IS DNA SURPASSING SILICON?

Although DNA computers haven't overtaken silicon-based microprocessors,

researchers have made some progress in using genetic code for
computation. In 2003, Israeli scientists demonstrated a limited, but
functioning, DNA computer.
What is a DNA Computer?
DNA computers will be the next-generation computers made of genes' building
blocks. Because of their speed, miniaturization and data storage potential, DNA
computers are being considered as a replacement for silicon-based computers.
Current DNA computer research has already proven that DNA computers are
capable of solving complex mathematical equations and storing enormous amounts
of data.

Limitation of Silicon Chips

Silicon-based computer chips have been around for more than 40 years and
manufacturers have been successful in making silicon-based chips smaller, more
complex and faster than their predecessors. According to Moore's Law,
microprocessor size is halved every eighteen months. However, there is a limitation
to how small, fast and compact silicon computer chips can be.

Advantages of DNA Computers

DNA computers show promise because they do not have the limitations of silicon-
based chips. For one, DNA based chip manufacturers will always have an ample
supply of raw materials as DNA exists in all living things; this means generally lower
overhead costs. Secondly, the DNA chip manufacture does not produce toxic by-
products. Last but not the least, DNA computers will be much smaller than silicon-
based computers as one pound of DNA chips can hold all the information stored in
all the computers in the world.
With the use of DNA logic gates, a DNA computer the size of a teardrop will be more
powerful than today's most powerful supercomputer. A DNA chip less than the size
of a dime will have the capacity to perform 10 trillion parallel calculations at one
time as well as hold ten terabytes of data. The capacity to perform parallel
calculations, much more trillions of parallel calculations, is something silicon-based
computers are not able to do. As such, a complex mathematical problem that could
take silicon-based computers thousands of years to solve can be done by DNA
computers in hours. For this reason, the first use of DNA computers will most
probably be cracking of codes, route planning and complex simulations for the
government.

History of DNA Computers

The first person who thought of and experimented with DNA as an alternative to
silicon chips was Leonard Adleman, a computer scientist working in the University of
Southern California. The 1994 experiment using DNA as a way of solving complex
mathematical problems was a product of a book's influence (Molecular Biology of
the Gene written by James Watson).
DNA computers will work through the use of DNA-based logic gates. These logic
gates are very much similar to what is used in our computers today with the only
difference being the composition of the input and output signals. In the current
technology of logic gates, binary codes from the silicon transistors are converted
into instructions that can be carried out by the computer. DNA computers, on the
other hand, use DNA codes in place of electrical signals as inputs to the DNA logic
gates. DNA computers are, however, still in its infancy and though it may be very
fast in providing possible answers, narrowing these answers down still takes days.
Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic
instructions used in the development and functioning of all known living organisms
and some viruses. The main role of DNA molecules is the long-term storage of
information. DNA is often compared to a set of blueprints or a recipe, or a code,
since it contains the instructions needed to construct other components of cells,
such as proteins and RNA molecules. The DNA segments that carry this genetic
information are called genes, but other DNA sequences have structural purposes, or
are involved in regulating the use of this genetic information.
Chemically, DNA consists of two long polymers of simple units called nucleotides,
with backbones made of sugars and phosphate groups joined by ester bonds. These
two strands run in opposite directions to each other and are therefore anti-parallel.
Attached to each sugar is one of four types of molecules called bases. It is the
sequence of these four bases along the backbone that encodes information. This
information is read using the genetic code, which specifies the sequence of the
amino acids within proteins. The code is read by copying stretches of DNA into the
related nucleic acid RNA, in a process called transcription.
Within cells, DNA is organized into structures called chromosomes. These
chromosomes are duplicated before cells divide, in a process called DNA replication.
Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA
inside the cell nucleus and some of their DNA in the mitochondria. Prokaryotes
(bacteria and archaea) however, store their DNA in the cell's cytoplasm. Within the
chromosomes, chromatin proteins such as histones compact and organize DNA.
These compact structures guide the interactions between DNA and other proteins,
helping control which parts of the DNA are transcribed.

Introduction to How DNA Computers Will Work

Even as you read this article, computer chip manufacturers are furiously racing to
make the next microprocessor that will topple speed records. Sooner or later,
though, this competition is bound to hit a wall. Microprocessors made of silicon will
eventually reach their limits of speed and miniaturization. Chip makers need a new
material to produce faster computing speeds.
You won't 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 your 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 might one
day be integrated into a computer chip to create a so-called biochip that will push
computers even faster. DNA molecules have already been harnessed to perform
complex mathematical problems.

