally, it sure would be interesting to see chips evolve with time. Wouldn't that throw a wrench in compiler technology?
  • PETA can suck my meat&cheese fed, animal tested shampoo using, D**K! Seriously, PETA is one of the few activist groups that annoy me. I actually do try to keep my diet towards vegan ideals, but only because I know all the meat and dairy are going to kill me, not because some cow died or suffered to feed me.
  • Thanks, nice description of the situation. I checked with a relative who's more knowledgable of such things, and it seems Los Alamos was working with an amino acid, probably proline, given it's unique structure. (It contains a 90 degree angle) Given this, we could grow quantum computers with DNA as well.
  • It's the old Niven universe you are thinking about. They ground-up corpsecicles and extracted the RNA in order to facilitate the transplant the neural path memories of the dead into the bodies of condemned criminals: Ten Million Years from Earth. (Bwuah-ha-ha!)
  • That's all we don't need. Smart, designer bacteria. This stuff recombines in a water medium? My brain is mostly water! Besides, how do you connect a keyboard and a monitor to a petrie dish full of algar?
  • Umm trying to link Transmeta 'code-morphing' to self assembly is quite a stretch.
  • Actually, let me add a caveat emptor. I think cooling might be an important issue after all, at least with bacteria. Hotter temperatures cause bacteria to multiply (one of the reasons why you're not supposed to take very hot showers, you're defeating the purpose of the hygiene).

    Cooling may be needed to decrease the bacteria supply, not cool the DNA in particular. More bacteria would destroy your "chip".

  • It is tempting to believe that each base codes for a quatenary 'bit'; and that all the 'information' that the organism needs is stored in an long n bit string. But remember that sequences fold into a wide variety of structures which affect how they are read/what they mean, there are also regulatory systems that prevent/promote certain reigons of DNA being read, DNA in some organims is methylated to prevent digestion by nucleases etc. In short, DNA is a physical (complicated) thing, and the 'bit' analogy hides this...things just aren't that simple.

  • Useful? (Score:1)

    by leko ( 69933 )
    In my lab (MIT AI) there is a division working on computing with Ecoli. I had it explained to me, something about writing programs with climatids (sp?) and then the Ecoli will suck them up, and process the DNA in the climatid and execute a program. They have been able to do this, the problem is each ecoli takes about 30minutes to change state.... But neat research nonetheless.
  • The humorous side to all this, or so it seems to me from the report [cnn.com] on cnn.com [cnn.com] is that the genetic raw material they were using comes from sperm... not just any sperm, but salmon sperm in particular. The number of gags one can spin off from this combination in relation to computing should be worth a chuckle. Imagine what all the dotporn sites can do with this!
  • You don't know the half of it ....
  • I don't think you need to worry about being infected by a DNA computer virus. Virii generally aren't contagious across species, let alone across a loose collection of self-organizing molecules and us.
  • What ever happened to quantam computing?

    That seemed like a good idea, using the spin of atoms as bit counters.

    One thing that scares me is,
    Will this become a state that you can either be cloned, or made into a computer...

    and what kind of prosessor would you get if you crossed salmon DNA with the DNA of say....
    a cat?????
    I demand answers to these questions damnit!
  • how does this compare with computers that we use today? Is it possible to apply this technology to quantum computing?
  • DNA does not get biological diseases, each one those A,C,G,T molecules are only a few atoms, DNA is not "alive".
  • If they are, does it mean that you'll be able to upgrade to a dual (quad etc...) processor system just by providing more genetic material???

    And would say human blood be a suitible source of genetic material??? because if it were I could forsee all sorts of paranoia about super intelligent genetic computer-vampires, out to drink blood in order to 'grow' or maintain all those processors...

    But I rant...

  • From A While Back (Score:5)

    by Metrol ( 147060 ) on Wednesday August 09, 2000 @10:20PM (#866164) Homepage
    I knew I had read about a very similar set of experiments going on with DNA in Wired. I didn't realize how long ago it was. Anyhow, I did me a search over there on the mag and found the article in their archives called Gene Genie -Aug1995 [wired.com]. This is a rather old article, and I honestly have no idea how far this guy got with his research.

    To quickly summarize, this Adleman fella actually got DNA to do some simple calculations. What the biggest stumbling block at that time (and most likely still) was getting an interface between the user and the DNA setup. Sounds like that's what these folks in England are up to now.

