Nothing quite showcases the industrial bounty of California agriculture like a vast field of tomatoes baking in the August sun. A rich, dusky red emanates from beneath the curled, dying leaves. A nearly two-story-tall mechanical harvester run by the Morning Star tomato-processing company clatters through the Sacramento Valley field. As the machine hums along at about three miles per hour, it uproots two rows of plants and lays them on a belt that conveys them to the top of the harvester, where the vines are sucked through a shredder and blown back onto the field as the tomatoes cascade onto other belts. Electronic eyes send signals to plastic fingers that pop out anything not red or green. Dirt clods, last year's squash and the errant toad and mouse tumble to the ground. The ripe fruit is funneled into a tandem trailer. In ten minutes, the machine gathers more than 22,000 pounds of Roma-type processing tomatoes.

I get into a pickup truck with Cameron Tattam, a Morning Star supervisor, and we follow a semitractor that hooks up to the trailer, pulls out of the field and then barrels down Interstate 5 to a Morning Star cannery outside the town of Williams. This 120-acre facility is the largest of its type in the world. During the three months of the local harvest, it handles more than 1.2 million pounds of tomatoes every hour. The tomatoes I just saw getting picked are washed down a stainless steel flume and plunged into a 210-degree cooker. The heat and pressure blow them apart. After passing through evaporators and cooling pipes, they will end up three hours later as sterile-packed tomato paste in 3,000-pound boxes. For the next two weeks, the facility will produce nothing but paste that is destined to become Heinz ketchup. Among Morning Star's other large customers are Pizza Hut, Campbell's Soup and Unilever, maker of Ragu.

Processing tomatoes—condensed or canned—make up 75 percent of the tomatoes that Americans eat. Farmers think of them as an entirely different crop than fresh-market tomatoes. The variety that Tattam and I watched being harvested is a hybrid called Heinz 2401. It was bred to maximize yield, with thick-skinned, fleshy fruit that ripen simultaneously so they can be picked all at once and withstand a machine's rough handling. Its genes maximize the conversion of solar rays into sugars and solids. These tomatoes have thin cavities, or locules, where the seeds and juices—and many flavors—are stored. There is little point in having a lot of volatile flavors in a processing tomato because cooking boils them off, and, besides, much of the flavor of ketchup and tomato sauce comes from whatever the tomatoes are mixed with. The Heinz 2401 is also bred for resistance to tomato pathogens, of which there are many: beetles and nematodes, fungi such as fusarium and verticillium, and viruses such as yellow leaf curl and spotted wilt, which are carried in the wind, the soil or the mouths of pests such as whitefly and thrips. Because it doesn't really matter what processing tomatoes look like, they require fewer applications of pesticides than do fresh-market varieties. The Romas I saw being harvested had been sprayed only once.

There's something a bit brutal about the production methods exemplified by Morning Star's operations, which are all about maximizing yield and efficiency. But the industrial tomato has its place, even if foodies turn up their noses at it. "You want us to be out there with hoes, like in a third-world nation?" Tattam says. "How else are you going to feed 350 million people?"

The next day I drive 30 miles south to the live-oak-shaded compound of Full Belly Farm, a small operation in the Capay Valley. An organic farm that grows up to 100 crops, including 25 tomato varieties, it couldn't be more different from Morning Star. Full Belly's farmers fertilize their fields with dung from their own sheep, herded into the fields after harvest. A bank of trees and shrubs by the creek harbors bats and birds that feast on insects—pest control. The farm relies as much as possible on such predators as well as good mulch. When those measures fail, it turns to organic controls, including garlic, cedar and clove oils. "Our goal is to somehow take the farm, which is an artificial system, and mimic the systems you see in the natural world," says partner Andrew Brait, 42, whose heirloom tomatoes are one of the farm's biggest sources of profit.

Brait has staked his heirloom tomatoes in a patch of uneven bottomland alongside gorgeous heirloom peppers, eggplants and squash. But in the tomato patch, things don't look quite so good. Tobacco mosaic virus, long ago controlled by breeding resistance into commercial tomatoes, has attacked the vines, causing the leaves to shrivel and some of the fruit to abort while tiny. The plants are still growing, and Brait will be happy if they yield as little as five tons to the acre, or about one-eighth of a Morning Star harvest from one acre. Chic Bay Area stores and restaurants such as the Zuni Café and Chez Panisse cheerfully shell out $2.50 a pound for Brait's heirloom tomatoes. (Last year Morning Star reportedly paid farmers the equivalent of 3 cents a pound.) In the farm's packinghouse, Brait feeds me vine-ripened Green Zebras, verdigris-and-orange-mottled Marvel Stripes and Zapotec Pinks, wrinkled as a bulldog's muzzle (the breeder term is "catfaced"). I chew on his tiny Sun Gold cherry tomatoes and get a sour blast, followed by a burst of sweetness that deposits a complex honey musk on my upper palate.

