regory Ziegler puts a small block of chocolate into a styrofoam bowl and sticks it into the microwave. Soon, a lovely sweet aroma spreads through the air, lending warmth to the otherwise bleak lab. Ziegler takes the bowl out of the microwave; it's filled with a thick, swirling liquid. "I'm rather unromantic when it comes to this," Ziegler says. He offers the chocolate to Melis Cakirer, a Penn State undergraduate in biochemistry, and to me. We each dip our fingers into it and taste. I grimace, then laugh: Cakirer looks as if she's just swallowed a goat, and a pretty bitter one at that. What we're tasting is unsweetened chocolate liquor, or pure cocoa in liquid form. "It's just fermented, roasted, ground cocoa beans," explains Ziegler, a food scientist at Penn State. He grins at Cakirer. "It's actually quite good, but it doesn't become real chocolate until you add the other two main ingredients: cocoa butter and sugar." (Also, vanilla is normally added for flavor, salt to cut the bitterness, and soy lecithin to make the texture smoother.) It only smells like chocolate.

"lavor," Cakirer had explained to me earlier, "is a combination of texture and aroma. Aroma's such a huge part of it." Cakirer — who looks more like an art student than a science student, with her dangling metal earrings and red thrift-store pea coat, "borrowed from a friend" — is working with Ziegler and Mark Guiltinan, a professor of horticulture, to trace the flavor of chocolate back to the DNA in the cacao plant.

"Most of your taste is smell," Cakirer says. "There's a whole language of smell: Green smells, brown smells, each means something different. A green smell could be the smell of cut grass, or a green apple. You see how these could have some of the same undertones, even though they're different? Just being able to describe a specific smell is a craft." Cakirer speaks with her hands, gesturing in little circles as if she's trying to conjure up a green or brown smell.

"There are lots of chemicals in the raw cacao bean that affect the flavor," she says. In fact, the raw bean actually tastes bitter; the flavor of chocolate emerges only after the beans have been fermented and roasted, so Cakirer is studying the flavor of chocolate before it even becomes chocolate.

A common misbelief about chocolate flavor is that the more chocolate liquor a chocolate contains, the better it is, Ziegler explains now, as if having 70 percent chocolate liquor will automatically make the candy taste rich and delicious. "But you can get some very disgusting chocolate liquor, so having 70 percent of that isn't going to make the chocolate better."

Ziegler gives us each a thin square of chocolate. We eat it thoughtfully, considering its flavor. I conclude that it's chocolate, and it tastes good.

Ziegler has a more advanced reading. "It has a slight raisiny aftertaste," he says. "It's very typical of the Latin American chocolates to have a slightly fruity flavor." He consults the box. "This one's made from a Venezuelan cocoa. It has that criollo flavor." There are three varieties of commercially grown cacao plants; one of them is criollo, grown in Venezuela, Central America, Java, and the West Indies. It's normally used in very fine chocolates, and has a mild flavor, which can be floral, fruity, or spicy. The other types are forastero, a stronger flavor, which comes from a hardier, higher-yielding plant; and trinitario, a cross between the other two, with the delicate flavor of the criollo and the hardiness of the forastero plant. Commercially grown cacao used to be more diverse, but gradually fewer and fewer varieties got planted. "People planted those that have a higher yield," explains Ziegler. "The same complaint exists with corn and potato. The number of sources, both geographically and in terms of variety, has diminished."

Ziegler gives us Valrhona, a French chocolate made with a high proportion of criollo beans; Ziegler describes it as "not sugar sweet, but flower sweet," and once Ziegler puts it into words, I can taste the "flower sweet," just as I could taste the "raisiny aftertaste." We try a Swiss chocolate that's a little sweeter, and then one that Ziegler says is Cakirer's favorite. It's smooth, mild, and very sweet. "It's Nestle's," says Ziegler.

The last is a chocolate called Jacques. It has a coconut taste, which I notice after Ziegler points it out. He considers the flavor for a few more seconds, then says suddenly, "The aftertaste tastes like goat." It does taste rank; I think of smelly, sweaty socks, or the tepid, slightly sour milk that came with school lunches in elementary school.