    I feel I should clarify one point that seems to be getting mixed up here on this thread. The promise of DNA based computers isn't specifically to replace CPU's that we know today. In fact, DNA is far slower at running the repititive kinds of tasks that silicon deals with. The exciting stuff is in it's ability to do massive parallel processing on a small scale.

    For example, if you had a race between silicon and DNA to count to 1e24 the silicon would most likely be a clear winner. On the other hand, DNA based processors usher in the ability to solve problems that silicon based machines simply can't do, like calculate a perfect game of chess.

    Most likely, what we'll eventually see out of all this is a new hybrid computer utilizing both silicon and DNA based on their individual strengths. The prospects for this are both very cool, and very scary. We're talking about a machine that literally removes every advantage the human brain presently enjoys over silicon CPU's in the way of problem solving. Imagine HAL, only one hell of a lot smarter.
  • Not strictly the same thing I know... but there's a fairly interesting article on molecular electronics that was in July's Wired [wired.com] magazine... the article is archived here [wired.com]
    ,Tez
  • What happens when the radiation from the computer causes the DNA to degenerate? "computer cancer" treatment will be a billion dollar industry :P Entrope is a fool
  • ...a year ago, and it was being done at Los Alamos, and I think it was also a quantum computer, as well. Sadly, I remember precious few details. Does anyone know what I'm talking about, or have I been paying too much attention to the little voices?

  • Gamma Rays, PCR and Viruses (Score:3)

    by oldzoot ( 60984 ) <morton.james@comcas t . n et> on Wednesday August 09, 2000 @07:04PM (#866171)
    DNA based computers might be much more sensitive to the effects of radiation, or other mutagenic factors. I can just see the label on the computer, " Caution, the hacker general has determined that smoking causes crashes ".

    One interesting tool used in DNA research is called PCR, which is a way of multiplying the amount of DNA in a sample. 24 cycles of PCR amplification would yield a 2 ^ 24 increase in the quantity of a DNA based circuit, and takes less than a day to do. For once, memory could grow faster than data!

    I would be concerned about the possibility of your computer infecting you with a biologically active virus....

  • I'm amused.

    Looking at the hullabaloo surrounding easy-to-copy software, I can just imagine what it will be like when you have easy-to-copy hardware. Will they make test tubes illegal?

  • Cool != useful. I would be more interested in what problem domains they wou;d have superior characteristics than deterministic silicon stuff. I believe the original claims of it being used to solve combinatorical problems (e.g. travelling salesman) were retracted when they calculated the volume of DNA required to encode all the possibilities. If smaller but slower than RAM, then they might have a role as massive solid state memory devices. If they can duplicate the incredible self-repair mechanisms of cells, then they might be useful in hostile environments.

    However, it would still be useful if someone could point out papers describing their theoretical computing properties. All of classical computing (ie Turing) can be derived from binary logic and NAND gates, and a similar theoretical basis exists for quatum computing (but they're having problems with the engineering aspects). Has anyone developed the equivalent for biocomputing? I know a lot of work has gone into string, tree and sequence algorithms (a la computational molecular biology) but can they be adapted for other uses?

    In some ways the fun part is the reverse-engineering of the genome. Imagine that you're given the compressed core dump of a Linux kernel, and are asked to recreate the instruction set, systems architecture and application source code from first principles. If those gene jocks ever succeed, maybe we'll be hacking/designing complete biostructures in a few decades.

    LL
  • It's a pity there's a lack of details about, say, Powerage.
    Because, if it's only molecular, the signal it will generate will need to be amplified to be processed by another peripheral, should it be a monitor.
    If an external signal as to be absorbed, there is also a risk that it has to be lowered not to "break" the moleculs (Overflow ?).
    So, yes, it *is* cool, but we will need a complete range of devices to connect it to before it is usable...
    At this moement, I can only imagine a single multiusages interface for these chips : living organisms.
    And then, it will have to reach the "mass-production" level. Maybe in fields, as "transgenic corn" ?
    OR it'll maybe look like "human powered" like in "The Matrix" ?
    --

  • Re:What would a DNA computer look like? (Score:3)

    by Metrol ( 147060 ) on Wednesday August 09, 2000 @10:43PM (#866186) Homepage
    But I've never heard anyone describe how, even in the most general terms, a science of such a thing would look. What's the molecular/genetic equivalent of binary math?

