IT WAS SPRINGTIME IN THE SKAGIT VALLEY when the private jet carrying Chipotle CEO Steve Ells touched down at the airfield in Burlington, Washington. From there, Ells and four chefs from the fast-casual Mexican chain headed for a low-slung green building on the edge of nearby Mount Vernon, where the 30,000-person town starts giving way to farmland. 

Here, at Washington State University’s Mount Vernon Research and Extension Unit, the group piled into an unlikely room known as the Bread Lab—barely 600 square feet and divided down the middle like a freshman dorm room inhabited by roommates with wildly different majors. 

Along the black countertops on the right side sat bulky pieces of laboratory equipment, machines that measure dough’s elasticity and extensibility, its starch levels and torque, how much water it can absorb and its tolerance to mixing.

The other half of the room was essentially a baker’s workshop. Various mixers and flour mills, even a grain flaker crowded counters made of butcher block; a wire rack bore stacks of metal mixing bowls and bag upon bag of flour. Clear plastic tubs filled with wheat kernels commanded any available shelf space, each container’s contents identified by a scribble of ink on tape. Purple Prairie. Druchamp. Sonora. Bobtail. Diva.

The trio that received Ells and his chefs during that April 15, 2014 meeting consisted of Jonathan Bethony, the Bread Lab’s resident baker, PhD student Bethany Econopouly, and Dr. Stephen Jones, director of the lab and the guy whose unlikely career shift hatched this project.

After some introductory chat about dough and what, exactly, the Bread Lab does, the Chipotle CEO leaned against the four-deck steam-injected hearth oven in the corner and asked his hosts, “You interested in tortillas?” 

Nobody had thought much about tortillas. Ells was unfazed. 

“I serve a million a day. Are you interested now?”

He laid out his request: a 100 percent whole wheat tortilla that Chipotle customers would actually want to eat. It should contain just four ingredients: water, flour, salt, and a little bit of oil.

The last time Dr. Jones took a meeting about an ambitious corporate project, it did not end well. But here was a challenge with a potentially enormous social impact. As Jones later put it, “If Chipotle can make it work for a million people a day, why can’t other people? Why can’t schools?” Technically Chipotle serves closer to 800,000 daily tortillas, but a million is a far more romantic figure.

Within two days, the company was helping fund Econopouly’s doctoral studies in wheat breeding. Soon a tortilla warmer, the kind found in Chipotle locations, was on its way to the lab. 

Stephen Jones, 58, founded the Bread Lab as a sort of scientific go-between for farmers and bakers; no surprise he’s a guy who looks equally at home in a laboratory or damp wheat field. With his six-foot five-inch bearing and black-framed glasses, he has an authentically professorial air and looks convincing in a lab coat, though he favors plaid shirts, fleece vests, and baseball caps. Aside from some childhood baking sessions with his Polish grandmother, nothing in his upbringing in Cupertino, on the Bay Area’s south end, suggested he might one day reimagine one of America’s most symbolic foods. 

He graduated from high school around the same time two other guys named Steve—Jobs and Wozniak—were founding a computer company in a garage just 10 miles away. Jones had a part-time job mowing the greens at a local golf course. “I thought that was agronomy,” he recalls of his mowing days. He enrolled at California State University at Chico because of its agronomy program, “and pretty soon I’m farming wheat and beans and I’m waiting for the lawn and turf to come into play, but it never did.” 

By the time Jones figured out his mistake, he was already enamored with wheat. He grew it on a five-acre student plot along with beans and even a bit of marijuana for good measure. Kind bud aside, what hooked him was helping farmers up their yields, and thus their profits. After earning a PhD in genetics at UC Davis, Jones found his way to Washington State University, heading up the wheat breeding program in Pullman. 

The grain that waves over Eastern Washington is known as commodity wheat. Geneticists like Jones breed it to fit a tightly prescribed set of characteristics: resist disease, yield large quantities, possess various characteristics that make for good flour.It’s aggressively uniform.

In his recent book The Third Plate, chef and author Dan Barber writes of a fateful meeting in 1997, when Jones’s department chair called him in to sit with the associate dean and a few guys from Monsanto, who came bearing an exciting opportunity: Create for the agrochemical company a new strain of wheat, one able to withstand doses of Roundup, Monsanto’s signature herbicide. Both Jones and the university stood to make a lot of money in royalties.

But Jones took issue with Monsanto patenting this seed; farmers would have to pay each year to resow something developed with taxpayer funds. “I recoiled from the idea of a company owning a university seed,” is how he explains it.

