The next computer: your genes

May 16, 2011 by Miranda Marquit feature
DNA

(PhysOrg.com) -- "Human beings are more or less like a computer," Jian-Jun Shu tells PhysOrg.com. "We do computing work, and our DNA can be used in computing operations." Shu is a professor at the School of Mechanical and Aerospace Engineering at the Nanyang Technical University in Singapore. "For some problems, DNA-based computing could replace silicon-based computing, offering many advantages."

Shu has been working with his students, Qi-Wen Wang and Kian-Yan Yong, at Nanyang Technical University to propose a way that the manipulation of could be used to solve certain types of problems. Their work has been published in : “DNA-Based Computing of Strategic Assignment Problems.”

The computations that the human body performs naturally are much faster than even the fastest silicon-based computer. On top of that, Shu points out, silicon is not very environmentally friendly. “There are also heat problems. DNA-based computing could be faster, friendlier for the environment, and eliminate some of the other problems that come with .”

DNA-based computing could prove especially useful for strategic assignment problems. “Even with developments in silicon-based computing, there are some problems that take even the fastest computers months to solve,” Shu says. With DNA-based computing, massive parallel problems, combinatorial problems and AI solving problems could all be addressed with the possibility of greater efficiency.

“Silicon-based computing relies on a binary system,” Shu explains. “With DNA-based computing, you can do more than have ones and zeroes. DNA is made up of A, G, C, T, which gives it more range. DNA-based computing has the potential to deal with fuzzy data, going beyond digital data.”

Shu and his students manipulated strands of DNA at the strand level and at the test tube level. They found that they could fuse strands together, as well as cut them, and perform other operations that would affect the ability of the DNA to compute. In this model, DNA molecules are used to store information that can be used for computational purposes.

“We can join strands together, creating an addition operation, or we can divide by making the DNA smaller by denaturization,” Shu says. “We expect that more complex operations can be done as well.”

However, Shu points out that DNA-based computing is in the most basic of stages right now. “So far, there are a lot of human manipulations that must be done. We’d like to refine it so that there is less human interference. In silicon-based computing, we let the CPU do everything. We need to get to the point where we just need to provide a command and let the DNA do everything.” Cost is also an issue. “DNA right now is very costly and hard to commercialize.”

Another challenge with DNA-based computing is the display. It’s very difficult to display the results from DNA-based computing, since electronics have to be used. “We need to find the missing link between electronic speed, which slow, and DNA speed, which is fast – more like optical speed.”

Despite the challenges, Shu is optimistic. “We have made some progress, and we expect to continue making more progress. is the future of computing.”

Explore further: New microscope collects dynamic images of the molecules that animate life

More information: Jian-Jun Shu, Qi-Wen Want, and Kian-Yan Tong, “DNA-Based Computing of Strategic Assignment Problems,” Physical Review Letters (2011). Available online: link.aps.org/doi/10.1103/PhysRevLett.106.188702

3.2 /5 (40 votes)

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StandingBear
1 / 5 (13) May 16, 2011
Watch out. We were possibly bioengineered about twelve thousand five hundred years ago somewhere in either Southwest China or somewhere in what is now below sea level in the Persian Gulf, or maybe India or somwhere east of the Black Sea. All those are suspected archaelogical sites of great age. Point is, one of the best ways to preserve a computer program is in DNA. Think about it! Would a CD last that long? Without errors except small ones that could be dealt with statistically? We have a lot of 'non-coding' DNA in us. If our creators left a letter for us when we 'grew up enough to be able to read it', it would be here. And the key 'rosetta stone' to decipher the alien language it is written in would be the oldest Old Testament Bible (or Torah) that we have or can find. This is not heresy. God did in fact create us.....through his helpers that he had created before us (refer: 'In my Father's house are many mansions' and many Old Testament references )
SmartK8
5 / 5 (5) May 16, 2011
StandingBear: You're full of it. The DNA is definitely not the best way to preserve anything. It's prone to change (mutation). Your children don't look like you. So obviously the DNA has changed for them via 'crossover'. And we're all unique, therefore the timespan is about one life time. If, on the other hand, are you writing new fantasy novel or playing make-believe, then I'm sorry and go ahead, but note those technical inaccuracies.
Physmet
5 / 5 (1) May 16, 2011
I find the concept of DNA computing fascinating. I remember an article a few years back where they setup a simple mathematical problem and got an "instant" answer. The main problem being that along with the correct answer was something like a half million wrong answers and they had to find the correct one themselves.