In recent years, heirloom tomatoes have become a mainstay of gourmet culture, a testament to authenticity and a strike against the complaint, voiced fervently by Boston Globe columnist Ellen Goodman, that the everyday tomato "has had its hide toughened" and "has been pushed around, squared, even gassed to death," every year becoming "less of a fruit and more of a metaphor."

But let us not be tomato snobs. Let us acknowledge that the pleasure of the heirloom itself is as much metaphorical as real. The heirloom's huge variety of shapes and colors and flavors offers a reassuring sense of diversity in a cookie-cutter world; backyard cultivation gives the city dweller or suburbanite an almost spiritual connection to an ancestral agrarian past. I'm aware of no evidence that heirlooms make you healthier than hybrid tomatoes. And the cheap, mass-produced processing tomato yields more concentrated nutrients than the fresh-market varieties that are picked green. "There's more antioxidant activity in a tablespoon of paste than a box of fresh tomatoes," says Kanti Rawal of San Leandro, California, who has no reason to exaggerate—he's a breeder of fresh-market varieties. Not only that, antioxidant tomato micronutrients such as lycopene and beta carotene are more easily absorbed when consumed with cooking oil, according to some research. Yes, Virginia, pizza is good for you.

Even in the fresh-market world, not everyone is convinced that heirlooms taste best. "What is good flavor?" says Teresa Bunn, a breeder at Seminis, a seed company owned by Monsanto. "Everyone has a different perception. You can do things to boost sugars and acids, but people want a different balance. It's hard to get people to agree on the same thing." There's also the issue of how appearance and "mouth feel" affect the perception of tomato quality. "If you're blindfolded, an orange tomato may taste good, but a lot of people won't buy an orange tomato," Bunn says. Most eaters mistrust mealy tomatoes, even if they are flavorful. Still, heirloom tomatoes do tend to have more intense flavors, Bunn says. "You can think of a tomato as a factory, with each leaf a worker. Heirlooms have fewer fruit and more factory. On the commercial side, farmers are paid for yield. They want as many fruit as they can get. A lot of times it's perceived that heirlooms are better tasting, but it could be that they just pack more flavor into them. And just because it's an heirloom doesn't mean it's a good tomato." Flavor is in the mouth of the taster. "I can't stand the flavor of Brandywines," says John "Jay" W. Scott, a well-known Florida tomato breeder, voicing apostasy about a choice heirloom variety.

A year ago, I set out to learn how the world's second most popular "vegetable" (the potato is No. 1) had connived its way into the major cuisines of the world. Perhaps more than any other food, tomatoes inspire passion. Whether it's outrage over the "cardboard" supermarket tomato, pride in the recipe that great-grandma brought over from the old country, or the mystique of that homegrown tomato vine, the smell and feel and even the texture of tomatoes manage to get under almost everyone's skin. Still, despite what the organic-obsessed Cassandras might have us believe, the tomato is thriving, even at Safeway. The recent nationwide alarm after hundreds of consumers were sickened after eating fresh tomatoes contaminated by salmonella bacteria (see opposite page) underscored consumers' intense attachment to the fruit. "Business is down 50 percent," Bob Pizza, chief executive of What a Tomato Produce Company, told me at the San Francisco Wholesale Produce Market. "But sales will come back. People can't do without their tomatoes."

The tomato, Solanum lycopersicum (formerly Lycopersicon esculentum), is a peculiarly flavored species of the nightshade family, which also includes potatoes, eggplants, peppers and the deadly belladonna. It is a product of what is known as the Columbian exchange, that unequal sharing of genetic material following the conquest of the New World. The Old World got tomatoes, potatoes, chocolate, squash, corn and peppers. The new one got coffee, sugar cane and cotton—and the African slaves to cultivate them—as well as smallpox, measles and other previously unknown contagious diseases that devastated the native population.

Many wild tomato types grow throughout the Andes from Chile to Colombia, but the plant was apparently first cultivated in Mexico by the Maya, the Nahua and others. Marvelous accounts of tomato diversity are recorded in the Florentine Codex. According to that collection of ancient Mexican lore begun in the 1540s by the Spanish priest Bernardino de Sahagún, vendors sold "large tomatoes, small tomatoes, and leaf tomatoes" as well as "large serpent tomatoes" and "nipple-shaped tomatoes" at the Nahua market at Tlatelolco, in what is now downtown Mexico City. They were "quite yellow, red, very red, quite ruddy, ruddy, bright red, reddish" and "rosy-dawn colored." Some were bitter tomatoes "which scratch one's throat, which make one's saliva smack, make one's saliva flow; those which burn the throat."

