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Computer Made From DNA And Enzymes
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.
330 trillion calculations per second? Impressive, but can it run Doom 3?
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!
In Soviet Rush, today's Tom Sawyer gets high on you.
Imagine a beowulf cluster of those machines...wait a minute, I am one!
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?
Too busy staying alive... ~ R.A.
I hear Feed Only Memory is the future of storage.
I don't think I'd be responsible enough to remember to feed my computer.
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
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...
My life in the land of the rising sun.
Not just that, but they go from "have created" to "proof of concept" in the blink of an eye. Blech...
Stop by my site where I write about ERP systems & more
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* )
This sig intentionally left bla... dammit!
Who's got the whiteout?
To understand all the hype, here is an article about how DNA computing works. DNA Computing, interestingly, was first proposed by Prof. Len Adleman (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
I was first introduced to DNA computing by Leonard M. Adleman's article Molecular Computation of Solutions to Combinatorial Problems 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!
Imagine what a beowulf of these would look like!
Perhaps a little like a scandinavian warrior from the 6th century!?
----
Go canucks, habs, and sens!
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.
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..
"I can't give you a brain, so I'll give you a diploma" - The Great Oz (blatently stolen sig)
from the National Geographic aritcle:
It can't, for example, correct a misspelled word
Slashdot must be running these DNA computers!
"the fax machine is nothing but a waffle iron with a phone attached to it." - Grandpa Simpson
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. 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?
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:
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.
Today we're computing with Denatured Alcohol.
When will the madness end?
KFG
you obviously haven't seen me throw a ball...
-calyxa
Decay! Decay! Decay! -Helium
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 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".