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FROM: Bobbie Razo
DATE: May 19, 2000 TIME: 11:06:32 REMOTE IP: 163.238.244.230 |
DNA Computing |
DNA Computing
Computer technology, specifically the computer machine world, may come to a time where the substance it is conventionally built on may reach its limits.
Computer companies today are competing and struggling to build their computers on smaller and faster silicon chips.
But, scientists believe that there are physical speed limits to how far these silicon chips can go, and once we got into the sub-nanoseconds of computing, something would eventually replace silicon chips as the brains of a computer…and they believed that we could find that in a petri dish!
Despite their respective complexities, both biological and mathematical operations have some similarities.
The very complex structure of a living being began initially with information encoded in a DNA sequence called genes.
These genes were then applied through simple operations which resulted into complex living structures.
On the other hand, all complex math problems can be reduced to simple operations like addition and subtraction.
For the same reasons that DNA was presumably selected for living organisms as a genetic material, its stability and predictability in reactions, DNA strings can also be used to encode information for mathematical systems.
This is how DNA computing became the cutting-edge of technology in computing research.
It is a whole new approach and era of advanced computing — and the key is to use molecules themselves.
DNA computing, in the literal sense, is the use of synthetic DNA (Deoxyribose Nucleic Acid) molecules, the molecules which encode genetic information for all living things, as a data structure in computers.
Researchers have turned to DNA for its chief attributes — its microscopic size and powerful search function that can explore all possible answers simultaneously — to build DNA based computers.
Let us begin with a comparison: DNA based computers versus the conventional computers.
A conventional computer represents information on silicon chips as a series of electrical impulses — zeroes and ones — and manipulates the information by performing mathematical computations with those zeroes and ones.
The basic suite of operations are addition, bit-shifting, logical operators (And, Or, Not), etc., which allows the performance of even the most complex calculations.
Its components are motherboards, hard drive, and expansion slots.
Instead of silicon chips and electrical currents, DNA computers use the four deoxyribonucleic acids, or bases (nucleotides) — A (adenine), C (cytosine), G (guanine), T (thymine) — as memory units, and recombinant DNA techniques (enzyme reactions) to carry out the fundamental operations.
The bases in the DNA are spaced every .35 nano-meters along the DNA molecule, giving DNA a remarkable data density of nearly 18 Mbits per inch.
In two dimensions, if you assumed one base per square nano-meter, the data density is over one million Gbits per square inch.
Compare this to the data density of a typical high performance hard drive, which is about 7 Gbits per square inch - a factor of over 100,000 times smaller.
Also, DNA is useful for its double stranded nature.
The bases A with T, and C with G, can bind together respectively, forming base pairs.
Therefore, every DNA sequence has a natural complement to form double stranded hybridized helices.
For example, a DNA sequence S is ATTACGTCG, its complement would then be S’, TAATGCAGC.
This makes DNA a unique data structure for computation and can be exploited in many ways.
Error correction is one example.
If an error occurs in one of the strands of a double stranded DNA, repair enzymes can restore the proper DNA sequence by using the complement strand as a reference.
While a DNA based computer may be run by a conventional computer, the components of an actual DNA based computer are all molecular — synthetic DNA and modifying enzymes.
Also, computation takes place in test tubes.
The input and output are both strands of DNA, whose genetic sequences are used to encode certain information.
A program on a DNA computer is executed as a series of biochemical operations, which have the effect of synthesizing, extracting, modifying, repairing and cloning the DNA strands.
The advantage of the approach of DNA computing is its ability to work in a massively parallel fashion.
This ability is lacked by all current electronic-based computers.
As mentioned before, operations that manipulate DNA are executed by a variety of enzymes; those that cut, paste, copy, repair or clone DNA on the molecular level.
Molecular biology, Biochemistry, and Biotechnology have developed techniques that allow us to perform many of these cellular functions in the test tube.
It is the cellular machinery, along with some synthetic chemistry, that makes up the palette of operations available for computations like those of the conventional CPU.
When these enzymes are combined with a solution of DNA in a test tube, note that it does not function sequentially, working on one DNA at a time.
Rather, many copies of the enzyme work on many DNA molecules it is exposed to simultaneously in the test tube.
