18-01-2010, 06:15 PM
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Abstract:
Biological computers are special types of microcomputers that are
specifically designed to be used for medical applications. The
biological computer is an implantable device that is mainly used for
tasks like monitoring the body's activities or inducing therapeutic
effects, all at the molecular or cellular level.
The biological computer is made up of RNA (Ribonucleic Acid - an
important part in the synthesis of protein from amino acids), DNA
(Deoxyribonucleic Acid - nucleic acid molecule that contains the
important genetic information that is used by the body for the
construction of cells; it's the blue print for all living organisms),
and proteins.
Advantages
The main advantage of this technology over other like technologies is
the fact that through it, a doctor can focus on or find and treat only
damaged or diseased cells. Selective cell treatment is made possible.
The biological computer can also perform simple mathematical
calculations. This could enable the researcher to build an array or a
system of biosensors that has the ability to detect or target specific
types of cells that could be found in the patient's body. This could
also be used to carry out or perform target-specific medicinal
operations that could deliver medical procedures or remedies according
to the doctor's instructions.
This not only makes the healing process easier. It also allows the
doctors to focus only on the damaged, diseased or cancerous cells found
in the patient's body without causing stress to other healthy and
normal cells.
How It Works
Biological computers are made inside a patient's body. The researchers
or doctors merely provide the patient's body with all of the necessary
information or a "blueprint" along which lines the biological computer
would be "manufactured." Once the "computer's" genetic blueprint has
been provided, the human body will start to build it on its own using
the body's natural biological processes and the cells found in the
body.
As of today, reading signals produced by cell activity is not yet
possible due to technological limitations. However, through the use of
a tiny implantable biological computer, these cellular signals could
easily be detected, translated and understood using existing medical
and laboratory equipment.
Through boolean logic equations, a doctor or researcher can easily use
the biological computer to identify all types of cellular activity and
determine whether a particular activity is harmful or not. The cellular
activities that the biological computer could detect can even include
those of mutated genes and all other activities of the genes found in
cells.
As with conventional computers, the biological computer also works with
an output and an input signal. The main inputs of the biological
computer are the body's proteins, RNA, and other specific chemicals
that are found in the human cytoplasm. The output on the other hand
could be detected using laboratory equipment.
Applications
The implantable biological computer is a device which could be used in
various medical applications where intercellular evaluation and
treatment are needed or required. It is especially useful in monitoring
intercellular activity including mutation of genes.
By Jonathan M. Gitlin |
In the lab, we have many interesting and ingenious ways of looking at
biological processes. The biotech revolution has allowed us to develop
methods for detecting and quantifying molecules produced by living
cells; we can detect gene expression and activity, and we can pinpoint
within a cell the precise location of proteins. However, while these
tasks are relatively easy to perform in vitro on a lab bench, imagine
the benefits to medicine if we could apply them in vivo (in a whole,
living animal). Nanotech machines could be injected into a patient that
would then monitor for certain conditions and respond accordingly.
There is a paper, published online today in Nature Biotechnology, that
brings this dream a little bit closer to reality. Scientists at Harvard
and Princeton have detailed the construction of a biological circuit
that uses siRNA to affect boolean logic statements. The circuit works
by having two different mRNA strands that code for the same protein but
contain untranslated regions that correspond to different siRNA
sequences.
Different endogenous inputs will control the expression of the various
siRNAs, thereby affecting which of the two mRNA strands gets expressed;
an example would be inputs A and B targeting one mRNA, and inputs X and
Y inputting the other mRNA, thereby giving the logic expression (A AND
B) OR (X AND Y). Other mRNA strands can be designed to work for (A AND
NOT B), and so on. The output of the mRNA strand that isn't silenced
can be a reporter protein: luciferase or GFP, for example.
Although this research describes relatively simple artificial molecular
machinery, it doesn't take much imagination to see the potential.
Biological machines can be implanted or even built within a patient's
own cells that will act as biosensors, watching out for disease
markers. Should they find such markers, the molecular logic circuits
like this could chose the most appropriate action. That could involve
inducing programmed cell death in the case of cancerous cells or
synthesis of a drug in specific tissues. Obviously such therapies
remain vaporware for now, but that won't remain true for much longer.
http://arstechnicajournals/science.ars/2007/05/21/designing-
biological-computers
By Bill Christensen
Biocomputers constructed entirely of DNA, RNA and proteins can function
inside the body as "molecular doctors," according to Harvardâ„¢s Yaakov
Kobi Benenson, a Bauer Fellow in the Faculty of Arts and Sciencesâ„¢
Center for Systems Biology.