I imagine this is a long way from reality and may never happen. Still, it's an amazing concept.
Johannes414
1 / 5 (8) May 16, 2011
Every computer has a designer, and every piece of software requires a programmer. Yet scientists want us to believe that the most powerful computer in the universe was built by blind chance and its software written by random mutations over millions of years. Doesn't make sense.
Pyle
5 / 5 (10) May 16, 2011
the most powerful computer in the universe
Quite full of ourselves aren't we.
by blind chance
Nope. Natural selection.
random mutations over millions of years
Yup. Random mutations that were selected upon via the non-random process of natural selection.
Doesn't make sense.
Actually evolution makes perfect sense to many. And even more importantly the "megatons of fossils" and other evidence support it. As do our controlled experiments to support Darwinian evolution. (See the links provided to you on other threads.)

Spew your nonsense elsewhere.
Johannes414
1 / 5 (5) May 16, 2011
To say evolution is non-random because of natural selection is to say that you won at the roulette table because you positioned the chips so well. A pair of dice will limit the numbers one can throw, but the rolling itsself still produces random results.

The driving force of evolution is blind chance - random mutations. So the creative aspect of evolution is entirely random. Natural selection cannot alter that fact.

A selection of random changes based on function does not generate any new feature. Darwinian evolution demands that new life forms are formed. That newness is brought about by a string of random events - and thus the overall outcome is random.

Throwing dice a million times will always produce a random outcome, although the set of possible outcomes are functionally limited by the shape and numbers on the dice.
Silverhill
5 / 5 (5) May 16, 2011
The driving force of evolution is blind chance - random mutations. So the creative aspect of evolution is entirely random. Natural selection cannot alter that fact.
Natural selection *does* alter that fact. An environmental condition that favors a random change is likely to be persistent. A persistent condition is a bias in a system, and biases can act strongly against randomness. (Think about loaded dice.)

A selection of random changes based on function does not generate any new feature. ... That newness is brought about by a string of random events - and thus the overall outcome is random.
Wrong again. New information (whence, possibly, new features) is *any* information that did not previously exist. When a mutation happens (whether single-point, or duplication, or reversal, or transposal, or deletion), the resulting arrangement is *new*. Sometimes it's even beneficial.
Beard
5 / 5 (3) May 17, 2011
Trying to use rational arguments to convince an irrational person is a waste of your time, and using irrational arguments is a waste of everyone's time.

What a strange game...the only way to win is not to play.
dgreyz
not rated yet May 17, 2011
Interesting article,
About the creationist comments: Beard is right, however I think we have to fight those enemies of reason, since they can only spread ignorance and misunderstanding and more terrible things.
Pyle
not rated yet May 17, 2011
At first I thought, just ignore them. Then I saw people agreeing with some of them in later comments. Best to show them to be irrational early than to let the unsuspecting reader get pulled in by them.

Regarding the article. Yeah. This is far enough into the future to be science fiction at this point, but we won't get there if we don't think about it.

One line really troubled me:
We need to find the missing link between electronic speed, which slow, and DNA speed, which is fast more like optical speed.
Not really sure what this really means. I guess chemical reactions could be faster than switching gates? Anybody want to add something here? Thanks.
trucksmart
not rated yet May 18, 2011
I'm sure if our DNA were programed to copy or better yet clone the program for reproduction purpose, It would. But it wasn't set up for that kind of programing. We were undoubtedly designed to take the characteristics from both mates and create an original human, unlike any other. I'm sure if we were to use DNA models to develop computer systems, we would also be able to design them to copy perfect duplicates of document files or whatever. I've been waiting for someone to develop a computer that uses more than a binary system of computing for decades. This might be able to not only duplicate or use actual usable DNA but also what has been wrongfully considered "junk DNA" into a not only Quantum computer but possibly a "Cosmic" computer.
What say you?
spectator
5 / 5 (1) May 19, 2011
The computations that the human body performs naturally are much faster than even the fastest silicon-based computer. On top of that, Shu points out, silicon is not very environmentally friendly. There are also heat problems. DNA-based computing could be faster, friendlier for the environment, and eliminate some of the other problems that come with silicon.