Spurning such a prominent project ultimately put Jones at odds with his bosses and large-scale wheat growers who feared losing out to farms in other states. So in 2008, the head of WSU’s esteemed wheat-breeding program packed up and headed west across the state, taking a position at his university’s sleepy Mount Vernon research center, serving mostly small and medium size farms. In his book Barber likened Jones’s self-inflicted demotion to “leaving a vice president position at General Motors in Detroit to run one of the branch offices in Kalamazoo.”

He reported for duty with every intention of turning his attention to the valley’s cabbage or cucumber or tulip crops. Jones was done with wheat.

Wheat wasn’t done with him. In the Skagit Valley, grain isn’t the main event, but farmers do sow it in between crops of tulips or vegetables to replenish the soil and prevent weeds or diseases. It keeps fields healthy for other crops—the wheat is actually cheaper than fertilizer. Farmers usually sell it at a loss overseas. 

The Bread Lab’s mission began here. Jones asked these farmers: What if, instead of growing the uniform commodity wheat, they planted different strains? Ones with too much personality and flavor (not to mention nutrients) for the international commodity market. In turn, he promised to create demand—and a higher selling price.
 

Jones and his Bread Lab were challenging 150 years of commercial milling and baking in America. Within each kernel of wheat, virtually all the healthy stuff—the vitamins, the fiber, the iron, and essential oils—reside in either the hull (aka the bran) or the germ (the embryo within). The remainder of each kernel is a fluffy white substance known by the decidedly unappetizing term endosperm. Jones is fond of saying that this part of the wheat kernel has the nutritional value of a Q-tip. “And it looks like a Q-tip.”

Since the 1800s, commercial mills have ground these kernels into flour, then sloughed off the hull and germ, leaving behind the endosperm, ground into snowy all-purpose flour. Even commercial wheat bread is made with this flour, plus bran and germ added back in. Whole grains can comprise as little as 10 percent. Not surprisingly, Jones is withering in his assessment: “That’s not bread; that’s dough that’s been whipped into a frenzy,” he told a recent conference of entrepreneurs in downtown Seattle. (Speaking engagements are a big part of life at the Bread Lab.)

Then there are all the additives in processed bread—shelf stabilizers, sweeteners, and dough conditioners that speed up fermentation so loaves can hit store shelves at top speed. Some studies indicate that people with intolerance—not celiacs, but people whose gut flora doesn’t take kindly to gluten—might actually have issues with additives and can happily consume whole-grain bread leavened instead with a long ferment. To Jones, real bread consists of little more than water, flour, yeast, and salt. “If you’re eating bread with 25 ingredients, it has 21 too many.”

In Bread Lab vernacular, to make the switch to 100 percent whole grain flour is known as going hundo, a truncation of “one hundred,” and a term that packs the massive mental shift of going native plus the unpredictability of going commando.

The Bread Lab began as that small room full of baking and lab equipment, some adjacent greenhouses for breeding wheat strains, and a field planted with even more research wheat out back. At first, Jones did the baking himself, drawing on those bagels and dark loaves made with his grandmother as a boy. In May 2013 he hired Jonathan Bethony as Bread Lab’s full-time resident baker. Slim and bearded, with light eyes behind rimless glasses, Bethony is 32, and—in a long conversation about whole wheat and mass-produced bread—the only person Jones interviewed for the job. Bethony had been baking in the Bay Area for a while and was on a “self-directed journey” working for free to glean knowledge from some of the region’s best bakers. 

“The huffing flour was really getting to me,” Bethony recalls of those days; here at the Bread Lab he has most definitely gone hundo. His job is to instruct but also inspire: He teaches workshops and helped the nearby La Conner school district with whole grain muffin and scone recipes, but he’s also awfully close to pulling off a credible whole wheat croissant. In the lab, he examines strains of wheat and determines how to best use it in recipes. It’s way more complicated than simply making an even substitution for all-purpose flour. Whole wheat flour is tricky; it absorbs more water, the bread ferments faster, and different strains can have wildly different levels of gluten. 

But with it, Bethony produces rustic rounds of bread with a crust the color of cocoa and an interior flecked with tiny air pockets, so moist it might as well be cake. His boules smell and taste like actual wheat—a note surprisingly unfamiliar in most bread. Those four ingredients produce something complex and nuanced like a single-origin pour-over coffee after a lifetime of vanilla lattes. 