    A couple of very fair questions. To answer the first I would refer you to my earlier post linking to the article in Wired about this. For a more in depth look at this there are 4 papers [usc.edu] USC has published on this subject. Fair warning, quite a bit of this goes beyond "even in the most general terms".

    As to your question concerning the the comparison to binary math, it's oddly very similar. DNA uses what amounts to a 4-bit word in it's chemical make up. I could go into more depth here, but that would only serve to show my igorance in this. Follow them links for decent descriptions.
  • And, finally, a computer virus will be a real virus.

    --

  • troll (Score:2)

    by n3m6 ( 101260 )
    imagine a beowulf cluster of these ?

    err.. does that make sense.. i thought it would fit with anything..

  • Re:I thought I saw something about this... (Score:4)

    by donny ( 165416 ) on Wednesday August 09, 2000 @11:13PM (#866192)
    To clarify a few things:

    There is a big difference between quantum computing and DNA computing. In fact, there is a big difference between what people usually mean by DNA computing, and the results described here in this article. To summarize (and I'm condensing things a bit for brevity):

    Quantum computers use quantum states instead of discrete states to perform computations. Quantum bits or "qubits" are quantum superpositions of the "pure" states corresponding to 0 and 1. (e.g. if we consider the 0 and 1 states to be two different energy levels of a certain electron in an atom, if we don't observe the electron, we can place the electron into a superposition of states corresponding to the two energy levels). The power of quantum computing (in theory, at least) comes from using these qubits instead of normal bits because by acting on a superposition of quantum states, we perform the action on each quantum state in the superposition individually.

    Quantum computers actually require a completely different model of computation than the one that current computers are based on, and are potentially (if all this theory pans out) counterexamples to the Church-Turing thesis (that all computing devices are polynomially equivalent to a Turing machine).

    DNA computing is more about mass parallelization than a new model of computing. It is based on the idea that by encoding solutions of combinatorial problems (read: NP-Complete) in DNA, and using modern DNA manipulation techniques (which include searching for particular sequences), we can find a solution with particular properties (read: optimal). For example, to solve the Travelling-Salesman Problem, we can generate (randomly) trillions of solutions and then pick out the optimal one. The advantage is that generating these is quick, and any operation you perform is performed on each strand at the same time. This massive parallelism makes it possible to solve search problems (TSP, Satisfiability, etc) that were not previously feasible, but DNA computing still falls under the Church-Turing thesis and so all the same complexity-theory results apply. DNA computing just reduces the constant involved by a factor of 100000000000000 or so.

    The article mentioned here seems to point more towards a "computer built with DNA", where DNA is being used to build components that will mimic the action of a circuit-based computer. It seems that this would simply bring several orders of magnitude of miniaturization to current computers, rather than anything fancy-schmancy in the theoretical computer science realm.

    Donny

    P.S. If you saw something on work at Los Alamos, it's probably on quantum computers.

  • ...when the dna-based meat-powered compu-robots start asking to take control of the missle command computers...

    Woohoo! As opposed to the dna-based, meat-powered computers [yahoo.com] currently controlling the missile command computers?

  • Hmmm... (Score:2)

    by Anonymous Coward
    So I read a few days ago that they have computers or robots powered on meat. Then I read that they're getting DNA implanted in them.... Note to future generations...when the dna-based meat-powered compu-robots start asking to take control of the missle command computers, please don't let them.
  • Bagh, back in my day, we didn't need fancy schmancy quantum and DNA computing (they are different things, young ca1v1n).

    Test tubes should be reserved for babies and scientific experiments. Nowadays all you kids want to shrink this, and integrate that, but not me.

    I'll stick with my heavy and big VAX system and line-printer. Then, the next flu that comes around will only wipe me out, not my computer, too.

  • Cooling? (Score:4)

    by OctaneZ ( 73357 ) <ben-slashdot2 AT uma DOT litech DOT org> on Wednesday August 09, 2000 @07:16PM (#866200) Journal
    We all consider cooling to be of vital importance in our silicon based machines, don't we? What kind of new cooling device are they going to create/use that will keep the DNA from degrading or just plain denaturing? Not that this isn't an interesting experiment, but the actual implementation seems rather difficult and/or unstable.

  • A few other issues. (Score:3)

    by Mercury ( 13121 ) on Wednesday August 09, 2000 @07:16PM (#866201)
    Unfortunately there seem to be a few other issues which could stand in the way of computers based on DNA.