The Spanish conquest took the tomato first to Spain in the early 16th century, and from there to the Middle East and Italy, though tomato sauce would not become an Italian mainstay until the late 18th century. Tomatoes were long thought to be poisonous, perhaps because of the alkaline flavor of the earliest cultivated iteration and their similarity to belladonna. Lore has it that Thomas Jefferson, who grew tomatoes at Monticello, helped destroy the poison myth by consuming his harvest. The tomato soon found its way onto American plates and even into tomato pills, an early dietary supplement craze. The tomato itself is a seed-bearing fruit, but the Supreme Court, noting its customary place in the meal, classified it as a vegetable in 1893, for the purpose of deciding which tariff to charge for imports.

In the early 20th century, Heinz ketchup and Campbell's Soup drove U.S. tomato consumption. Because tomatoes are finicky—frequently attacked by viruses, fungi and insects—large-scale tomato farming took root in California, where the dry summers minimize pestilence. (Because water fosters growth of fungi and mold, the cardinal rule of tomato watering is: Don't get their heads wet.) A dramatic change in the very nature of the tomato came in the late 1950s, when Jack Hanna, a plant breeder at the University of California at Davis, developed a hardy, tough-skinned tomato that could be more readily harvested by machines, then being developed in Michigan and California. Within a couple of decades, machines were gathering most of California's tomatoes.

The architect of the modern commercial tomato was Charles Rick, a University of California geneticist. In the early 1940s, Rick, studying the tomato's 12 chromosomes, made it a model for plant genetics. He also reached back into the fruit's past, making more than a dozen bioprospecting trips to Latin America to recover living wild relatives. There is scarcely a commercially produced tomato that didn't benefit from Rick's discoveries. The gene that makes such tomatoes easily fall off the vine, for instance, came from Solanum cheesmaniae, a species that Rick brought back from the Galápagos Islands. Resistances to worms, wilts and viruses were also found in Rick's menagerie of wild tomatoes.

Flavor, however, has not been a goal of most breeding programs. While importing traits like disease resistance, smaller locules, firmness and thicker fruit into the tomato genome, breeders undoubtedly removed genes influencing taste. In the past, many leading tomato breeders were indifferent to this fact.Today, things are different. Many farmers, responding to consumer demand, are delving into the tomato's preindustrial past to find the flavors of yesteryear.

Each September, a former restaurateur named Gary Ibsen holds TomatoFest, a celebration of the heirloom tomato outside Carmel, California. The definition of an heirloom is somewhat vague, but all are self-pollinators that have been bred true for 40 years or more. (By contrast, a commercial hybrid is a cross between two parents carefully chosen for notable traits, with the seeds produced by physically pollinating each flower by hand; tomato breeders contract out that painstaking task, mostly to companies in China, India and Southeast Asia.) At TomatoFest, about 3,000 people tasted 350 heirloom tomato varieties and various tomato-based dishes prepared by leading chefs. "I never cook with fresh tomatoes unless I can get heirlooms," Craig von Foerster, chef at the Post Ranch Inn in Big Sur, told me as he ladled out a mesmerizing Thai-spiced gazpacho made with Lemon Boy and Marvel Stripe tomatoes. David Poth, kitchen manager at Google corporate headquarters, in Mountain View, had had a hand in a triplet of sorbets made from Green Zebras, Brandywines—and salmon. Ah, California.

At the heirloom table, I saw that the Red Peaches looked leathery. The Russian Limes were yellow with nipples. The Black Cherries, Black Princes, Black Zebras and Black Russians had dark olive green skins with muddy orange shading. The big pink-striated Dinner Plate looked like a nectarine. The German Red Strawberry was indeed shaped like a giant strawberry. Green Sausages were French's Mustard yellow and lime green, and shaped like pickles. After an hour or so, I was experiencing what the experts call taste fatigue. And I was getting a stomachache.

Ibsen had named Clint Eastwood's Rowdy Red after his friend, the actor-director and former Carmel mayor. "It's a very sweet tomato," Ibsen said. A panel of vintners and chefs voted as its favorite the Paul Robeson—a large blackish purple beefsteak tomato named after the African-American singer and actor. But for me and several others, the champ was the small, leathery-looking Speckled Peach, a German-bred tomato that packs a wallop of tang and sweetness. "It reminds me of fruit," said Hannah Grogin, age 9, of Pebble Beach. Regina Greel, a hospital employee from Berkeley, said, "They taste melony, like peaches, but fruity, not tomato-y. Like a combination of a cantaloupe and a peach." Eureka, I thought: the perfect tomato.

