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Getting Closer To DNA Computing
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.
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!
From books people learn to remember, from mistakes to understand.
The head of the pin is the end with the angels dancing on it......
You're unto something about that "denaturing" process, however. How would we keep DNA-based electronics from being torn apart by bacteria?
- I don't care if they globalize against free speech. All my best free thoughts are done in my head.
New form of artificial intelligence. DNA evolves with useage. Computer refuses to run Windows and won't take input from user attached to keyboard.
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!
air and light and time and space
given that we have bio-pcs.. will they sweat to disspiate heat??? and could you overclock them with caffeine?
... it could actually be Beowulf!
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Go ahead, blame me... I voted for Nader!
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...
"The future's good and the present is nothing to sneeze at." - Roblimo's last
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.
"The future's good and the present is nothing to sneeze at." - Roblimo's last
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.
====
Crudely Drawn Games
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?
The humorous side to all this, or so it seems to me from the report on 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!
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. 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.
The line must be drawn here. This far. No further.
Not strictly the same thing I know... but there's a fairly interesting article on molecular electronics that was in July's Wired magazine... the article is archived here
,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?
WARNING: there is a trojan on your
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....
enough is too much
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?
-Eldurbarn
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" ?
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Trolling using another account since 2005.
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 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.
The line must be drawn here. This far. No further.
imagine a beowulf cluster of these ?
err.. does that make sense.. i thought it would fit with anything..
Woohoo! As opposed to the dna-based, meat-powered computers currently controlling the missile command computers?
Any sufficiently well-organized community is indistinguishable from Government.
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.
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.
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..
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!-)
I think, therefore thoughts exist. Ego is just an impression.
1) This will not let Bill Gates pull your Natalie Portman fantasies from your brain while you sleep. /. signature! Hurry or your copy of 1984 will come to life and kill you!
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
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"
I think there's a basic misunderstanding going on here. It might be too late to get it moderated up, but here goes:
;] ). 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.
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"(
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
Barclay family motto:
Aut agere aut mori.
(Either action or death.)