Editor's Note: This is the third in a series of six features on the science of food, running daily from March 30 through April 6, 2009.

DAVIS, Calif.—Ann Wigmore was not enamored with the American diet. Having moved from Lithuania after World War I, she was appalled by our white breads and other abominations and dearly missed the treats her grandmother once prepared, including a savory "gruel made from crushed rye grain and diluted goat's milk."

One day, after struggling for years with ill health, she wandered out to an abandoned parking lot and, as she wrote in her memoir Why Suffer? How I Overcame Illness and Pain Naturally, "There, spread out before my eyes, were hundreds of square feet of the most luscious weeds I had ever beheld." So began Wigmore's faith in the healing powers of wheatgrass, a belief that made her a pioneer of the raw foods movement and inspired thousands to forgo one of man's earliest innovations and feast exclusively on raw sprouted grains, raw nuts and crunchy carrot sticks. Although Wigmore's own life was cut short when she died in a fire in Boston in 1994 at age 85, her legacy lives on through a number of foundations, including the Hippocrates Health Institute she started in 1956 in West Palm Beach, Fla.

Although it may be easy to sneer at the most ardent adherents of "Raw Foodism," Wigmore's atavistic philosophy has influenced how most mainstream Americans eat and think about eating. We may prefer a sizzling sauté of veggies over Wigmore's astonishingly bland recipes, but it's hard to dismiss that lingering sensation that raw veggies might just be healthier for us.

Over the years, scientists have also had trouble dismissing the Raw Foodists. Proponents of raw cuisine like to point out that cooking breaks down a number of beneficial enzymes and vitamins, but critics note that stomach acid inactivates enzymes anyway, and moderate cooking can also help release other nutrients—such as a tomato's lycopene (an antioxidant with potential health benefits) or folic acid and beta-carotene from spinach. The fact is that, in general, the mechanics of how our digestive systems break down solid foods and reap their benefits are poorly understood.

The U.S. Food and Drug Administration's nutrition label on the back of that package of Planters peanuts is strictly based on chemical analysis of the nuts, and it doesn't tell you what fraction of those heart-healthy monounsaturated fats your body actually absorbs. Since 2004 two European research teams have sought to fill that gap by simulating the stomach in vitro with a kind of robo-stomach. And now Paul Singh, at the University of California, Davis's Department of Food Science & Technology, has taken the project to the digital realm to simulate digestion "in silico".

One afternoon in October, Singh pulled up a graphic video on his computer monitor in his office. A glistening pink mass that appears to have a clenched mouth was violently gurgling and contracting like the parasitic monster from the first Alien film. This was no parasite but a rare view of the inside of a human stomach as it performed rhythmic peristalsis, crushing and churning solid foods into particles one tenth of an inch (2.5 millimeters) in diameter. Exactly what these particles look like after being chomped by our teeth and churned by our stomachs is key to understanding what happens when they finally slip though the pyloric valve and into the small intestine where nutrients are absorbed. For the most part, this process has been invisible to scientists like Singh. After all, we can only look inside empty stomachs, because mushed up food would cloud the view. "How do we know what is really going on?" he asks.

With a two-year, $300,000 grant from the U.S. Department of Agriculture, Singh and his postdoctoral student Fanbin Kong, have built a 3-D stomach on their computer. Their virtual stomach is split into a mesh of 281,602 squares; they use fluid dynamics to calculate how the rolling waves of contraction agitate the gastric acid inside it. The researchers can then place virtual particles of food inside—each with its own physical properties—and simulate how long it takes for molecule-size nutrients to seep out.

"Each food has its own microstructure," Singh says, "Whether it is porous or compacted or its cells are held together through some binding agent.  Nutrients are embedded in that matrix, and unless the matrix breaks down to the point where those nutrients get released, they are going to stay embedded."

Singh, 60, who grew up in Punjab, India, is literally the rocket-scientist scientist of the food world. In his basement laboratory he proudly shows off the next multipurpose food processor he completed in 2007 for NASA's proposed manned Mars mission. Half a dozen books on his shelf are about the physics of heat transfer and another half dozen cover fluid dynamics. He is the author of the college textbook Introduction to Food Engineering, now in its third edition. After the 1993 scare set off by the deaths of four children who had eaten undercooked hamburger patties from a Jack-in-the-Box restaurant, he helped the fast-food industry with a computational model of hamburgers cooking on fast-food grills. Most recently, he has applied for a patent for a plastic clamshell package that will help strawberry growers cool down their fruits after harvest, a critical step in keeping strawberries fresh.

Not one to get lost in his mathematical universe, Singh complements his computation with laboratory studies that uses a mechanical stomach that he designed, which looks like a heavily instrumented ice cream churner. In an experiment published last year in the Journal of Food Science, Singh took raw and boiled cubes of carrots, 0.2 inch (six millimeters) wide, and placed them inside this contraption, which was inspired by similar equipment used by the pharmaceutical industry to study how drugs dissolve.

After soaking a carrot cube in simulated saliva and shaking it for 30 seconds, it was suspended inside a spinning chamber filled with gastric acid (maintained at body temperature) and plastic beads, which simulate the shearing action of other food particles. The scientists then recorded the forces on the carrot and periodically weighed it to measure how much had dissolved. The cooked carrot cube took just 20 minutes to be reduced to 50 percent of its original mass, but the raw one took a full hour. "Mom was right when she said you've got to chew your food well," Singh says, suggesting that if you're sticking to raw food you better be prepared to chew.

Meanwhile, researchers at the Institute of Food Research in Norwich, England, have built The Model Gut, a software-controlled in vitro system digestive system to study how carrots, meat, almonds and a host of other foods break down in the digestive system. Although almonds contain about 55 percent fat, lead researcher Giusy Mandalari, a biologist, says that  humans absorb less than half of that largely because the oils in almonds are stored behind a tough cell wall that must be broken for our bodies to absorb them. Much of the nutritional content of almonds serves as a "prebiotic," meaning that it supports beneficial microbial communities in our large intestines. When the group compared natural almonds to blanched almonds, which have undergone a heat treatment to remove their skins, they found that blanched almonds release slightly greater amounts of nutrients.

Marion Nestle, a nutritionist at New York University, said she found these recent results "surprising," and noted that if almonds and raw foods are really so prebiotic then you would experience some intestinal discomfort. But after a moment of consideration, she recalled a recent trip to Rancho La Puerta in Mexico, a semivegetarian resort known for serving large amounts of salads and other raw vegetables. "One of the big jokes in camp," she says, "is everyone is passing an enormous amount of gas."