Biological computers, Blue gene, Face recognition technology

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://arstechnica.com/journals/science.ars/2007/05/2
1/designing-biological-computers

By Bill Christensen

Biocomputers constructed entirely of DNA, RNA and

proteins can function inside the body as "molecular
doctors," according to Harvards Yaakov Kobi
Benenson, a Bauer Fellow in the Faculty of Arts and
Sciences Center for Systems Biology.
Each human cell already has all of the tools required
to build these biocomputers on its own, says
Harvards 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 Blymphocytes, 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://www.technovelgy.com/ct/Science-FictionNews.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://www.smalltimes.com/articles/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 Harvards Yaakov Kobi
Benenson, a Bauer Fellow in the Faculty of Arts and
Sciences Center for Systems Biology.
Each human cell already has all of the tools required
to build these biocomputers on its own, says
Harvards 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 Blymphocytes, 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.