DNA Outside the Gene
I see this sort of like Columbus taking off from Spain. He was looking for India, and he smacked into America - the New World. That's what I think we are really doing. We are taking off, trying to build a practical molecular computer. But I think we are really taking off into the unknown world of biology and mathematics and computer science. And if we don't get to the molecular computer - if we don't get to India - that's OK. I'm optimistic that we are going to hit something interesting and important. The journey is the point.
Leonard M Adleman
Written by: Avinash
or years computer scientists have pondered over the daunting task of solving satisfiability problems. A typical statisifiability problem is: A will attend a party only if C does and B doesn't, while C insists that E and F must be present. E, refuses to be in the same room with A unless B is there to distract her attention. Try to accommodate 20 such requests and there are more than a million (2 to the 20th power) possible combinations to consider. For 30 there are a billion, for 40 there are a trillion. Once you go beyond 50, the problem quickly becomes intractable - unsolvable in any reasonable time. Now, in a handful of labs across the US, researchers are building what they hope will be some of tomorrow's computers that would eventually resolve complex mathematical requests. They are making headway, calculating not with silicon chips but with strands of DNA. Working with a set of beakers, test tubes and petri dishes full of bacteria, these scientists are trying to reate cells that can compute, endowed with "intelligent" genes that can add numbers, store the results in some kind of memory bank, keep time and perhaps one day even execute simple programs.
Thomas A Bass writing in Wired explains the basic premise of DNA computing; "Rather than make machines assume lifelike proportions, researchers working on DNA based computing are preoccupied with what if life itself already susceptible to genetic engineering could be used to solve problems. Can DNA be shifted from producing life to thinking about it." It's the preoccupation with this question that led to the first breakthrough, the first landmark exhibition of computing on the molecular level. In 1994, a computer scientist at the University of Southern California, Leonard M. Adleman took a yawning seven days to solve a routine computational problem, which an average desktop machine could solve in the blink of an eye. Why then was this work remarkable?
The problem Adleman solved is popularly known as the traveling salesman problem (TSP). In Adleman's version, a hypothetical salesman tries to find a route through a set of cities so that he visits each city only once. Alderman ordered 21 test tubes of single stranded DNA one for each city and the 14 routes connecting them. Alderman took a pinch from each and threw it into a test tube holding a watery solution. In the DNA computing approach to this problem, a unique strand of DNA that stretched 20 nucleotides long represented each city. Each possible route between any two cities was represented by another 20-nucleotide-long strand. This strand connecting cities was also related to the nucleotide sequence of each city connected by that route. For example, the route between City 1 and City 2 consisted of two sets of 10 nucleotides; the first 10 nucleotides on the strand's route complemented the last 10 nucleotides of City 1, while the second 10 nucleotides on the strand's route complemented the first 10 nucleotides of City 2. In this way, if strands for cities 1 and 2 came in proximity to the route 1-to-2 strand, the three strands would bind.
So how is the DNA computing different from conventional computing? A traditional computer represents information on silicon chips as a series of electrical impulses (zeroes and ones) and maneuvers the information by performing mathematical computations with those zeroes and ones. In sharp contrast DNA computer represents information sequence of its four basic nucleotides - adenine, cytosine, guanine, and thyme. That information is manipulated by subjecting it to precisely designed chemical reactions that may mark the strand, lengthen it, or even destroy it. Think of DNA as the software, and enzymes as the hardware. Put them together in a test tube. The way in which these molecules undergo chemical reactions with each other allows simple operations to be performed as a byproduct of the reactions. The scientists tell the devices what to do by controlling the composition of the DNA software molecules. It's a completely different approach to pushing electrons around a dry circuit in a conventional computer.
To the naked eye, the DNA computer looks like clear water solution in a test tube. There is no mechanical device. Alderman visually descriptive account of the computer said, "It is a bunch of test tubes, each about the size of a C battery, holding DNA. This rack of test tubes - maybe 30 by 30 in size - isn't very big. The whole thing is about one meter square. Sitting above the tubes are a bunch of robots. A little robotic arm picks up a tube, reaches over and picks up another tube, picks up a third tube, and brings the tubes into itself. Some sort of chemical process goes on which moves DNA from one tube to another. Then the robot returns the tubes to their spot on the rack, and it picks up new tubes for the next operation. It continues in that fashion, but there are maybe 50 robots all working at once. Next to the robots is a little traditional electronic computer, which keeps track of what's in the tubes and tells the robots what to do next. In the end, you get a tube that has your answer in it, coded in DNA."