Ziegler goes to a three-ringed binder filled with pages of chocolate bar wrappers from all over the world, neatly laid out inside clear plastic page covers. He flips a few pages, and then pulls out the Jacques wrapper. "See this?" He points to the milk listed in the ingredients. "Butyric acid." Butyric acid comes from the milk fats in the chocolate. In a process called lipolysis, the fatty acids in the milk decompose, resulting in a rancid, or "goaty" taste. Hershey's purposefully puts their chocolate through controlled lipolysis, giving it that unique flavor. Because of this, most Europeans don't like Hershey's chocolate — but Americans do.

uiltinan, the horticulturist, is working on making cacao a stronger crop, improving its yields and disease resistance — without making the mistakes of earlier plant breeders. Both Ziegler and Cakirer cite the famous example of the tomato: Tomatoes were bred to have a high content of solids, so there would be less water to boil away when making products like ketchup. They were bred to be firmer, so they'd be easier to pick with an automatic picker. They were even bred for shape, to be easier to pack into boxes. "When people only consider the economic aspects, you get these little tennis balls without very good flavor," says Ziegler.

To avoid a similarly tasteless chocolate, Guiltinan gave Cakirer the assignment of mapping chocolate flavor. "Most breeders don't really think about flavor," says Guiltinan. "That's why Melis's project is important."

"I had to find the parts of the DNA that control the flavor," Cakirer explains. "On a genetic level, no one knows completely how the flavor of cocoa develops. Is the flavor influenced more from the tree itself, or from the fermentation process, or the roasting? We need to know this." Researchers at the Botanisches Institut in Germany have found a seed-storage protein called "7S Vicilin" that seems to be key. The researchers extracted the 7S from the raw cacao bean, "chomped it up" with enzymes, then put it onto a petri dish and roasted it with sugar. The result? It smelled like chocolate.

"The experiment implies that the 7S is the source for a lot of the flavors in chocolate," Cakirer says. "It probably controls most of the aroma, for example." Cakirer hypothesizes that the 7S protein is different in different varieties of cacao, and therefore explains the different flavors of chocolate.

Cakirer and I meet late one Sunday night so she can better explain the concept to me. She brings a pile of charts and drawings she made herself. She's wearing her pajamas, and she drinks — what else? — hot chocolate. "Mmm," she says, sipping her drink. "OK, let's start."

With a banana or an orange, Cakirer says, you can taste the flavor as soon as you pick it off the tree. The raw cacao bean, on the other hand, doesn't have a typical cocoa flavor at first. The amino acids in the proteins are the "flavor pre-cursors," meaning they give rise to flavor compounds after fermentation and roasting. During fermentation of the beans, enzymes "chew" on the proteins, freeing the amino acids. Next, in the roasting process, these freed amino acids combine with sugars and other elements to create compounds which contribute to the flavor. For instance, the sulfur-containing amino acid methionine undergoes a reaction to produce 3-methiopro-panal, which has a sulfurous character. The amino acid leucine produces isovaleraldehyde, which has a fruity character.

As Guiltinan had pointed out to me earlier, both the sequence and the amount of the amino acids could affect the flavor of chocolate, and both are determined by the plant's DNA. "A single amino acid change could change everything," he'd said. "As things are being broken down, you could get different reactions, depending on what the free ends of the amino acids are. It's like a little tape going through a machine. The sequence of the DNA decides the sequence of the amino acids," which in turn determines how these amino acids are broken down.

Various conditions of fermentation and roasting, such as temperature, acidity, and duration, can alter the resulting flavor of the bean. All of these elements add to the difficulty of mapping the genome for flavor. Even the way the chocolate melts in your mouth affects the flavor, Guiltinan said, as well as the aromas you smell as you're eating it.

The 7S protein is a good place to start mapping the flavor, Guiltinan had said, because it's highly abundant. Yet, Cakirer adds now, finishing off her hot chocolate in one long sip, each cocoa bean contains about 500 aromatic compounds that might be involved in flavor; the 7S does not produce all of them. "There must be many more proteins involved in the overall flavor of cocoa. I'm sure of it," she says, "because the flavor of chocolate's really complex."

o see where all of this chocolate flavor comes from, Cakirer and I visit Penn State's greenhouses. When Cakirer first told me about the chocolate greenhouse, she described it as being "so great. The mist that comes out — it's so thick, it's like you can almost feel it between your fingertips. You'll be so inspired to write about it."