On the other hand, an electronic computer can analyze only one piece of information one at a time.
This ability to perform many parallel operations allows computational problems to be approached from a different point of view.
Transistor-based computers typically handle operations in a sequential manner.
Of course there are multi-processor computers and modern CPU’s that incorporate some parallel processing, but in general, in the basic von Neumann architecture computer, instructions are handled sequentially.
A von Neumann machine, which is what all modern CPUs are, basically repeats the same “fetch and execute cycle” over and over again.
DNA computers, however, are non-von Neumann machines that approach computation in a different way from ordinary computers for the purpose of solving a different class of problems.
For DNA computing, the power comes from the memory capacity and parallel processing.
If DNA is forced to behave sequentially, it loses its appeal.
If both a DNA computer and a conventional computer were to operate on only a single piece of data, the speed of the DNA computer to operate on that data would be at a snail’s pace compared to the data throughput of an average hard drive.
But when the amount of data to process is a large number, the DNA computer would operate on all those data at the same time, whereas again, the electronic computer will continue to operate on all the data one at a time.
To give an idea of the difference in time, a calculation that would take 10^22 modern computers working in parallel to complete in the span of one human’s life would take one DNA computer only 1 year to complete!
This simultaneous calculation is applied to certain types of computational problems by having all the possible answers to a certain problem in a test tube (as a DNA solution) where each potential answer is represented as a unique sequence of a DNA strand.
A series of enzymes work on the DNA solution filtering out all the incorrect answers leaving behind the correct one in the solution.
The founder of DNA computing, University of Southern California professor Leonard Adleman, spawned the field and shocked the world in 1994 with his research showing that he could solve a math problem using DNA.
It was a landmark demonstration of computing in the molecular level.
The type of problem that Adlman solved is a famous one.
It is formally known as a directed Hamiltonian Path (HP) problem, but is more popularly recognized as a variant of the so-called traveling salesman problem.
The objective is to find a path from start to end going throught all the given points only once.
This problem is difficult for conventional (serial logic) computers because they must try each possible path one at a time.
It is like having a whole bunch of keys and trying to see which fits a lock.
Conventional computers are very good at math, but poor at key into lock problems.
DNA based computers can try all the keys at the same time (massively parallel) and thus are very good at key into lock problems, but much slower at simple mathematical problems like multiplication.
The Hamiltonian Path problem (or non-deterministic time problem) was chosen because every key into lock problem can be solved as a Hamiltonian Path problem.
Adleman solved this problem with only 7 points.
Each points are named with a unique DNA sequence.
Without going into much detail the algorithm used to solve this problem is as follows: 1. Generate random paths through the graph (all possible paths); 2. Keep only those paths that begin with the starting point and end with the ending point; 3. Keep only those paths with 7 points; 4. Keep all those paths that enter all points at least once; 5. Any remaining paths are solutions.
Each of these steps are performed with a certain enzyme.
When Adleman did this procedure it took him 7 days.
Although this problem can be solved in a shorter time in a regular computer or with a pencil and paper, when the number of points between the path is increased to 70, the problem becomes too complex for even a supercomputer.
When Adelman proved this possibility of DNA computing, it prompted an explosion of work.
Many other researchers followed in the field and continued to research in DNA computing.
A group of researchers in Wisconsin repeated the same procedure but instead of a test tube they used the surface of a gold-plated square inch glass as something analogous to a conventional memory chip.
Three computer scientist from prestigious schools have outlined a way for a DNA cmputer to crack messages coded with thte U. S. government’s own Data Encryption Standard.
When a message is encrypted according to the standard, the coding relies on one of 72 quadrillion keys or encoding instructions.
A message coded in this way is hard to crack, because there is no way to know which specific key was used.
Testing all possible keys on an electronic computer would take an enormous amount of time.
But a DNA computer could test all keys at the same time, find the right one, and pass it to a human code-breaker for use in translating the message.
A highly automated version of a DNA computer might be able to produce the answer in as little as 2 hours, according to Dr. Adleman.
However, it is still considered a pioneer and an early stage for DNA computing.
Scientists now are only practicing DNA computing on problems in small versions, those that can also be calculated in an electronic computer to compare for accuracy.