As Alderman's preliminary experiment reveals the distinct advantage of the DNA approach is parallel processing. DNA based computers function in parallel, thus processing all possible answers simultaneously. In contrast conventional computers operate linearly, taking on one task at a time. Parallel computing allows DNA based computers to solve complex mathematical problems in hours, whereas it might take electrical computers years to complete. This makes the DNA computer suitable for solving "fuzzy logic" problems that have many possible solutions rather than the either/or logic of binary computers. In the future, researchers speculate hybrid machines, which would use traditional silicon for normal processing tasks but have DNA co-processors that can take over specific tasks they would be more suitable for.
Another key advantage of DNA based computing is that it will make computers smaller than ever before, while at the same time holding more data. This is a tremendous development when you see that conventional computer chip manufacturers are finding it a great deal harder to keep up with Moore's law. Sooner or later miniaturization in conventional computing is bound to hit a wall. In this scenario, it's truly astounding to think that a drop-sized DNA computer, using DNA logic gates, will be able to out power the world's most powerful supercomputer! That is because more than 10 trillion DNA molecules can fit into an area no larger than 1 cubic centimeter. With this small amount of DNA, a computer would be able to hold 10 terabytes of data, and perform 10 trillion calculations at a time. Israeli scientists in February for instance devised a computer that can perform 330 trillion operations per second, more than 100,000 times the speed of the fastest PC.
DNA is a virtually inexhaustible and inexpensive resource and you don't have to worry about the supply factor as long as there are living cells all around! Tom Knight, a researcher at the MIT Artificial Intelligence Laboratory and one of the leaders in the biocomputing movement in the MIT Tech Review is quoted to have said. "Once you've programmed a single cell, you can grow billions more for the cost of simple nutrient solutions and a lab technician's time. In the second place, biocomputers might ultimately be far more reliable than computers built from wires and silicon, for the same reason that our brains can survive the death of millions of cells and still function, whereas your Pentium-powered PC will seize up if you cut one wire. But the clincher is that every cell has a miniature chemical factory at its command: Once the organism was programmed, virtually any biological chemical could be synthesized at will."
DNA computing potential in terms of size and speed it may have applications in completely diverse areas. One area where it could make a significant contribution is genetics where a DNA computing system could read and decode natural DNA directly. Thus DNA computing will be a cost-effective way to decode the genetic material of humans and other living things. DNA computing will thereby eliminate the protracted task of translating DNA into a form that can be stored in an electronic computer. Most important researchers feel DNA computing devices could revolutionize the pharmaceutical and biomedical fields. Some scientists predict a future where our tiny DNA computers will patrol our bodies to monitor our well being and release the right drugs to repair damaged or unhealthy tissue. Autonomous bio-molecular computers may be able to work as 'doctors in a cell,' operating inside living cells and sensing anomalies in the host, Consulting their programmed medical knowledge, the computers could respond to anomalies by synthesizing and releasing drugs.
DNA based computing might also be of interest to forensic experts as it will facilitate DNA fingerprinting -- matching a sample of DNA, such as that in blood/hair found at a crime scene, with the person from whom it came. The military establishment is also following DNA computing closely, as it is ideal for repetitive and time-consuming tasks such as code breaking. Crafting sequences of DNA to represent specific patterns of information is the modus operandi adopted in code breaking. Thus DNA computers would be handy for intelligence agencies and military taking into account the ever-increasing sophistication of encryption techniques.
Regardless of these myriad advantages, certain technological challenges have to be overcome before DNA computing is widely used. One roadblock is the number of computational errors produced by unwanted chemical reactions with the DNA strands. Researchers are furiously working out techniques to reduce and eliminate these computing errors. Another drawback of his DNA computer is that it requires human assistance. Scientists today are working towards making DNA computing function independent of human involvement.
DNA computing is in its infancy; and is confined to the academy and research labs. Even though DNA computers in the near future are unlikely to feature common place applications such as word processing or accounting programs, molecular computers represent an untapped legacy of three billion years of evolution and there is great potential in further exploration.
(With Inputs from the Net)
(Avinash is a freelance writer, who has contributed to various publications.)
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