Since the lab launched in 2008, it has become a destination for bakers and high-profile chefs interested in the provenance of their ingredients as much as the results. Perhaps Jones’s biggest chef booster is Dan Barber, the madly accomplished New York chef and writer. He worked with Jones to develop his own strain of wheat for a whole-grain bread at Blue Hill at Stone Barns, his flagship farm-to-table restaurant in New York’s Pocantico Hills, then served it to diners including the Obamas and Chipotle’s Steve Ells (precipitating the tortilla conversation). His book The Third Plate devotes an entire section to Jones and his lab. 

Mel Darbyshire, the head baker at Seattle’s Grand Central Bakery, remembers attending a Bread Lab session and baking with a flour referred to as “dirty white” (yes, the name needs improvement). It’s made with hard red wheat with just a little bran sifted out, so it bears a passing resemblance to all-purpose flour. With it, Darbyshire made a perfectly respectable baguette. “God, could we sub out our white flour for dirty white and have that be the primary flour?” she asked herself that day. “It seemed so radical, yet we just did it really successfully.” Grand Central makes a rustic loaf that’s 100 percent whole grain, and two more that are more than 50 percent. They’re not immensely popular, she allows, but sales are growing. 

In 2012, Grand Central Bakery started buying its whole wheat flour from a brand new mill in Eugene, Oregon, called Camas Country; owner Tom Hunton is a second-generation Willamette Valley farmer. Hunton had grown weary of commodity wheat’s low prices, not to mention the very anonymous act of sending his wheat on a railcar to the Port of Portland to be shipped abroad. Even before his mill opened, he was meeting with Jones in Mount Vernon, learning about various wheats’ yields. That relationship has wrought an unexpected, if not unwelcome, issue: Hunton got into milling because he wanted to feed his community. Now he’s fielding calls from artisan operations from New York to San Francisco, wanting his flour.

On a recent Wednesday, Jonathan Bethony stood at the lab’s butcher-block counter and mixed tortilla dough by hand in a stainless steel bowl. He works on the Chipotle project a little bit each week. A good tortilla must be both stretchy and durable, able to withstand the beans, carnitas, and lashings of salsa that get ladled on top. It isn’t too thick or too chewy. It needs “a nice kind of flakiness,” he muses, but “getting the dough to spread is the ultimate challenge of the tortilla.” 

The corn and flour versions Chipotle currently serves are its only menu items that still contain additives. These are mostly dough conditioners (which help speed the fermenting process) and preservatives, since a thin, moist tortilla is an open invitation for mold. A sourdough with a longer ferment, eight or 12 or even 25 hours, easily knocks out the need for those dough conditioners. Keeping tortillas chilled fends off unwelcome bacteria. Bethony, Jones, and Econopouly are still discussing the ideal strain of wheat for Chipotle. They’re gravitating toward hard whites, a class of wheat with a lighter, not-too-intimidating golden hue. Ideally, says Jones, they’ll have to find several strains that can thrive in different climates to meet the demands that come with the restaurant’s more than 18,000 locations around the country. After nearly a year of work (Chipotle pays WSU for the Bread Lab’s services) Jones and Bethony say the tortillas are close. But it’s not their only means of making an impact.
 

With so many missions, the Bread Lab has outgrown its humble environs. In July it will begin the move from its 600-square-foot room to a 12,000-square-foot facility in nearby Burlington that’s big enough to accommodate a host of projects. An education center run by King Arthur Flour will train more than 2,000 bakers a year. Blaine Wetzel, the chef from nearby Willows Inn on Lummi Island who recently won his second James Beard Award, has signed on as resident chef to be on hand for workshops or special events.

Meanwhile, the lab breeds new strains of barley, exploring its potential as a healthy food and for Washington’s beer and spirits industries. SoDo’s Westland Distillery wants its own barley strain, and a new small-scale facility called Skagit Valley Malting sets a stage for brewers to derive uncommon flavors from small-scale barleys.

Jones likes to say that he’s decentralizing bread, but really he’s building an entirely new groundwork of connections, from farmers eager to get off the commodity train to like-minded millers and malters and bakers open to the possibilities of whole grains. 

It extends from the wheat fields of northern Washington to the farms of the Willamette Valley and across the nation to restaurants and bakeries in New York, Toronto, Phoenix, and points between—a big network of small operations. All bringing one of our most basic foods back to actual basics.

This article has been updated since publication to correct a quote from Jonathan Bethony.