Wednesday, January 26, 2011

Computing with chemistry

Friday's 'Speaking of Science' considers the intersection of computer science, biology, and chemistry. In the column, I feature the work of two enterprising scientists attempting to use the building blocks of life to perform a variety of tasks. These include performing computations, building devices and self-assembling into complex patterns.

“Biology is about programming chemistry,” said Erik Winfree, a professor of computer science at the California Institute of Technology. “The genome is the information that specifies the organism and its characteristics. Not only does DNA contain the instructions for making a whole organism, but also how to maintain the processes integral to life.”

On Tuesday, Winfree spoke to a full auditorium in the Electrical Engineering Building. His colloquium presentation,Learning how to program chemistry, discussed DNA computing and synthetic biology from the perspective of a computer scientist.

Winfree contrasted the various questions associated with these fields, and discussed how they might be answered.

“Biology asks, ‘What is it? How does it work?’” said Winfree. “Synthetic biology replies, ‘What might be possible? How do we build it?’ These new steps are all about information and algorithms. We seek to program using the language of life, DNA.”

Winfree’s group has found success in creating structures, patterns, devices, and even circuits made out of DNA, RNA and enzymes. Last year, one of his students, Paul Rothemund, created intricate patterns out of DNA strands. These shapes, including squares, triangles, stars and smiley faces form when a broth of specifically sequenced DNA is heated and cooled.

From patterns, researchers have created tiles of DNA that form the basis for structures and circuitry.  This might not seem like a noteworthy feat. Considering that these computers are functioning at the nanoscale, however, this illustrates the immensity of the advances.

The biggest challenges scientists currently face in chemical computing revolve around scale and reliability. It’s only possible to create simple patterns and devices at present. Scientists still need to build complexity into the gap that lies between DNA and organisms like humans. Furthermore, robustness and reliability need to be built into the computing paradigm. Unlike electronic computing, cells and DNA don’t always behave predictably.

“Molecules don’t behave very nicely like electronic computers do,” said Eric Klavins, a UW professor of electrical engineering. 
“The question of robustness becomes, ‘How do you make a program work in a noisy environment?’”

As scientists like Winfree and Klavins ask questions to expand the field and develop technologies, others have raised ethical questions that seek to keep research in check. Critics have argued that there could be danger in synthetic biology. If we learn how to program the language of life, the power unlocked could help or hinder human happiness. Ethical considerations are clearly important, and should develop in lockstep with the technological side of the field.

The science contained here has the potential to illuminate the foundations for life and utilize it to improve computing in terms of scale and efficiency.

“Once you’re able to think about programming things, a wide range of applications present themselves,” said Winfree. “Many haven’t even been dreamt of yet. We’re simply trying to make computing with chemistry sufficiently general as to be able to unlock these possibilities.”

Check out ‘Speaking of science’ online or in print, and follow your curiosity through the links provided here. The field of chemical computing is burgeoning now, fully poised to revolutionize our way of thinking about computing.