Science File / An exploration of issues and trends affecting science, medicine and the environment. : Unconventional Wisdom : Mathematical maverick who created a DNA computer solves old problems in new ways.
There may be no better way to illustrate the unconventional intellect of USC mathematician Leonard Adleman than to reflect on how he finessed a failing grade in physics.
Today, Adleman, 48, is a distinguished scientist who recently galvanized the world research community by demonstrating that the language of life--the DNA molecules inside every living cell--can be programmed to compute complex problems. In the six months since his research was made public, his provocative discovery has stimulated a new field of computer science, experts say.
But as the 1960s ended, he was just a computer programmer at the Bank of America taking a graduate physics course at San Francisco State and was eager to drop the unsatisfying class.
It was too late, however, to withdraw without taking an incomplete in the course, and that would leave a failing grade on his transcript. It is the sort of seemingly insoluble human dilemma that gives most students insomnia.
On the shelves of the university library, Adleman found the solution. He reasoned that the college, as a matter of policy, would not release the transcript of any student with an overdue book or unpaid fine. So he checked out a computer text, then never returned it.
No book. No transcript. No failing grade.
Colleagues say that what is revealing--and characteristic--about the incident is the way in which Adleman turned the complex characteristics of an arbitrary, rigid system to his own purpose. In much the same way, he put the predictable molecular structure of DNA to a slightly different purpose than the one nature had intended--to serve as the blueprint of all living things.
Last fall, he used DNA to compute the answer to a mathematical formula that at its most complex is more than any electronic thinking machine can handle.
To do it, he organized the orderly chemical components of a DNA molecule strand by strand, the way a conventional programmer would arrange computer code one byte at a time.
He took advantage of the natural machinery of life to do the rest. He essentially grew the answer in a test tube as the DNA combined and recombined according to its own internal organic logic. Eventually, a molecule evolved that contained the answer.
The amount of genetic material involved was barely enough to wet the lip of a teaspoon. In the process, Adleman transformed the way in which scientists think about all computers.
“What a computer is depends on who you are and when you are asking,” Adleman said. “A computer is a physical device obeying physical laws. A machine becomes a computer when we learn to interpret its behavior as computation.
“Lots of things in the world might make computers,” he added. “It is up to us to look around. We just have to find the right way of looking at it.”
When he presents his research now, he promises every student and scientist who attend his lectures a supercomputer, then tosses them bags of tiny test tubes.
Leonard Adleman’s laboratory is in his head.
He does some of his best thinking under a tree in his back yard but he is comfortable musing about science almost anywhere in his San Fernando Valley home. Dressed in a hooded gray sweat shirt, blue plaid flannel shirt and blue jeans, he leans back in the thick white, pebbled upholstery of the living room sofa, his feet stretched out on a white wool rug. The air is perfumed by the aroma of oatmeal cookies baking in the kitchen. While his mind wanders, he noodles around the house and answers his electronic mail, talks about science with his wife, Lori, and three daughters, or channel surfs restlessly.
“One of the nice things about mathematics,” he said, “is that it is a place where you can do science without having the material world there. When you actually go into a laboratory and you have to move the material world around, things tend to slow down. Also, the real world is sometimes not so perfect as in math.
“The second you conceive of a [math] experiment, it is largely done. You can sit in your room without any resources and do this very high level of raw mathematics,” he said. “In fact, very high levels of mathematics usually are done without resources . . . by people in their rooms.”
Adleman’s primary “room” is a Spartan home office, where, when inspiration strikes, he retreats to his computer. “The only situation I feel comfortable in and do well in is one in which things are very rigorously defined in detail,” he said. “That’s what you get in science. Everything is in a very solid foundation. Once I get away from those solid foundations I am filled with ambiguities and I don’t quite understand how things work.
“That is one of the things that drove me to be a scientist, to find a place where I was comfortable,” he said.
The kind of genetic engineering that underlies Adleman’s molecular computer is not normally his forte. He is more at ease with algebraic number theory and the higher mathematics of secrecy.
Until recently, he was best known as the inventor, with Ronald Rivest and Adi Shamir, of a patented electronic encryption system called RSA, so powerful that governments and businesses worldwide have adopted it.
When Robert Redford was seeking a technical adviser for the movie “Sneakers,” which involves stolen computer codes and electronic encryption, he turned to Adleman as a technical adviser. In the Bay Area bookstores where self-styled “cypherpunks” gather, Adleman has even been asked for his autograph.
Born and raised in San Francisco, Adleman sampled chemistry, physics, computer science and medicine on what he now sheepishly calls a “random walk” through academia before settling on mathematics.
The turning point, he said, was a course in formal logic at UC Berkeley, where he received his doctorate in computer science in 1976. The course, he said, revealed to him the alluring structure that underlies mathematics.
He taught at the Massachusetts Institute of Technology before joining the USC faculty as a tenured professor in 1980.
The insight that led Adleman to molecular computing actually had very little to do with computer science.
Rather, it was his interest in AIDS, which led him to examine the mechanism by which the human immunodeficiency virus inflicts lethal damage on the immune system. Studying the molecular biology of HIV led to molecular computing.
The idea that DNA could be harnessed as a computer “was probably almost automatic from the moment you had a theoretical computer scientist in a molecular biology lab,” he said.
Colleagues say it is that kind of imaginative leap that makes his work so intriguing. “The genetic code is a mathematical challenge,” said Leonard Kleinrock at the UCLA computer science department. “It is not surprising he would be looking at this. He is just a very, very creative guy.”
Adleman insists on calling his molecular computer a toy designed just to prove his concept. But he is proud of how it combines the tools of biology and the theories of computer science.
“Can a practical molecular computer be built?” he asks.
“The short answer is that I don’t know. I don’t think anyone knows,” he said. “This is basic research, which may be laying the foundation for what computers may look like in 50 years.”
(BEGIN TEXT OF INFOBOX / INFOGRAPHIC)
The Gene Machine In theory, virtually any device that behaves according to predictable rules can become a computer. One such device is DNA, whose chemical components combine in regular ways. USC mathematician Leonard M. Adleman married computer science to biology by using the genetic code to calculate a mathematical problem.
Growing an Answer 1. Adleman assembles his program by building a molecule of DNA. He uses its chemical subunits (adenine, thymine, guanine and cytosine) the way another programmer would use computer code. 2. The molecule replicates according to the natural laws governing the behavior of DNA. The answer “evolves” in the test tube. 3. The result is a single molecule of DNA that contains the solution to the mathematical problem. 4. Adleman reads the answer by analyzing the molecule’s chemical structure-its adenine-thhymine and guanine-cytosine sequences.
A Future for the Gene Machine Through a DNA computer would perform individual operations very slowly, it could: * perform billions of operations simultaneously.* store enormous amounts of data in little space. * require very little energy. Source: Los Angeles Times
