Abstract: Biomolecular computers, made of DNA and other
biological molecules, only exist today in a few specialized labs,
remote from the regular computer user. Nonetheless, Tom Ran and Shai
Kaplan, research students in the lab of Prof. Ehud Shapiro of the
Weizmann Institute's Biological Chemistry, and Computer Science and
Applied Mathematics Departments have found a way to make these
microscopic computing devices ‘user friendly,' even while performing
complex computations and answering complicated queries.
DNA Computation Gets Logical at the Weizmann Institute of
ScienceRehovot, Israel | Posted on August 3rd, 2009
Shapiro and his team at Weizmann
introduced the first autonomous programmable DNA computing device in
2001. So small that a trillion fit in a drop of water, that device
was able to perform such simple calculations as checking a list of
0s and 1s to determine if there was an even number of 1s. A newer
version of the device, created in 2004, detected cancer in a test
tube and released a molecule to destroy it. Besides the tantalizing
possibility that such biology-based devices could one day be
injected into the body - a sort of ‘doctor in a cell' locating
disease and preventing its spread - biomolecular computers could
conceivably perform millions of calculations in
parallel.
Now, Shapiro and his team, in a paper published
online today in Nature Nanotechnology, have devised an advanced
program for biomolecular computers that enables them to ‘think'
logically. The train of deduction used by this futuristic device is
remarkably familiar. It was first proposed by Aristotle over 2000
years ago as a simple if…then proposition: ‘All men are mortal.
Socrates is a man. Therefore, Socrates is mortal.' When fed a rule
(All men are mortal) and a fact (Socrates is a man), the computer
answered the question ‘Is Socrates Mortal?' correctly. The team went
on to set up more complicated queries involving multiple rules and
facts, and the DNA computing devices were able to deduce the correct
answers every time.
At the same time, the team created a
compiler - a program for bridging between a high-level computer
programming language and DNA computing code. Upon compiling, the
query could be typed in something like this: Mortal(Socrates)?. To
compute the answer, various strands of DNA representing the rules,
facts and queries were assembled by a robotic system and searched
for a fit in a hierarchical process. The answer was encoded in a
flash of green light: Some of the strands had a biological version
of a flashlight signal - they were equipped with a naturally glowing
fluorescent molecule bound to a second protein which keeps the light
covered. A specialized enzyme, attracted to the site of the correct
answer, removed the ‘cover' and let the light shine. The tiny water
drops containing the biomolecular data-bases were able to answer
very intricate queries, and they lit up in a combination of colors
representing the complex answers.
Prof. Ehud Shapiro's
research is supported by the Clore Center for Biological Physics;
the Arie and Ida Crown Memorial Charitable Fund; the Phyllis and
Joseph Gurwin Fund for Scientific Advancement; Sally Leafman
Appelbaum, Scottsdale, AZ; the Carolito Stiftung, Switzerland; the
Louis Chor Memorial Trust Fund; and Miel de Botton Aynsley, UK.
Prof. Shapiro is the incumbent of the Harry Weinrebe Chair of
Computer Science and Biology.
####
About Weizmann Institute of
Science The Weizmann Institute of Science in Rehovot, Israel,
is one of the world's top-ranking multidisciplinary research
institutions. Noted for its wide-ranging exploration of the natural
and exact sciences, the Institute is home to 2,600 scientists,
students, technicians and supporting staff. Institute research
efforts include the search for new ways of fighting disease and
hunger, examining leading questions in mathematics and computer
science, probing the physics of matter and the universe, creating
novel materials and developing new strategies for protecting the
environment.
For more information, please click here
Contacts: Batya Greenman Publications and Media
Relations Department Weizmann Institute of Science P.O. Box
26, Rehovot 76100 Israel Tel: 972 8 934 3852 Fax: 972 8 934
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