Team develops 'logic gates' to program bacteria as computers

December 8, 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.

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5 / 5 (1) Dec 08, 2010
Can we say "Synthetic Immune System" anyone?
not rated yet Dec 08, 2010
See for an existing and open source CAD tool for genetic engineers.
not rated yet Dec 08, 2010
oops, my computer just gave me dysentery.
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.
not rated yet Dec 09, 2010
Can I be Bill Gates?
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?
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.
not rated yet Dec 14, 2010
commodities forecasters are way ahead of these scientists in using life as logic gate
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.

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