Each human cell already has all of the tools required to build these
biocomputers on its own, says Harvardâ„¢s Benenson. All that must be
provided is a genetic blueprint of the machine and our own biology will
do the rest. Your cells will literally build these biocomputers for
you.
Benson and colleagues claim to demonstrate that biocomputers can work
in human kidney cells in a culture. Also, they have developed a
conceptual framework by which various phenotypes could be represented
logically. Phenotypes are characteristics that are measurable and that
are expressed in only a subset of the individuals within that
population (like blond hair or brown eyes).
In theory, using a biocomputer as the calculation mechanism,
researchers could build biosensors or medicine delivery systems that
could single out specific cell types in the body. These molecular
doctors could target only cancerous cells, for example, ignoring
healthy ones.
Biomolecular computers have been proved in concept by researchers at
the Weizmann Institute of Science; see the article Biomolecular
Computer: The Tiniest Doc?.
Dr. Leonard Adleman, a computer scientist at USC, discussed the
possiblity of biocomputers as early as 1994. Science fiction fans
didn't have to wait so long; they could read about the intellectual
cells in Greg Bear's 1984 novel Blood Music:
His first E. coli mutations had had the learning capacity of planarian
worms; he had run them through simple T-mazes, giving sugar rewards.
They had soon outperformed planaria...
Removing the finest biologic sequences from the altered E. coli, he had
incorporated them into B-lymphocytes, white cells from his own
blood...Using artificial proteins and hormones as a means of
communication, Vergil had "trained" the lymphocytes in the past six
months to interact as much as possible with each other and with their
environment - a much more complex miniature glass maze.
http://technovelgyct/Science-Fiction-News.asp?NewsNum=1051
For a scientist who has just staked a claim to the first programmable
and autonomous biological nanocomputer, Professor Ehud Shapiro is
remarkably low-key when asked to predict how such research may
eventually change the world.
He refuses to get drawn into detailed discussions of futuristic
applications for the technology, and prefers to leave prophesying to
others. At the same time, his incremental approach to the embryonic
science of turning DNA into trillions of tiny computers, swimming
inside a test tube, has given Shapiro a keen sense of direction as he
embarks upon a long-term mission.
Shapiro does not see his computer as a potential competitor to silicon
-based electronic computing, as some have suggested. Instead, he
envisions DNA computers as a "molecular computing device that can
operate initially in a test tube and eventually inside an organism and
interact with its biochemical environment."
DNA computing could possibly be used to streamline laboratory analysis
of DNA, by eliminating the need for sequencing. This, he said, could
happen within a decade.
"In the longer term, you may have medical applications in which this
device can operate in vivo, inside a living organism," he says. "Based
on the information it receives from the environment and medical
knowledge encoded in the software it may diagnose the problem and
prescribe a solution, and then it could synthesis that molecule and
output it."
That's as far as Shapiro is willing to venture on the prospects of the
technology.
"I don't have an opinion on nanogurus or nanoapproaches," he says dryly
during an interview in his office at the Weizmann Institute of Science
in Rehovot, Israel. "We know where we are and where we are going to go.
It's just going to be a very long way."
The starting point for Shapiro, who recently published his design for a
molecular computer in Nature magazine, came after his Internet software
company called Ubique was sold to IBM in 1998.
Plotting a path back to academia, Shapiro stumbled upon research being
done in molecular computing, and challenged Yaakov Benenson, a
biochemistry Ph.D. student, to help make it work. Their modest initial
goal was to find a way to use turn DNA into the most elementary
mathematical computing device known as a finite automaton, capable of
answering "yes" or "no" to very basic questions about a bunch of zeroes
and ones.
"We constructed a molecular realization of this mathematical device,"
Shapiro says. "It has input, it has software and it has hardware
components; and when it computes it produces output, which is another
molecule."
To do this, Shapiro and his colleagues used the four components of a
DNA strand known as A, C, G and T to encode the zeroes and ones and
create an input molecule with an exposed "sticky" end. Then, another
DNA strand -- the software -- swoops in to try and hook up with an
exposed edge like a Lego piece attempting to lock into a complementary
block. Each exposed edge has a specific complementary DNA strand.
After hooking up, the hardware gets to work. An enzyme called ligase
seals the link, and another called Fok-1 moves in to snip the strand,
leaving the next section exposed.
The process continues several times until the computer delivers an
answer to the question. There are 765 different possible software
programs that can be used for simple calculations, such as whether
there are an even or odd number of zeroes or ones.
Shapiro's research is the latest step forward in a field founded by
Leonard Adleman of the University of Southern California, Los Angeles.
