In 1997, Joseph Takahashi identified and cloned the first mammalian gene related to circadian rhythms, or the biological clock. Some said he'd never find it. But using a technique called forward genetics, Takahashi induced chemical mutations in strains of mice and then studied those that had unusual circadian behavior. In a collaboration with researchers at Northwestern University and the University of Wisconsin–Madison, Takahashi pinpointed the gene—called Clock—on mouse chromosome 5, and then cloned it.

Clock controls several other circadian genes, but its expression doesn't cycle. Without the forward genetics technique to introduce mutations, Clock probably would have been overlooked.

"These forward genetics screens literally broke open the clock mechanism between [the fruit fly] and mammals," Takahashi says. "There weren't other obvious clues that this particular set of genes was important."

Takahashi and his colleague, Chuck Weitz, soon discovered that the CLOCK protein interacted with another protein known as BMAL1, and together CLOCK:BMAL1 regulated a number of other clock genes such as Per1. He has since identified several more, and has begun to understand how the genes work together.

Thirty years ago, most scientists were sure that a mammal's biological clock would be found only in the brain. But not Takahashi. He and colleagues found that circadian genes are expressed throughout the body. In short, we have a clock in every cell. So is it possible to hear all of those clocks ticking? Yes, he says—but it's easier if you listen to one cell at a time.

"If you look at populations of cells in culture, the circadian rhythms eventually cancel one another out—each cell has a slightly different period." After he and his colleagues, David Welsh and Steve Kay, discovered this phenomenon, they instead focused on the effects of mutations on a single cell.

They found differences between the clock in the brain—located in an area called the superchiasmatic nucleus, or SCN—and the clock in the rest of the body. "The clock in the brain is much more robust, because it works as a network," Takahashi says. "All of the neurons are coupled, and they synchronize one another." This can overcome genetic defects that have strong effects at the cellular level.

"We found that some mutations such as Per1 and Cry1 that are very subtle at the behavioral level and in the brain actually had strong effects on single cells," he says. "We found that some genes were more important at the single-cell level than the SCN level. We eventually showed that the SCN network can actually overcome some genetic defects."

We now know that the brain clock resets faster than the body clock, he says—the brain can reset after about a day or two, but the body needs up to a week. So when it comes to something like jet lag, "We have to worry about the whole system, not just the brain," he says. One of Takahashi's current focuses is to elucidate how the body clock works.

He's not finished looking for genes, however. Takahashi's lab recently completed a five-year, large-scale mutagenesis screen using forward genetics in mice. They looked for mutations affecting circadian rhythms, as well as those affecting other complex behaviors such as vision, learning, addiction, and locomotion. In 2007, he identified a circadian gene called Fbxl3, which is involved in breaking down the CRY proteins in the biological clock. Mice with mutated Fbxl3 genes had clocks that ran about 2.5 hours slower than normal. The screen also resulted in more than 20 other mutations that are still being studied.

Takahashi has always been fascinated by the natural world. His father, an economist, traveled widely and often brought the family along. Takahashi fished the Arabian Sea in Pakistan and rode elephants in Burma. He also loved all things mechanical: for his senior project at Richard Montgomery High School in Rockville, Maryland, he and his best friend rebuilt the engine of a 1959 Ford Thunderbird.

Medical school was the biology/engineering major's "default pathway" at Swarthmore. But he found the laboratory courses given by biology professor Kenneth Rawson to be "really interesting," and asked to do some more work in Rawson's lab. That turned into Takahashi's senior research project, which was on circadian rhythms. "It was only then that I learned that you could actually go to graduate school and do research," he says.

Even someone who has discovered so much about the mammalian biological clock has not figured out how to create a 30-hour day. Despite long hours in the lab (and many days of travel time for meetings and conferences), Takahashi tries to find time to ski and play tennis. He lives in Wilmette, Illinois, with his wife, Barbara, and their teenagers, Erika and Matthew.