This is wrong and ridiculous.

First of all, life does not "Think" at the DNA level.

Life "Thinks" at the cellular, tissue, or organ system levels, as in neurons, spinal cord, and brain.

The DNA is a blueprint and command set for building cells and their components one molecule or one atom at a time via Ribosomes.

In actuality, DNA would be the secondary memory, and RNA would be the primary working memory.

Finally, human beings simply do not think faster than computers. WE have parallel thinking because of neural networking in our brain, but our signal propagation is FAR slower than computers
spectator
5 / 5 (1) May 19, 2011
Our nerves adn other cell structures communicate with one another through molecular carrier signals, which are several orders of magnitude more massive than electrons, which is why the signal delay is so much greater for our nerves and brain, as compared to a computer.

think about it, your computer can download data in megabytes per second, even gigabytes per second for some devices, on a few parallel ports.

Moving the mass of a DNA molecule around to do a calculation actually requires millions of times more energy than the theoretical minimums in electronic, spintronic, or photonic calculation, which only needs to move the mass of an electron, or a spin charge, or a photon.
spectator
1 / 5 (1) May 19, 2011
If you "think" you think faster than a computer, then you have never played a modern Real Time Strategy game and watched the actions per minute.

The computer "Player" plays 10 to 15 times faster than ANY pro human could ever play, and up to 100 times faster tahn an average gamer, AND it has the disadvantage of also needing to run the OS, the video card drivers, the game engine itself, the human player's interface, etc.

The only reason a human player can beat a computer controlled player is the human is "more intelligent," and more experienced, since machine learning hasn't advanced enough in RTS yet.

However, the computer is "thinking" hundreds of times faster than any human could ever think.

If the game developers could develope a virtual neural net simulator with a modest sized permanent memory, instead of a few branching A.I. scripts, the computer would eventually learn to easily destroy any human player.
Johannes414
1 / 5 (2) May 19, 2011
Exactly where does rationality and logic reasoning come from in a naturalistic world? Knowledge and reason are not attributes of matter. So where do the rules of logic and reasoning come from in an atheistic universe where everything is material?
spectator
2.5 / 5 (2) May 19, 2011
Exactly where does rationality and logic reasoning come from in a naturalistic world? Knowledge and reason are not attributes of matter. So where do the rules of logic and reasoning come from in an atheistic universe where everything is material?


Don't ask me, I'm not an atheist.

Without God, nothing is anything more than random quantum noise, and chain reactions.

To an atheist, logic and reasoning are nothing more than illusionary surface defects in a world governed only by mechanics, which Hawking discussed in his books in the past.

Free moral agency, free will, "decision making," and even morality itself, are meaningless in an atheistic world view, since everything is merely taken to be a chain reaction governed by and caused by some underlying set of deterministic and/or quantum noise rules.

Logic and intelligence would also be illusionary surface defects in a purely materialistic world view.
spectator
2.5 / 5 (2) May 19, 2011
They would attempt to describ logic and rationality in evolutionary terms, by claiming something along the lines of:

1) "Intelligent systems are more likely to live to reproduce, since they can understand and anticipate their environment, therefore logic is evolutionarily superior to non-logic," etc.

2) They would claim that the logical system came about through random chance. (See Hawking, Page 131 in "Black Holes and Baby Universes.)

But the logic is faulty, because point 2 would undermine point 1.

In point 1, they acknowledge an intelligent lifeform which recognizes, responds, and anticipates stimuli is probably more successful than a non-intelligent one, but in point 2, they believe a non-intelligent accidental system can somehow give rise to the best intelligence, which is a contradiction in terms, since a non-intelligent system couldn't possibly recognize degrees of intelligences to make a selection.
spectator
2.5 / 5 (2) May 19, 2011
Ultimately, atheists believe everything is a meaningless accident.