    I'm no expert, but it seems like there could be serious issues connecting the 'wires' to conventional wires.

    In addition to this there may also be issues with the voltage these can handle, compared to the voltage required to operate the conventional circuit..

    Then we have the issue of laying them out on some form of small chip, a test tube is obviously not the optimal form to have on motherboards...

    The last issue I see is that of lifespan, how long are these DNA based circuit expected to last? And what sort of maintance might be required?

    Again, I'm no expert, however..

  • Effects of Scale Only (Score:4)

    by korpiq ( 8532 ) <-.@korpiq.ik i . fi> on Wednesday August 09, 2000 @11:39PM (#866204) Homepage

    1. The article does not talk about computing by DNA, it's about using DNA to build smaller conventional electronical circuits. So the logic would not change.

    2. As devices get smaller, required amount of electricity drops. Future pc's/appliances should be able to run on bare light/movement energy. "Cool."

    3. Imagine tools for DNA design. Anyone could design their own special component/appliance and start a farm. Back to the nature!-)

  • 1) This will not let Bill Gates pull your Natalie Portman fantasies from your brain while you sleep.
    2) I will not imagine a beowulf cluster of these and anyone who does will be shot.
    3a) This will not let you hack your brain.
    3b) Hacking your brain is dangerous, and should only be attempted by very skilled mad scientists. It has also been declared illeagal to help others to hack their brains under the ADWA (Assault with a Deadly Weapon Act)! Put a protest against this injustice in your /. signature! Hurry or your copy of 1984 will come to life and kill you!
    4) This will not make your computer become sentient.
    5) This will not let you install Linux on your body, unless you install 64 cc's of halucenogens first.
    6) Do not mention "computer virus" in your post under threat of slow torture.

    For more information buy my book: "Get Rich Quick by Giving Your Money to Me"
  • Can I change my mind?

    There's a thought, eh? Program some bit of DNA code to do this and you could have an anti-Bigot virus. The ultimate convergence of genetics and memetics. Political warfare would become biological warfare. Would new ideas become outlawed under the Geneva Convention? Psychiatric medicine would take an entirely new turn. Wasn't there some sci-fi story that had "learning pills" in it? You think popular entertainment today is bad? Think of the popular personalities. (Oh, wait... we already have that. They're called "religions")

  • A little misunderstanding... (Score:4)

    by dbarclay10 ( 70443 ) on Thursday August 10, 2000 @12:21AM (#866210)
    I think there's a basic misunderstanding going on here. It might be too late to get it moderated up, but here goes:

    Most people here seem to have the idea in their head that these DNA-based chips will degrade and/or mutate. Don't think of these as life forms, but think of them as life-inspired. Your silicone chips are nothing more than carefully ordered atoms, which are called "chemicals"( ;] ). These DNA-based computer's don't have all the cruft we usually associate with DNA. For example, these things won't reside in cells. The individual gates, transistors, etc., are just carefully ordered atoms. There's no basic difference, other than the fact that we can control, very carefully, how these atoms are ordered. We can't do that with silicon. At least, not to this degree. We're using nature's own techniques to control how these DNA-based(not actually the life-deciding chemicals, just based on them) chemicals to an incredible degree. That's how come they'll be so small.

    As for the degradation worries, there's really relatively little to worry about. I'm not a biologist, but these people won't be building these things using unstable molecule chains. They can't, really. They'll have to make them fairly stable. As for the "mutation", it's no different than in silicon. Sure, a stray neutrino isn't going to affect a relatively MASSIVE silicon-based gate, but if you made that gate REALLY small, then yeah, something really small could permanently damage it. It isn't that DNA-based computers are more vulnerable because they're DNA-based. They're more vulnerable because the individual parts are smaller. If you shrunk your processor to the point where the transistors were as small(and had as few atoms) as a DNA-based transistor, then you'd have the same problem. Very little upsets would completely destroy such a silicon transistor.

    Just to recap:

    These computer's won't be using the same stuff in our cells. They'll just be using strings of atoms, carefully ordered(much like silicon is carefully ordered, only in this case we can be very precise).

    The worries expressed here often(that of mutation and degredation) are really besides the point. They won't build these things with unstable molecules that "melt" at room temperature(well, maybe in the beginning, but that'll have to change), so a chip decaying is not really likely. And the problem with mutation(where something happens to an individual component) is a risk involved in any device which uses extremely small parts.

    Dave

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