Florida is the biggest supplier of winter fresh tomatoes for U.S. consumers, though Canada, where they're grown in greenhouses in the spring and winter, and Mexico are cutting into the Sunshine State's market. Tomato-growing in Florida is a tough business, because of, among other things, high humidity and frequent storms, which can wreak microbial havoc. "We see more diseases in a season than they do in California in a year," one expert says.

To get Florida tomatoes, which have traditionally been bred for size and durability, to Northern shoppers, the fruits are usually picked as hard and green as Granny Smith apples, packed in boxes, warehoused and exposed to controlled doses of ethylene gas, a ripening agent, so they turn red just in time for sale. Farmers often get a premium for big tomatoes. (On the day I visited the DiMare Inc. operation near Ruskin, Florida, the market was $14 for a 25-pound box of extra-large tomatoes, $10 for medium tomatoes.) The consumer consensus is that these tomatoes don't taste like much; 60 percent will end up in fast food, sliced thin for burgers and subs or chopped into the salsa that garnishes tacos and burritos. Along the way shippers and shoppers frequently refrigerate them—a no-no that ruins the texture and what little flavor they started with.

Some academic specialists are trying to improve the dispiriting state of the Florida tomato. Jay Scott, of the University of Florida's Gulf Coast Research and Education Center near Tampa, has contributed to the development of many tomato varieties found at supermarkets around the country. Seeds from a dwarf tomato he bred, the Micro-Tom, even flew on the space shuttle Endeavour in 2007 as part of an experiment to test the practicality of growing food on long-haul space missions. The flavor of tomatoes, Scott says, comes from sugars, acids and volatile chemicals. Photosynthesis generates sucrose, or table sugar, which is broken down into glucose and the sweeter fructose during ripening. The concentration and balance of glucose and fructose determine the degree of sweetness. Acidity comes mostly from citric and malic acid. "If you have a tomato without many acids, it may be bland or insipid. You need acid to go with the sweet," says Scott. "But if acids are too high, you can't perceive the sweet. So it's a balance. And it's better when both are high."

That's hard to achieve in a big tomato, though, because "you've maxed out the plant's ability to produce sugars and other flavors," says Harry Klee, a biochemist at the university's Gainesville campus. The subtleties of tomato flavor derive mainly from about 20 of the 400 volatile chemicals in the fruit's flesh and juice. Klee and his co-workers are using genetic engineering techniques to enhance some of those key volatiles to improve the flavor of commercial tomatoes. It's a peculiar task, this job of trying to make bland tomatoes taste good.

I visited Klee's laboratory to taste a fresh transgenic tomato that his colleague Denise Tieman had produced. Using a technique developed in the 1980s by Monsanto, Tieman and a graduate student endowed a tomato with a gene that enhances production of methylsalicylate, a compound better known as oil of wintergreen, a natural volatile component of tomatoes. Tieman fed me a slice of ripe tomato from one of the transgenic plants. It had a flavor that I associated, at some level, with freshness, but it was not particularly good. Tieman fed me another transgenic variety that had 50 to 100 times higher than normal levels of another volatile tomato flavor component, phenylacetaldehyde—the familiar rose oil odor of cheap perfume, bath soaps and detergents. The DNA containing this gene was recovered from Solanum pennellii, a tomato native to Peru. The smell was intense—and not pleasant. The tomato left an aftertaste of a lady's powder room on the roof of my mouth. "You wouldn't really want a tomato to taste like that," Tieman says. But like the wintergreen tomato, she added, "it proves that you can alter these flavors." If any of the transgenic tomatoes prove promising, Klee says, traditional breeding techniques might be developed to produce them, obviating concerns about eating a genetically engineered food.

Whether Klee and other flavoristas succeed or not, we can take comfort in the tomato's continuing, explosive diversity: the U.S. Department of Agriculture has a library of 5,000 seed varieties, and heirloom and hybrid seed producers promote thousands more varieties in their catalogs. Scott has developed a variety he thinks can challenge the heirlooms for flavor, at an affordable price, if only he can convince some Florida growers to plant it and pick it closer to ripeness. He calls it the Tasti-Lee. I haven't sampled it yet, but I'm growing some of Scott's seeds this summer, along with 12 different heirlooms, a yellow tomato from Siberia, wild cherry tomatoes from the mountains of Mexico and sugary-sweet grape tomatoes. It's fun, though I'm strictly an amateur. If they get moldy or eaten by bugs, I know I can find good ones at the farmer's market. With tomato growing, as in other walks of life, sometimes the professionals know more than we give them credit for.

Arthur Allen of Washington, D.C. is the author of Vaccine: The Controversial Story of Medicine’s Greatest Lifesaver. Photographer Ed Darack's next book is Victory Point.