There actually is no right or wrong, and even though logic exists within the universe, and they use logic to try to understand everything, yet logic itself is a meaningless accident in the greater scheme of things, in an atheistic world view.

There is no right or wrong, no good or evil, because whether things are random, or nonsense, or determined, people would have no control either way. Life is nothing more than the sum of some force interactions, and everything you say, think, or do is nothing more than the sum of chain reactions and cascade effects caused by either internal or external stimuli.

There cannot be right, wrong, or free will if all life is a sequence of pre-determined accidental chain reactions.

This is a key reason why the godless can easily justify to themselves abortion, genocides, murder, and other immoral behavior.
spectator
2 / 5 (2) May 19, 2011
On page 133, Hawking essentially denies free will.

Then he provides an argument in a moral delemma in which he draws a fallacious moral conclusion.

On page 134, he says people should adopt the attitude as though they have free will, since, as he claims, the equations to predict human behavior cannot be solved, but on page 133 he clearly does not actually believe that. He simply says this because he reasons that if everyone believes in fataism then they'll do stupid things, but if fatalism is real, then they will do what they will do regardless...

At the end of the chapter, he says, "Is everything determined? The answer is YES, but it might as well not be, because we can never know WHAT is determined." (emphasis mine.)

Therefore, the atheist does not "really" believe in free will, nor morality, nor responsibility for one's actions, since everything is determined. A murderer is a murderer because the accidental sequence of the universe made him that way. He can't help it, etc
spectator
3 / 5 (2) May 19, 2011
Wheras, in the Bible, God gives man free will, and encourages him to make the "right" moral choice in moral situations, though they are "free" to make the evil choice if they so choose.

God does not make anyone evil, and doesn't want anyone to be evil, and further doesn't even "want" to punish the evil people (though he has to at some point.) God wants evil people to repent and do good, he doesn't want them to be evil and doesn't want them to suffer or die.

People's moral condition, according to the Bible, is influenced by one another, but not controlled or "pre-determined" by conditional stimuli, etc. Else God giving man a "choice" and stating that he doesn't want the wiked to die and takes no pleasure in it, etc, would be a contradiction if everything was precisely determined.

The mechanism or ontology of free moral agency is never explained, except to say that man is created in the image and likeness of God.
Pyle
not rated yet May 19, 2011
Erratic ratings reflect the quality of your posts. Overall I say it is one of the best set of posts on this topic. Thank you. If I have time I will respond to those points I most strongly disagree with. In general I believe you have a strong bias against atheists that neglects their possible belief in the spiritual (not me) or their feelings towards the wonder of nature and the universe. That the universe may or may not be deterministic bothers me not at all and doesn't lead me to conclude as you suggest. I am a devout atheist and believe in good and evil, right and wrong, "free will", and morality.

Sorry for the tease. Gotta run. Response pending nobody else speaking my mind.
Siluro
1 / 5 (1) May 21, 2011
Either comment on the article itself or shut up.
If you want to understand how reason and meaning arise from the material, and how order and direction arise from randomness, refer to chaos theory and complexity science.
If you don't believe what you read there and you are stupid enough to think believing is important, go chat to your grandfather about it.
If he's dead ask God to help you find him.
Do you understand the algorithm above?
_oneci_e_ade
not rated yet May 25, 2011
To say evolution is non-random because of natural selection is to say that you won at the roulette table because you positioned the chips so well.


--Johannes414

WRONG, a more accurate analogy would be to say that you won roulette because YOU HAD A CHIP ON EVERY SPACE, thus ensuring a win. Just because chance produces a winning combination, does not mean that it wasn't one of countless losing combinations; chaos covers every space on the board with a chip, so when natural selection comes to divy out prizes, there will always be a winning play simply due to suffusion of input.
Pyle
not rated yet May 25, 2011
chaos covers every space on the board with a chip, so when natural selection comes to divy out prizes, there will always be a winning play simply due to suffusion of input.
Hmmm. A breeding lottery. Breeding for luck. Teela Brown!!!!