New World: Biomolecular computers are becoming user friendly and sophisticated

Minuscule biomolecular computers made of DNA are as uncommon today as laptops were 15 years ago.

August 15, 2009 20:31
4 minute read.
New World: Biomolecular computers are becoming user friendly and sophisticated

DNA generic 248.88. (photo credit: Courtesy)


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Minuscule biomolecular computers made of DNA are as uncommon today as laptops were 15 years ago. They were invented just eight years ago, when Prof. Ehud Shapiro and his team at the Weizmann Institute of Science's biological chemistry department introduced the first autonomous programmable DNA computing device. So small that a trillion can fit in a drop of water, the 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 A newer version of the device, created in 2004, detected cancer in a test tube and released a molecule to destroy it.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" - biomolecular computers could conceivably perform millions of calculations in parallel. The computers exist only in a few specialized labs, but Shapiro's research students Tom Ran and Shai Kaplan at the biological chemistry and computer science and applied mathematics departments have found a way to make these microscopic devices "user friendly," even while performing complex computations. Shapiro and his team have just published in the online edition of Nature Nanotechnology about their advanced program for biomolecular computers that enables them to "think." 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. Simultaneously, the team created a compiler - a program for bridging between a high-level computer 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 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 intricate queries, and they lit up in a combination of colors representing complex answers. MEASURING ENJOYMENT If hedonism is taking self enjoyment to the extreme, a "hedonimeter" measures the extent of this enjoyment. In 1881, the optimistic Irish economist Francis Edgeworth imagined a strange device called a hedonimeter that would be capable of "continually registering the height of pleasure experienced by an individual." It was just a dram, but for many decades, social scientists have tried to to measure happiness. Surveys have revealed some useful information, but these are plagued by the unpleasant fact that people misreport and misremember their feelings when confronted by a questioner with a clipboard or when volunteers report their feelings via cell phone. But what if you had a remote-sensing mechanism that could record how millions of people around the world were feeling on any particular day - without their knowing? That's exactly what Peter Dodds and Chris Danforth, a mathematician and computer scientist working at the University of Vermont's advanced computing center, have created. Their methods show that Election Day, November 4, 2008, was the happiest day in four years. The day of Michael Jackson's death, one of the unhappiest. Their results were recently reported in the Journal of Happiness Studies (yes, there is such a thing). "The proliferation of personal online writing such as blogs gives us the opportunity to measure emotional levels in real time," they wrote in their study, "Measuring the Happiness of Large-Scale Written Expression: Songs, Blogs and Presidents." Their answer to Edgeworth's daydream begins with a Web site,, that mines some 2.3 million blogs, looking for sentences beginning with "I feel" or "I am feeling." They gathered nearly 10 million sentences. Then, drawing on a standardized "psychological valence" of words established by the Affective Norms for English Words (ANEW) study, each sentence receives a happiness score. In the ANEW study, a large pool of participants graded their reaction to 1,034 words, forming a kind of "happy-unhappy" scale from 1 to 9. For example, "triumphant" averaged 8.87, "paradise" 8.72, "pancakes" 6.08, "vanity" 4.30, "hostage" 2.20, and "suicide" 1.25. The sentence "I feel lazy" would receive a score of 4.38. "We were able to make observations of people in a fairly natural environment at several orders of magnitude higher than previous happiness studies," Danforth says. "They think they are communicating with friends," but since blogs are public, he says, "we're just looking over their shoulders."

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