DNA computers
Besides the self-assembling structures we discussed recently, DNA’s base-pairing lets it function in a weird kind of computation. Most versions of such computation involve DNA strands containing short sequences that can base-pair to complementary sequences on other DNA strands. “Computation” occurs when the DNA strands are put together in solution, and rapidly “find” all their best-fit matches. In 2002, Leonart Adelman and colleagues devised a “DNA computer” that could solve a logic problem with 20 variables:
Part B represents the “answer” to the problem, which DNA molecules can “find” faster than a silicon computer. DNA is particularly effective at problems allowing highly parallel computation.
In general, a DNA computation system requires three stages:
(1) Store the input data into DNA sequences, by constructing the DNA molecules.
(2) Mix the DNA molecules together, and let diffusion accomplish its task. Much is made of how this stage takes zero energy. Overall, though, one has to count the energy involved in DNA synthesis for step 1.
(3) Read the answer. Various ways to read the answer use, for instance, restriction enzymes that cleave specific double-stranded sequences, or series of electrophoretic gels that capture DNA strands with unpaired base sequences.
More recently, DNA computers are now making logic gates out of DNA, using molecules that combine information storage with enzyme capabilities, so-called DNAzymes. Such a computer was able to determine square roots of a number up to 15.
But how useful is such a “machine”?
One use is to store computing power in a kind of “instant package,” to answer a question in a remote location where electricity is unavailable. An example is a chain of “biochemical transistors” to test blood for the presence of the malaria parasite. Another example would be in devising nanobots to enter the human bloodstream for nanosurgery. The advantage here would be DNA’s high information density, compared to any known or projected silicon chip.
Will DNA computers ever be faster and better than silicon? If you have any thoughts on this, let us know.
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Ultraphyte 
Will DNA computers ever be faster and better than silicon? If you have any thoughts on this, let us know.
I doubt it, and graphene is likely to be the successor to Si.
But I don’t think it is the question to pose. biocomputing will occupy a niche, the question is how large that niche might become and what functionality or processes will biocomputers excel at.
In a biologically oriented world, with biocomputers as part of living systems with appliance like functionality, they could be a very big part of “computing”, although they will not be used for the sorts of applications we think of today as being what computers do.
SF writers have barely touched on this aspect and I suspect it will be a potential vein to mine in the future as biocomputing gains traction and publicity.
The medical use of biocomputers is likely to grow, and may someday eclipse the silicon boxes we use today. This was what I proposed in Brain Plague back in 2000.
My take is that the current DNA strand-based computing is useful for the parallel processing you noted above, just as you can probably use a physarum polycephalum to solve a complex traveling salesman problem as fast as you can compute it. In both cases, the calculation needed is when it’s cheaper and/or faster to use a biological system and when it’s cheaper to run it in silico, assuming both are available.
Actually, this makes me wonder whether phylogenetic trees are susceptible to DNA computing methods. That could get really interesting…
So far as biocomputers go, the one I’d like to see (tongue in cheek) is from The Ghosts of Deep Time: It’s a machine whose “working surface was a magazine-sized touch screen, surrounded by a dark leathery frame reminiscent of the tough rind of a shelf fungus. The layer under the glass was emerald green, the color of a polluted stock pond.” It worked based on “algae doped with quantoplasts in a biofilm matrix, photonic data transduction, oligosaccharide crystal memory, polymycelial nutrient translocation.”
When I wrote that, I was having a little fun with the idea that electron transport chains exhibit quantum interactions, and that it might be possible to modify chloroplasts into some sort of photonic-quantum computers. Data would be stored in medium length sugar molecules and communicated as photons, and the power and nutrient system worked from fungi, sort of like a lichen in reverse.
Note that, on such a computer, if you don’t leave it in the sun to recharge, you will have to feed it. Spam should work.
If you want a more classic example, Brin and Benford had a biocomputer playing a supporting role in Heart of the Comet.
Well, a computer made of both algae and fungi sounds great to me! A lichen in reverse–that sounds intriguing.
Speaking of computers and DNA, I want one of these gizmos if they work:
http://www.newscientist.com/article/dn21495-usb-stick-can-sequence-dna-in-seconds.html