Team develops 'logic gates' to program bacteria as computers

Dec 08, 2010

A team of UCSF researchers has engineered E. coli with the key molecular circuitry that will enable genetic engineers to program cells to communicate and perform computations.

The work builds into the same found in electronic computers and creates a method to create circuits by "rewiring" communications between cells. This system can be harnessed to turn cells into miniature computers, according to findings that will be reported in an upcoming issue of Nature and appear today in the advanced online edition.

That, in turn, will enable cells to be programmed with more intricate functions for a variety of purposes, including agriculture and the production of pharmaceuticals, materials and industrial chemicals, according to Christopher A. Voigt, PhD, a synthetic biologist and associate professor in the UCSF School of Pharmacy's Department of Pharmaceutical Chemistry who is senior author of the paper.

The most common electronic computers are digital, he explained; that is, they apply to streams of 1's and 0's to produce more complex functions, ultimately producing the software with which most people are familiar. These logic operations are the basis for cellular computation, as well.

"We think of electronic currents as doing computation, but any substrate can act like a computer, including gears, pipes of water, and cells," Voigt said. "Here, we've taken a colony of bacteria that are receiving two from their neighbors, and have created the same logic gates that form the basis of silicon computing."

Applying this to biology will enable researchers to move beyond trying to understand how the myriad parts of cells work at the molecular level, to actually use those cells to perform targeted functions, according to Mary Anne Koda-Kimble, dean of the UCSF School of Pharmacy.

"This field will be transformative in how we harness biology for biomedical advances," said Koda-Kimble, who championed Voigt's recruitment to lead this field at UCSF in 2003. "It's an amazing and exciting relationship to watch cellular systems and synthetic biology unfold before our eyes."

The Nature paper describes how the Voigt team built simple logic gates out of genes and inserted them into separate E. coli strains. The gate controls the release and sensing of a chemical signal, which allows the gates to be connected among much the way electrical gates would be on a circuit board.

"The purpose of programming cells is not to have them overtake electronic computers," explained Voigt, whom Scientist magazine named a "scientist to watch" in 2007 and whose work is included among the Scientist's Top 10 Innovations of 2009. "Rather, it is to be able to access all of the things that biology can do in a reliable, programmable way."

The research already has formed the basis of an industry partnership with Life Technologies, in Carlsbad, Cal., in which the genetic circuits and design algorithms developed at UCSF will be integrated into a professional software package as a tool for genetic engineers, much as computer-aided design is used in architecture and the development of advanced computer chips.

The automation of these complex operations and design choices will advance basic and applied research in synthetic biology. In the future, Voigt said the goal is to be able to program cells using a formal language that is similar to the programming languages currently used to write computer code.

Explore further: Researchers create designer 'barrel' proteins

Provided by University of California - San Francisco

4.8 /5 (9 votes)

Related Stories

'Chaogates' hold promise for the semiconductor industry

Nov 16, 2010

In a move that holds great significance for the semiconductor industry, a team of researchers has created an alternative to conventional logic gates, demonstrated them in silicon, and dubbed them "chaogates." The researchers ...

Cell-inspired electronics

Feb 25, 2010

(PhysOrg.com) -- A single cell in the human body is approximately 10,000 times more energy-efficient than any nanoscale digital transistor, the fundamental building block of electronic chips. In one second, ...

The logic of life

Apr 20, 2006

Even though the entire human genome has now been 'read' - the chemical composition of our DNA has been more or less mapped out, gene by gene - we still have a rather poor grasp of how living cells actually work. That's because ...

Recommended for you

Researchers create designer 'barrel' proteins

3 hours ago

Proteins are long linear molecules that fold up to form well-defined 3D shapes. These 3D molecular architectures are essential for biological functions such as the elasticity of skin, the digestion of food, ...

World's fastest manufacture of battery electrodes

9 hours ago

New world record: Scientists at the Karlsruhe Institute of Technology (KIT) increased the manufacturing speed of electrode foils coated batch-wise by a factor of three – to 100 meters per minute. This was ...

User comments : 9

Adjust slider to filter visible comments by rank

Display comments: newest first

Quantum_Conundrum
5 / 5 (1) Dec 08, 2010
Can we say "Synthetic Immune System" anyone?
hsauro
not rated yet Dec 08, 2010
See tinkercell.com for an existing and open source CAD tool for genetic engineers.
robbor
not rated yet Dec 08, 2010
oops, my computer just gave me dysentery.
resinoth
not rated yet Dec 09, 2010
anything that moves and takes and bleeds light into space can be a gate. there are moral implications when you use beings as gates.
jmcanoy1860
not rated yet Dec 09, 2010
Can I be Bill Gates?
danlgarmstrong
3 / 5 (2) Dec 09, 2010
there are moral implications when you use beings as gates.

Are bacteria beings? A buddist might say yes, therefore perhaps it is morally wrong to use them in this manner. To a christian it has no soul, therefore it is not a *being* so morally there is not problem. Also as man id given *dominion* over beasts, it is perfectally acceptable to use them in this manner.

Is a cell a being? Or a biological machine?
resinoth
not rated yet Dec 14, 2010
forgetting dominion and souls, or rather the
"full-fledged" soul, a typical human soul, forgetting these:

it's not a gradation of consciousness 'depth', 'all the way down' to bacteria- surely it is rather framed upon the structures of the minds of the beings, and we do not see a morphological hierarchy, even of brains, but rather a huge, kneaded, brachiated tree, therefore anything that is LIKE us (LIKE meaning a being with sensory input and associated decision making capabilities AND unstuck-in-timeness [which is really just an artifact of cranial spatial extent]) CAN house soul (light, movement, a subjectivity): the question is of both how much soul, and what flavor!

So I do not mean to suggest that a bacterium has a light of mind in it, that it has some soul that you can see. But I suggest the bacterium has a microscopic soul. And I am not being facetious here: A soul is only as big or small as the nervous system pedestaling it.
resinoth
not rated yet Dec 14, 2010
commodities forecasters are way ahead of these scientists in using life as logic gate
danlgarmstrong
not rated yet Dec 14, 2010
But I suggest the bacterium has a microscopic soul. And I am not being facetious here: A soul is only as big or small as the nervous system pedestaling it.


A discussion of "soul" belongs more to a theological forum than here. Your claim that a bacterium has a 'microscopic' soul implies a means to measure that soul. When you can do this I would be the first to congratulate you - followed quickly by the Nobel commitee and then the Vactican! I wish you the best of luck.