artha Herbert, a pediatric neurologist at Boston's Massachusetts General Hospital, studies brain images of children with autism. She was seeing patients one day a few years ago when a 3-year-old girl walked in with more than the usual cognitive and behavioral problems. She was lactose intolerant, and foods containing gluten always seemed to upset her stomach. Autistic children suffer profoundly, and not just in their difficulty forming emotional bonds with family members, making friends, or tolerating minor deviations from their daily routines. Herbert has seen many young children who've had a dozen or more ear infections by the time they made their way through her door, and many others -- "gut kids" -- with chronic diarrhea and other gastrointestinal problems, including severe food allergies. Such symptoms don't fit with the traditional explanation of autism as a genetic disorder rooted in the brain, and that was precisely what was on Herbert's mind that day. She's seen too many kids whose entire systems have gone haywire.

During the course of the little girl's appointment, Herbert learned that the child's father was a computer scientist -- a bioinformatist no less, someone trained to crunch biological data and pick out patterns of interest. She shared with him her belief that autism research was overly focused on examining genes that play a role in brain development and function, to the exclusion of other factors -- namely, children's susceptibility to environmental insults, such as exposure to chemicals and toxic substances. Inspired by their conversation, Herbert left the office that day with a plan: She and the girl's father, John Russo, head of computer science at the Wentworth Institute of Technology, would cobble together a team of geneticists and bioinformatists to root through the scientific literature looking for genes that might be involved in autism without necessarily being related to brain development or the nervous system.

The group scanned databases of genes already known to respond to chemicals in the environment, selecting those that lie within sequences of DNA with suspected ties to autism. They came up with more than a hundred matches, reinforcing Herbert's belief that such chemicals interact with specific genes to make certain children susceptible to autism.

Although some diseases are inherited through a single genetic mutation -- cystic fibrosis and sickle cell anemia are examples -- the classic "one gene, one disease" model doesn't adequately explain the complex interplay between an individual's unique genetic code and his or her personal history of environmental exposures. That fragile web of interactions, when pulled out of alignment, is probably what causes many chronic diseases: cancer, obesity, asthma, heart disease, autism, and Alzheimer's, to name just a few. To unravel the underlying biological mechanisms of these seemingly intractable ailments requires that scientists understand the precise molecular dialogue that occurs between our genes and the environment -- where we live and work, what we eat, drink, breathe, and put on our skin. Herbert's literature scan was a nod in this direction, but actually teasing out the answers in a laboratory has been well beyond her or anyone else's reach -- until now.

Consider for a moment that humans have some 30,000 genes, which interact in any number of ways with one or more of the 85,000 synthetic, commercially produced chemicals, as well as heavy metals, foods, drugs, myriad pollutants in the air and water, and anything else our bodies absorb from the environment. The completion of the Human Genome Project in 2003 armed scientists with a basic road map of every gene in the human body, allowing them to probe more deeply into the ways our DNA controls who we are and why we get sick, in part by broadening our understanding of how genes respond to external factors. In the years leading up to the project's completion, scientists began developing powerful new tools for studying our genes. One is something called a gene chip, or DNA microarray, which came about through the marriage of molecular biology and computer science. The earliest prototype was devised about a decade ago; since then these tiny devices, as well as other molecular investigative tools, have grown exponentially in their sophistication, pushing medical science toward a new frontier.

Gene chips are small, often no larger than your typical domino or glass laboratory slide, yet they can hold many thousands of genes at a time. Human genes are synthesized and bound to the surface of the chip such that a single copy of each gene -- up to every gene in an organism's entire genome -- is affixed in a grid pattern. The DNA microarray allows scientists to take a molecular snapshot of the activity of every gene in a cell at a given moment in time.

The process works this way: Every cell in your body contains the same DNA, but DNA activity -- or expression -- is different in a liver cell, say, than it is in a lung, brain, or immune cell. Suppose a scientist wishes to analyze the effect of a particular pesticide on gene activity in liver cells. (This makes sense, since it is the liver that processes and purges many toxins from the body.) A researcher would first expose a liver cell culture in a test tube to a precise dose of the chemical. A gene's activity is observed through the action of its RNA, molecules that convey the chemical messages issued by DNA. RNA is extracted from the test tube, suspended in a solution, then poured over the gene chip. Any given RNA molecule will latch on only to the specific gene that generated it. The genes on the chip with the most RNA stuck to them are the ones that were most active in the liver cells, or most "highly expressed." The genes that don’t have any RNA stuck to them are said to be "turned off" in those cells. Scientists use the microarray to compare the exposed cells to non-exposed, control cells (see sidebar). Those genes that show activity in the exposed cells but not in the control cells, or vice versa, are the ones that may have been most affected by the pesticide exposure.