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

UNIVERSITY PARK, Pa.—Marlene Moskowitz unscrews the cap from an amber vial. Within moments, a roasty scent permeates this food science laboratory at Pennsylvania State University, conjuring in my mind my local bakery in the predawn hours as baguette loaves—golden-brown, crusty and warm—are taken out of massive ovens on rolling steel carts. The aromatic teardrop in her vial was extracted from the crust of a white bread loaf a month earlier and is a crucial part of an experiment that could overturn a tightly held belief about the Maillard reaction, one of the key chemical responses that occurs during cooking. Moskowitz, a grad student in food science, and her faculty advisor Devin Peterson, are trying to figure out why white and whole wheat bread smell, and taste, so different from each other when baked. "We bake things but what happens to them?" Peterson says, referring to the cryptic chemistry of cooking. "Nobody understands."

Slide Show: A look inside the Penn State lab

Peterson, 36, who arrived at Penn State in 2002, had just completed his dissertation and was busy churning out related papers on the aroma in fresh and heated butter when a colleague dropped an article on his desk about phenols: those ring-shaped organic compounds best known for imbuing wine with its taste, color and health benefits, but which are also found in cocoa and wheat bran. As Peterson gazed at the phenol's ring, he began to think about its connection to the Maillard reaction, which causes the browning of bread and the flavor of caramel.

Neither proteins nor sugars have a characteristic smell of their own. But when they are heated together they produce thousands of flavor compounds as a result of this Maillard reaction. Peterson realized that small amounts of phenols had the potential to hijack this process and alter flavor chemistry. The only problem is that no one had really explored the thousands of chemicals that spring from the reaction. "What are these molecules," he wondered, "and why are they being modulated?"

A few days later, he went into his lab and set up a simple model reaction. Just as a theoretical physicist might assume Earth to be a perfect sphere, for Peterson a loaf of bread became one sugar and one protein. He heated the two compounds, filling his laboratory with the odor of pyrazines, a toastlike scent tempered with a hint of chocolate. But when he added phenol to the mix, the pyrazine aroma practically disappeared.

"It was one of those 'wow' moments," Peterson says. He began applying for grants to fund further research. The U.S. Department of Agriculture (USDA) nominated him for a Presidential Early Career Award to study the Maillard reaction, giving him a research grant of $420,000 on top of $280,000 he received from industry. In 2005 he shook then President George W. Bush's hand during a visit to the White House with other awardees.

The model chemistry reactions could only take him so far, however, so he dug into real products. First, his team looked at improving the flavor of ultra high temperature (UHT) milk, which is common in Europe and heated to a higher temperature than U.S. pasteurized milk to effectively eliminate bacteria. Because it is sterilized, UHT milk does not require refrigeration until it is opened, so it can be kept on store and kitchen shelves, but Peterson says the Maillard reaction gives it a cooked flavor that U.S. consumers won't accept. He and a graduate student took phenolic compounds from grapes and cocoa and added them to the UHT milk before processing it. The two versions—the UHT and pasteurized—were indistinguishable. Penn State has since applied for a patent on the process.

Now, Peterson and Moskowitz are challenging the dogma about what makes whole grain breads bitter and, consequently, less acceptable than processed white bread to U.S. consumers. In spite of its current vogue among the health-conscious, whole wheat flour sales are not rising as rapidly as once anticipated and even declined slightly in 2007 to just 3.9 percent of the total U.S. flour market. "My daughter is five" years old, Peterson says, "and I'm having a problem getting her to eat whole grain bread."

He's not the only one. A study conducted by flour-maker ConAgra and the University of Minnesota found that school-age children ate more of just about anything—pizza, breadsticks or tortillas—when they were made from refined rather than whole grain wheat flour. According to Elizabeth Arndt, ConAgra's manager of research and development, the consensus in the industry is that whole grain flour's flavor is a necessary evil: the health benefits of wheat are contained in the high-fiber bran, which is also loaded with a bitter-tasting phenol called ferulic acid, which acts as a crosslink in plant cell walls. The darker the bread, the more fiber it has, and the more bitter it is. ConAgra has started using a winter wheat in its Ultragrain whole grain flour, which is lighter in color and tasty enough to fool those same schoolchildren into thinking it is the refined variety.

But Peterson sees Ultragrain as an incomplete measure and thinks there's another, more fundamental solution to the bitterness problem that would work for any flour type. "The amounts of phenols are very low—and too low, I think, to make an impact," he says of the ferulic acid in bran, "The amount that's there—if I were to put it in water, I would find no bitterness." Instead, he says the phenols may interfere with the Maillard reaction, stunting the development of bread aromas, and triggering the production of many more compounds that are bitter on the tongue.

To test this idea, Moskowitz runs her vials of bread extract through what she calls "a big fancy oven." As the extract heats up, individual odors become airborne and pass through a threadlike tube, nearly 100 feet (30 meters) long. The instrument, called a gas chromatograph, measures the intensity of these aromas as they rise from the liquid and create the gas mixture known as the "headspace." Meanwhile Moskowitz places a tube up her nose and writes down her experiences over 45-minute sittings. Her lab notes are filled with columns of visceral, one-word descriptions: puke, glue, latex, nutty, onion, popcorn and butter.

"I wouldn't expect to smell mushrooms, dirt and cucumber," she says, "but when it comes together it smells like bread." So far, her lists for white and wheat contain the same subjective scent descriptions, but she says she has to dilute the extract to compare their intensities.

At the same time, Peterson tries to home in on the development of bitterness. He pulls up a graph that looks like a roller coaster with eight humps. In an experiment he ran weeks earlier, he yanked all the phenols from the whole wheat crust extract, and these eight humps represent the important flavor components left behind. He isolated each of these fractions, turned them into a powder, and tasted them.

"It's bitter," he says of fraction 4. "There are a couple others in here that have what I call a mouth-coating astringency, and they just stick to your tongue." There can be anywhere from 10 to 100 chemicals that make up each of these humps, and he'll have to partition them again to pinpoint the exact chemical. One thing is already clear, he says, "Bitterness is not coming solely from phenolic compounds...90 percent of it is coming from other molecules generated during thermal processing."

ConAgra's Arndt welcomes the new research and believes it could have wide-ranging implications in the food industry. "Anything we can do to make whole grain more universally acceptable to consumers," she says, "is a good thing."

Peterson compares his rigorous approach to targeted drug discovery, but rejects the suggestion that tinkering with flavors is somehow unnatural.

"We live in a technological world," he says. "Why would you think we shouldn't investigate food?" Reducing bitterness could be as simple as processing the dough under a different level of acidity using all-natural ingredients, he notes, adding that chemistry is part of everyday life.  "Many molecules have never been identified," he says, "but we've been consuming them for 20,000 years."