Switches are a part of daily life, from snoozing your alarm, turning on
the coffee maker, firing up your car engine, and so on until we turn
off the lights at night. Researchers have now cataloged even more
templates of possible switches within a living cell than we use
throughout our day.
Naren Ramakrishnan, associate professor of computer science at
Virginia Tech, USA, and Upinder S. Bhalla, at the National Centre for
Biological Sciences (NCBS), part of the Tata Institute of Fundamental
Research in India, found that cells can make use of thousands of
switches to support important biological functions.
Cells use switches for determining what kind of cell to become —
skin or blood, for instance, in responding to stress, and in
communication with other cells. "A switch is like a memory unit," said
Bhalla. "The state of the switch — whether it is on or off, is like a
computer memory that can store a bit of 0 or 1. Although real
biological switches are quite complex and regulated in many ways, we
have shown the simplest possible ways in which switches could work",
The researchers collaboration began during a sabbatical visit by
Ramakrishnan to NCBS in Bangalore, India. Ramakrishnan is a computer
scientist whose expertise is in numerical simulation and data mining.
Bhalla is a computational neuroscientist with broad interests in
biochemical network modeling and simulation. They decided to use
Virginia Tech’s System X supercomputer to search for the many ways in
which cells can implement switches.
"Our exploration using System X is rather like how a tinkerer or a
kid puts together things to see if they do something useful. We took a
lot of ‘spare parts’, each spare part being one chemical reaction,
connected them together every which way, and we found that a surprising
number of these artificially constructed networks actually were
switches," said Ramakrishnan.
"Popular opinion used to be that there are a small number of ways in
which switches can be realized by biology, but we found thousands of
switches in our search," Ramakrishnan said.
The researchers report in PLoS Computational Biology, "We find
nearly 4,500 reaction topologies, or about 10 percent of our tested
configurations, that demonstrate switching behavior."
Their research also led to a comprehensive "map" of biochemical
switches. The map further revealed that most of the switches form a
"family" — that is, the switches are all related to one another. "This
has important implications since it suggests how evolution might
stumble upon a switch rather easily." Ramakrishnan said.
"Of course, there is more to cells than switches," Bhalla said. "But
switching and memory are the most basic behaviors possible. Armed with
our catalog of switches, we can now proceed to investigate more
interesting behaviors like complex information processing."
Journal reference: Memory Switches in Chemical Reaction Space. PLoS Computational Biology, June 20, 2008.