DNA: THE FUTURE OF COMPUTING
DNA computing is a nascent technology that seeks to capitalize on the enormous informational capacity of DNA, biological molecules that can store huge amounts of information and are able to perform operations similar to a computer's through the deployment of enzymes, biological catalysts that act like software to execute desired operations. This paper gives an insight into evolution and the future of DNA computing. Scientists around the globe are now trying to marry computer technology and biology by using nature's own design to process information. Research in this area began with an experiment by Leonard Adleman, a computer scientist at USC who surprised the scientific community in 1994 by using the tools of molecular biology to solve a hard computational problem. In terms of speed and size, however, DNA computers surpass conventional computers. While scientists say silicon chips cannot be scaled down much further, the DNA molecule found in the nucleus of all cells can hold more information in a cubic centimeter than a trillion music CDs. A spoonful of DNA contains 15,000 trillion computers. While a desktop PC is designed to perform one calculation very fast, DNA strands produce billions of potential answers simultaneously. This makes them suitable for solving "fuzzy logic" problems that have many possible solutions rather than the either/or logic of binary computers. In the future, some speculate, there may be hybrid machines that use traditional silicon for normal processing tasks but have DNA co-processors that can take over specific tasks they would be more suitable for.
As the lines between real and manufactured continue to blur, and science approaches finer and finer resolutions down to the subatomic scale, emergent technologies are rapidly evolving to radically alter the way humans interact with Nature. Increasingly we are wresting the fundamental tools of creation from the hands of the gods and employing them for our ownpurposes. A prime example is the discovery that DNA computers can be used to solve extremely complex mathematical problems much more readily than their silicon counterparts. This ingenious bit of repurposing appears to have many practical applications. Technology is rapidly accelerating, hurtling us towards a not-too-distant future where the human imagination will manifest itself everywhere in Nature.
DNA could be used as a computing medium - is opening a new interdisciplinary laboratory to explore the possibility of using the hereditary material to solve real-world computing problems. Information can be written onto individual DNA molecules, using the alphabet of four bases that all living things use to record genetic information. A DNA computation is done by coding a problem into this alphabet and then creating conditions under which DNA molecules are formed that encode all possible solutions of a problem. This process produces billions of billions of molecules encoding wrong answers, along with perhaps a few encoding the right one.
WHAT IS THE NEED?
Computers have become significantly smaller and more powerful over the past 40 years, but they still have a silicon substrate, and silicon has inherent limitations. The abilities and power of computers to this day have increased, almost exponentially, since the dawn of their creation. This exponential growth of silicon chip speed and inverse of size has come to be known as Moore's Law. Computer chip manufacturers are furiously racing to make the next microprocessor that will topple speed records. As advancements in micro silicon chip production continue, however, more and more obstacles are faced due to the increase in complexities of the problems for which they are required. Chip makers need a new material to produce faster computing speeds. It would be hard to believe where scientists have found the new material they need to build the next generation of microprocessors. Millions of natural supercomputers exist inside living organisms, including our body. DNA (deoxyribonucleic acid) molecules, the material our genes are made of, have the potential to perform calculations many times faster than the world's most powerful human-built computers. DNA molecules have already been harnessed to perform complex mathematical problems. The fastest supercomputers now available can perform about 109 (1 billion) operations per second. By using DNA molecules, it would be possible to achieve effective speeds of as much as 1017 operations per second
WHERE IT ALL STARTED?
The scientists at the forefront of the DNA computer revolution are a brilliant breed indeed. It was all started by a professor of Computer Science at USC by the name of Leonard M. Adleman, who utilized recombinant DNA to solve a simple Hamiltonian path problem, more popularly recognized as a variant of the so-called "traveling salesman problem." In Adleman's version of the traveling salesman problem, or "TSP" for short, a hypothetical salesman tries to find a route through a set of cities so that he visits each city only once. As the number of cities increases, the problem becomes more difficult until its solution is beyond analytical analysis altogether, at which point The Hamiltonian path problem, on a large scale, is effectively unsolvable by conventional computer systems. Computers now solve such problems by trial and error. But if hundreds of cities were involved, a conventional computer would require years to find the answer. A DNA computer, on the other hand, tests all possible answers simultaneously, offering the prospect of much speedier solutions.
HOW IT WORKS?
DNA computation is based on the fact that technology allows us to 'sequence' (design) single DNA strands which can be used as representations of bits of binary data. Technology also allows us to massively 'amplify' (reproduce) individual strands until there are sufficient numbers to solve complex computational problems.
• DNA input molecule
• The famous double-helix structure discovered by Watson and Crick consists of two strands of DNA wound around each other. Each strand has a long polymer backbone built from repeating sugar molecules and phosphate groups. Each sugar group is attached to one of four "bases".
These four bases –
guanine (G), cytosine (C), adenine (A) and thymine (T) - form the genetic alphabet of the DNA, and their order or "sequence" along the molecule constitutes the genetic code.
The bases are spaced every 0.35 nanometers along the DNA molecule, giving DNA a remarkable data density of nearly 18 Megabits per inch. In two dimensions, if it is assumed one base per square nanometer, the data density is over one million G bits per square inch compared to that of a typical high performance hard drive, which is about 7 G bits per square inch.