The greenhouses simulate the hot tropical environments where cacao is grown. A creamy, almost sweet aroma pervades the air. "It almost smells like cocoa butter," says Cakirer. Dozens of green-leafed cacao trees crowd the room: gnarled, knobby trees with long branches; bushy trees with thick, dark masses of leaves; small baby trees with thin, green branches and delicate leaves. The bean pods, according to a photo Guiltinan showed in a lecture, have a thick, melon skin. They're football-shaped, and come in just about every color and texture one could imagine: red, yellow, green, beige, maroon; smooth-skinned, rough, or bumpy.

Right now, Cakirer is determined to find a pod. She walks carefully through the small, quasi-jungles of chocolate trees, clearing passageways, gently bending branches in order to peer up the neck of a tree, where the pods grow. She stops every so often to explain something: "The really thin, light-green leaves you see? Those aren't weaker, or abnormal in relation to the thicker, greener leaves. They're just new," she says. "Hey! Found one!" Cakirer points out a seed pod: It's small, about the size of a fist, with a thick beige shell. Each pod contains 20 to 30 seeds, Cakirer explains, and each can express its own unique flavor: some might be sweeter, others more acidic, while others can be more bitter, all coming from the same pod. "Every bean represents a different plant," says Cakirer. "They're like different kids, different babies, even though they all come from the same mom."

As Guiltinan had explained, "The DNA gets shuffled like a deck of cards, and you get the different combinations. One parent could have a good flavor, and the other a bad flavor, and so the children could have one parent's flavor, or they could be in-between, a combination of the two flavors. That's why you make maps of the DNA, to figure out where these flavors come from." In order to figure out what flavors are produced by the 7S protein, Cakirer will extract the 7S from raw cacao beans, ferment it, and roast it, like the experiment done at the Botanisches Institut. The different smells may indicate the compounds in the different flavors of cocoa (e.g. a fruity smell would indicate ester), and will make it possible for Cakirer to trace the flavor back to the DNA.

Cakirer plans to continue studying the flavor of chocolate as a graduate student at Penn State. For her career, she wants to work in flavor chemistry. Recently, she visited a flavor house, which is where she'd eventually like to work. "I had always thought I was romanticizing it," she says, "but the flavor chemists, they hang onto it — the romanticizing. They thought of themselves as having an art. I ate lunch with them, and they brought it up every ten minutes, how flavor chemistry is really a craft."

We walk out of the greenhouse into the brisk, cold air outside. "When I was in high school," says Cakirer, "I was really good at visual arts, in a tenth-grade kind of way. I didn't talk much, but people kind of knew me by my art." Whenever she explains her project, Cakirer sketches ribbons and ribbons of DNA, long chains of ATCGCTCAGCGA. "I like to draw out the molecules," she says.

"I like the way it looks on paper, the visualness of it, the chains, the molecules, the arrows, getting a chemical reaction. It's kind of like sorcery. You can predict stuff, you can make stuff out of stuff that wasn't there before.

"I remember this chemistry teacher and this physics teacher in my high school," she says. "They were having some kind of contest, growing hot peppers to see which one of them could grow the hottest pepper. I always thought, Wow, it's so cool that a chemistry teacher could know that stuff, that maybe he'd know how to grow a hotter pepper because he knew so much about chemistry.

"It's just so cool that you could understand something like that, like flavor, with chemistry. But really, no matter how many charts and graphs you want to make up for it, the core of it is still the human nose, and the human sense of taste. It will always have a human aspect."

Melis Cakirer graduated in May 2000 with a B.S. and honors in biochemistry and molecular biology from the Eberly College of Science and the Schreyer Honors College. Her advisers are Mark Guiltinan, Ph.D., associate professor of horticulture in the College of Agricultural Sciences, 114 Tyson Bldg., University Park, PA 16802; 814-863-7957; mjg9@psu.edu; and Gregory Ziegler, Ph.D., associate professor of food science, 116 Borland Lab; 863-6132; grz1@psu.edu. Penn State's Cocoa, Chocolate, and Confectionary Research Group is funded by the American Cocoa Research Institute. Writer Julie Nariman graduated in May 2000 with degrees in film/video and comparative literature.