Hamilton Path problem

Adleman is often called the inventor of DNA computers. His article in a 1994 issue of
the journal Science outlined how to use DNA to solve a well-known mathematical
problem, called the directed Hamilton Path problem, also known as the
"traveling salesman" problem. The goal of the problem is to find the shortest route
between a number of cities, going through each city only once. As you add more
cities to the problem, the problem becomes more difficult. Adleman chose to find
the shortest route between seven cities.
You could probably draw this problem out on paper and come to a solution faster
than Adleman did using his DNA test-tube computer. Here are the steps taken in the
Adleman DNA computer experiment:
1. Strands of DNA represent the seven cities. In genes, genetic coding is
represented by the letters A, T, C and G. Some sequence of these four letters
represented each city and possible flight path.
2. These molecules are then mixed in a test tube, with some of these DNA
strands sticking together. A chain of these strands represents a possible
answer.
3. Within a few seconds, all of the possible combinations of DNA strands, which
represent answers, are created in the test tube.
4. Adleman eliminates the wrong molecules through chemical reactions, which
leaves behind only the flight paths that connect all seven cities.
The success of the Adleman DNA computer proves that DNA can be used to
calculate complex mathematical problems. However, this early DNA computer is far
from challenging silicon-based computers in terms of speed. The Adleman DNA
computer created a group of possible answers very quickly, but it took days for
Adleman to narrow down the possibilities. Another drawback of his DNA computer is
that it requires human assistance. The goal of the DNA computing field is to create
a device that can work independent of human involvement.
Three years after Adleman's experiment, researchers at the University of Rochester
developed logic gates made of DNA. Logic gates are a vital part of how your
computer carries out functions that you command it to do. These gates convert
binary code moving through the computer into a series of signals that the computer
uses to perform operations. Currently, logic gates interpret input signals from silicon
transistors, and convert those signals into an output signal that allows the computer
to perform complex functions.
The Rochester team's DNA logic gates are the first step toward creating a computer
that has a structure similar to that of an electronic PC. Instead of using electrical
signals to perform logical operations, these DNA logic gates rely on DNA code. They
detect fragments of genetic material as input, splice together these fragments
and form a single output. For instance, a genetic gate called the "And gate" links
two DNA inputs by chemically binding them so they're locked in an end-to-end
structure, similar to the way two Legos might be fastened by a third Lego between
them. The researchers believe that these logic gates might be combined with DNA
microchips to create a breakthrough in DNA computing.
DNA computer components -- logic gates and biochips -- will take years to
develop into a practical, workable DNA computer. If such a computer is ever built,
scientists say that it will be more compact, accurate and efficient than conventional
computers. In the next section, we'll look at how DNA computers could surpass their
silicon-based predecessors, and what tasks these computers would perform.
Silicon vs. DNA Microprocessors
Silicon microprocessors have been the heart of the computing world for more than
40 years. In that time, manufacturers have crammed more and more electronic
devices onto their microprocessors. In accordance with Moore's Law, the number
of electronic devices put on a microprocessor has doubled every 18 months. Moore's
Law is named after Intel founder Gordon Moore, who predicted in 1965 that
microprocessors would double in complexity every two years. Many have predicted
that Moore's Law will soon reach its end, because of the physical speed and
miniaturization limitations of silicon microprocessors.
DNA computers have the potential to take computing to new levels, picking up
where Moore's Law leaves off. There are several advantages to using DNA instead of
silicon:
• As long as there are cellular organisms, there will always be a supply of DNA.
• The large supply of DNA makes it a cheap resource.
• Unlike the toxic materials used to make traditional microprocessors, DNA
biochips can be made cleanly.
• DNA computers are many times smaller than today's computers.
DNA's key advantage is that it will make computers smaller than any computer that
has come before them, while at the same time holding more data. One pound of
DNA has the capacity to store more information than all the electronic computers
ever built; and the computing power of a teardrop-sized DNA computer, using the
DNA logic gates, will be more powerful than the world's most powerful
supercomputer. More than 10 trillion DNA molecules can fit into an area no larger
than 1 cubic centimeter (0.06 cubic inches). 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. By adding more DNA, more calculations could be performed.
Unlike conventional computers, DNA computers perform calculations parallel to
other calculations. Conventional computers operate linearly, taking on tasks one at
a time. It is parallel computing that allows DNA to solve complex mathematical
problems in hours, whereas it might take electrical computers hundreds of years to
complete them.
The first DNA computers are unlikely to feature word processing, e-mailing and
solitaire programs. Instead, their powerful computing power will be used by national
governments for cracking secret codes, or by airlines wanting to map more efficient
routes. Studying DNA computers may also lead us to a better understanding of a
more complex computer -- the human brain.

APPLICATIONS

CRYPTOGRAPHY
A field in which DNA computing appears to be particularly interesting is the
cryptography. The DES is the Data Encryption Standard that is the IBM's widely used
encryption procedure. It uses a 56 bit key to encrypt 64 bit messages. The
encryption procedure is known, and the security is based only on the secret
encryption key. In [Bon95a], a molecular program that breaks DES is proposed. That
is, one (plain-text, cipher-text) pair is given, and the key that maps the plain-text
into the cipher-text is found. Conventional (silicon based) computers - using brute
force - would take 104 years to solve the same problem (finding the key that maps a
particular pair).

SOLVING NP PROBLEMS:
NP problems are a class of problems which have an exponential increase in time
complexity as the number of instances increase. DNA Computers can be used to
solve NP class of problems in relatively lesser time because of the parallel
processing ability. This is best illustrated by Adleman’s experiment.

BIOMEDICAL AND PHARMACEUTICAL FIELDS

DNA Computers can monitor blood in vitro levels. If there are any chemical
imbalances, the DNA would synthesize the needed replacement and release it into
blood maintain equilibrium. Autonomous bio-molecular computers may work as
doctors in a cell.

WILL DNA SUPPLANT SILICON??

DNA's key advantage is that it will make computers smaller than any computer that
has come before them, while at the same time holding more data. One pound of
DNA has the capacity to store more information than all the electronic computers
ever built; and the computing power of a teardrop-sized DNA computer, using the
DNA logic gates, will be more powerful than the world's most powerful
supercomputer. More than 10 trillion DNA molecules can fit into an area no larger
than 1 cubic centimeter (0.06 cubic inches). 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. By adding more DNA, more calculations could be performed.
However, setting up and extracting results from a DNA computer can take days and
sometimes week. The fact that DNA doesn’t behave as expected makes things
difficult to obtain accurate results. Human intervention is required in each step of
result synthesis which brings in the drawbacks of human errors. Ehud Shapiro,
whose team has the Guinness record for “the smallest biological computing device”
says, “I think they will live together happily and be used for different applications”.

George Klington Fernandez. A

DMI - St. Eugene University, Zambia