In 1994, Adleman proved that DNA could compute, when he used the stuff
to solve the "traveling salesman" problem, in which the shortest route
between several cities must be mapped without going through the same
city twice.
Conventional computers have extreme difficulty solving the problem,
especially when dealing with many points on a map. This is because
electronic computers are based on sequential logic, which makes them
good at solving a problem requiring lots of computations in a row. But
posed with a puzzle of how to figure out the shortest route between 100
cities -- a problem best cracked by simultaneously performing an
enormous number of short operations -- conventional computers do not
make the grade. Adleman demonstrated that DNA could be an efficient way
to solve such problems.
Shapiro says his DNA computer is fundamentally different from Adleman's
breakthrough. Although Adleman's computer was composed of many
trillions of tiny DNA molecules swimming around in a test tube, Shapiro
says it was essentially a large operation that required active
involvement of scientists.
"The calculation needed to be carried out by humans. In our case, the
computer is just the molecules," says Shapiro, who can put a trillion
of his own biological computers into a drop of solution. "His computer
is measured in meters, ours is measured in nanometers."
Experts point out that Shapiro faces stiff competition and will be
challenged to scale up the work to perform more complex computations.
John Reif, professor of computer science at Duke University, described
Shapiro's work as "ingeniously constructed experiments" that clearly
demonstrated the ability to perform simple computations via solid
experimental protocols.
"But there is a lot of competition out there in the DNA computing
world," he added, singling out DNA computing research at Princeton
University and the University of Wisconsin that has gone beyond the
finite automaton.
"People are really aggressively pushing the limits, so the challenge
for the Israelis is to go in and push those limits as defined by some
of those strong competitors," Reif said.
Shapiro has no illusions. The biggest stumbling block now is the
dependency on natural enzymes, meaning scientists must search for the
right enzymes that could help perform computations on DNA. Science
still has no clue how to create designer enzymes that could pave the
way to dramatic progress.
For his part, alongside the finite automaton, Shapiro has taken an
important theoretical step forward by building a model of a molecular
Turing Machine, which is a representation of a computing device capable
of an infinite number of computations. It is in this green, squarish
model, sitting in a cardboard box in his office, that Shapiro sees the
real potential for molecular computing. The ability to create a
molecular Turing Machine would allow scientists to use DNA to generate
massive computing power. In the meantime, he is keeping focused on the
scientific challenges ahead -- and plans to be tied up in his DNA
strands for a while. "We have made a first small step in this
direction," he says. "I believe this will keep me busy until I retire."
http://smalltimesarticles/stm_print_screen.cfm?
ARTICLE_ID=267662
Biocomputers constructed entirely of DNA, RNA and proteins can function
inside the body as "molecular doctors," according to Harvardâ„¢s Yaakov
Kobi Benenson, a Bauer Fellow in the Faculty of Arts and Sciencesâ„¢
Center for Systems Biology.
Each human cell already has all of the tools required to build these
biocomputers on its own, says Harvardâ„¢s Benenson. All that must be
provided is a genetic blueprint of the machine and our own biology will
do the rest. Your cells will literally build these biocomputers for
you.
Benson and colleagues claim to demonstrate that biocomputers can work
in human kidney cells in a culture. Also, they have developed a
conceptual framework by which various phenotypes could be represented
logically. Phenotypes are characteristics that are measurable and that
are expressed in only a subset of the individuals within that
population (like blond hair or brown eyes).
In theory, using a biocomputer as the calculation mechanism,
researchers could build biosensors or medicine delivery systems that
could single out specific cell types in the body. These molecular
doctors could target only cancerous cells, for example, ignoring
healthy ones.
Biomolecular computers have been proved in concept by researchers at
the Weizmann Institute of Science; see the article Biomolecular
Computer: The Tiniest Doc?.
Dr. Leonard Adleman, a computer scientist at USC, discussed the
possiblity of biocomputers as early as 1994. Science fiction fans
didn't have to wait so long; they could read about the intellectual
cells in Greg Bear's 1984 novel Blood Music:
His first E. coli mutations had had the learning capacity of planarian
worms; he had run them through simple T-mazes, giving sugar rewards.
They had soon outperformed planaria...
Removing the finest biologic sequences from the altered E. coli, he had
incorporated them into B-lymphocytes, white cells from his own
blood...Using artificial proteins and hormones as a means of
communication, Vergil had "trained" the lymphocytes in the past six
months to interact as much as possible with each other and with their
environment - a much more complex miniature glass maze.
http://technovelgyct/Science-Fiction-News.asp?NewsNum=1051