One of the most significant properties of DNA is that every DNA sequence has a natural complement. For example if sequence S is ATTACGTCG, its complement, S', is TAATGCAGC. Both S and S' will come together (or hybridize) to form double stranded DNA. This complementarity makes DNA a unique data structure for computation and can be exploited in many ways. Error correction is one example. If the error occurs in one of the strands of double stranded DNA, repair enzymes can restore the proper DNA sequence by using the complement strand as a reference. This facility for error correction means that the error rate can be quite low compared to that of the hard drives that are used today In the cell, DNA is modified biochemically by a variety of enzymes, which are tiny protein machines that read and process DNA according to nature's design. Just like a CPU has a basic suite of operations like addition, bit-shifting, logical operators (AND, OR, NOT NOR), etc. that allow it to perform even the most complex calculations, DNA has cutting, copying, pasting, repairing, and many others. Many copies of the enzyme can work on many DNA molecules simultaneously. This is the power of DNA computing, that it can work in a massively parallel fashion. Pairs of molecules on a strand of DNA represent data and two naturally occurring enzymes act as the hardware to read copy and manipulate the code.
DNA computers derive their potential advantage over conventional computers from their ability to:
• Perform millions of operations simultaneously. The massively parallel processing capabilities
of DNA computers may give them the potential to find tractable solutions to otherwise
intractable problems, as well as potentially speeding up large, but otherwise solvable, polynomial
time problems requiring relatively few operations.
• Another advantage of the DNA approach is that it works in "parallel," processing all possible answers simultaneously. Therefore it enables to conduct large parallel searches and generate a complete set of potential solutions.
• DNA can hold more information in a cubic centimeter than a trillion CDs, thereby enabling it to efficiently handle massive amounts of working memory.
• The DNA computer also has very low energy consumption, so if it is put inside the cell it would not require much energy to work and its energy-efficiency is more than a million times that of a PC. While still in their infancy, DNA computers are capable of storing billions of times more data than a personal computer.
• The potential applications of re-coding natural DNA into a computable form are many and include:
• DNA sequencing
• DNA fingerprinting
• DNA mutation detection
• Development and miniaturization of biosensors, which could potentially allow communication between molecular sensory computers and conventional electronic computers.
• The fabrication of nanoscale objects that can be placed in intracellular locations for monitoring and modifying cell function
• The replacement of silicon devices with nanoscale molecular-based computational systems, and
• The application of biopolymers in the formation of novel nanostructured materials with unique optical and selective transport properties
• DNA based models of computation might be useful for simulating or modeling other emerging computational paradigms, such as quantum computing, which may not be feasible until much later.
• Evolutionary programming for applications in design or expert systems.
• In theory, this technology could one day lead to the development of hybrid computer systems, in which a silicon-based PC generates the code for automated laboratory-based operations, carried out in a miniature 'lab in a box' linked to the PC.
However, there are certain shortcomings to the development of the DNA computers:
• A factor that places limits on his method is the error rate for each operation. Since these operations are not deterministic but stochastically driven, each step contains statistical errors, limiting the number of iterations one can do successively before the probability of producing an error becomes greater than producing the correct result.
• Algorithms proposed so far use relatively slow molecular-biological operations. Each primitive operation takes hours when you run them with a small test tube of DNA. Some concrete algorithms are just for solving some concrete problems. Every Generating solution sets, even for some relatively simple problems, may require impractically large amounts of memory. Also, with each DNA molecule acting as a separate processor, there are problems with transmitting information from one molecule to another that have yet to be solved.
Israeli scientists have devised a computer that is so tiny that a trillion of them could fit in a test tube and perform can perform 330 trillion operations per second, more than 100,000 times the speed of the fastest PC with 99.8 percent accuracy. It is the first programmable autonomous computing machine in which the input, output, software and hardware are all made of biomolecules. Recently, the team has gone one step further. In the new device, the single DNA molecule that provides the computer with the input data also provides all the necessary fuel.
Classical DNA computing techniques have already been theoretically applied to a real life problem: breaking the Data Encryption Standard, DES. Although this problem has already been solved using conventional techniques in a much shorter time than proposed by the DNA methods, the DNA models are much more flexible, potent, and cost effective. Israeli scientists have devised a computer composed of DNA and enzymes. The enzyme FokI breaks bonds in the DNA double helix, causing the release of enough energy for the system to be self-sufficient. The design is considered a giant step in DNA computing which could transform the future of computers, especially in pharmaceutical and biomedical applications.
Future applications might make use of the error rates and instability of DNA based computation methods as a means of simulating and predicting the emergent behavior of complex systems. This could pertain to weather forecasting, economics, and lead to more a scientific analysis of social science and the humanities.
Perhaps most importantly, DNA computing devices could revolutionize the
pharmaceutical and biomedical fields. Some scientists predict a future where our bodies are patrolled by tiny DNA computers that monitor our well-being and release the right drugs to repair damaged or unhealthy tissue. The DNA computer might be a cost-effective way to decode the genetic material of humans and other living things, and it might be able to create "wet data bases" of DNA for research purposes.
Considering all the attention that DNA has garnered, it isn’t too hard to imagine that one day we might have the tools and talent to produce a small integrated desktop machine that uses DNA. It certainly might be used in the study of logic, encryption, genetic programming and algorithms, automata, language systems, and lots of other interesting things that haven't even been invented yet. With so many possible advantages over conventional techniques, DNA computing has great potential for practical use. Future work in this field should begin to incorporate cost-benefit analysis so that comparisons can be more appropriately made with existing techniques and so that increased funding can be obtained for this research that has the potential to benefit many circles of science and industry.
1).Wechsler A W ,”Advances in DNA ”,1992
2).Christina .T. Mora, “Secrets of Human DNA”, Springer Publications, 1995
3)www.vector.cshl.org/dnaftb and some websites and journals.