Most of the computational problems presented to DNA computing are still theoretical.
An actual functional DNA desktop computer lies may years in the future.
With some of the promises of DNA computing there are also some drawbacks.
Like a bug occuring in conventional programming, there can be contaminations in the DNA that are used.
Contamination of a DNA computer with DNA from outside sources could give incorrect results.
Also deformation of DNA from as excessive heat or from defection can also yeild incorrect results.
An expert believed that DNA is very fragile and prone to errors, that techniques must be developed to reduce the number of computational errors produced by unwanted chemical reactions with the DNA strands.
Nevertheless, experts have anticipated many useful applications of DNA computing.
For example, enabling a computing system to read and decode natural DNA directly.
Such a computer might also be able to perform DNA fingerprinting — matching blood (DNA) found at a crime scene with the person from whom it came.
It may also 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 that would eliminate the time-consuming task of translating DNA into a form the can be stored in an electronic computer.
A potential result could be the eradication of certain diseases and perhaps within a few decades, the implantable biochips, those that can detect toxins in a body and release chemicals to destroy them and then afterwards become dormant.
Benefits of DNA computers are its use of cheap, clean and readily available biomaterials (rather than costly, and often toxic materials that go into traditional microprocessors).
DNA also stores more information in less space, and because it computes via biochemical reactions (of which many can take place simultaneously), DNA can handle massive parallel processing.
Some scientists even believe that 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 a Pentium-powered PC will seize up if one wire is cut.
Computer scienctist are looking for a way to take processors beyond the speed and size limits of silicon microcircuitry and they believe DNA computing is one way to do this.
Question:
With the way DNA computers approach computational problems (key into lock problems: parallel computation) do you believe that DNA computing could completely replace conventional electronical computers (sequential computation)?
And what do you think the future will be like if DNA computing becomes a common practice in everyday technology, how will society be living?
REPLY TO THIS ARTICLE
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Re: DNA Computing
Posted by Prof. Klibaner on May 26, 2000 at 23:27:04 at IP 64.24.41.22
Aren't dna computers no more than massively parallel machines, capable of following all threads simultaneously? How do you foresee using it for "traditional" computer problems? Re: DNA Computing
Posted by Hoi Chun Yung on May 26, 2000 at 0:47:43 at IP 209.255.50.181
Before I can give any my opinion, I have something really confuse on computer, but with something call Biological stuff. How they get those material out to create the basic calculate module. How those biolo- stuff stable on room templature, and stable to make it more accuracy compare with cuurent silicon computer module. Re: DNA Computing
Posted by mkhanum@hotmail.com on May 25, 2000 at 10:52:34 at IP 216.67.6.123
Today technology is growing so fast. In the early days there were computers as big as a room. Now we have Pentium III. In future who knows DNA, Nanotechnology and Quantum computing might take over. Re: DNA Computing
Posted by Kam Tsui on May 23, 2000 at 22:02:34 at IP 4.54.120.229
I believe that some very long day in the future, things which happen in the movie like Matrix will no longer fiction because of the DNA computing or nanotech. Computer and human flesh can truely interact with together like upload programs to the brain because these two things are not separating from each other anymore. Re: DNA Computing
Posted by Hector Blanco on May 23, 2000 at 2:05:47 at IP 172.135.166.34
I am sure one day DNA, Nanotechnology or Quantum computing will take over. It is just a matter of the ability to control these complex structures to do what we want them to do. Will we see it in our life time? Who knows? My computer is sufficient for my daily tasks right now. I would like a T3 line in my house but thats another story. Re: DNA Computing
Posted by Dennis Healy
on May 22, 2000
at 23:44:38
at IP 205.188.199.194
I think that there are some areas where a DNA based computer would be better than a electronic based one. For example, identification of a persons face. This is an area where the domain is wide open, it could be any of 5 billion faces and to process this data sequeintially would take alot longer than in parallel.
But when the domain is more specific, i think sequenial computing will remain faster.
Re: DNA Computing
Posted by Joseph Fardella
on May 22, 2000
at 23:38:41
at IP 63.23.133.150
I beleive that dna computing may one day replace, classic computers. This will occur because technology is constantly evolving, and the next step in its evolution will be the step toward dna computing
