After a few false starts, Bethony devised a viable recipe using just five ingredients: water, oil, salt, whole-wheat Edison flour and a sourdough starter. The starter, a living concoction of flour, water and microbes, is not exactly standard procedure for a tortilla, but it is crucial for Bethony’s version: It magnifies flavor, makes the wheat molecules more digestible and extends the tortilla’s shelf life by adding acidity. Bethony taught his techniques to Ruben Berber and Tom Hoffert, who work in research and development at Don Pancho Authentic Mexican Foods in Salem, Ore., Chipotle’s primary tortilla supplier in the Northwest.

To accommodate Ells’s vision, Don Pancho has seriously modified its production process. The company must continually prepare and store large volumes of sourdough starter, maintaining just the right temperature and pH level. Further complicating matters, whole-wheat flour is often temperamental. It absorbs much more water than most bakers expect, and the shards of bran threaten to tangle the smooth strands of gluten, creating a sandy texture. If something goes wrong, the tortillas might turn out too bitter, or not stretch to their full size, which would be disastrous for a burrito that typically envelops more than half a day’s recommended calories. So Don Pancho has been cutting Edison with white flour. The tortillas they have produced so far are dense, golden-tinged and slightly tangy.

Ells plans to test the semi-whole-wheat tor­tillas in the Pacific Northwest. If things go well, he says, he will pair regional sources of wheat with tortilla makers around the country, which means the tortillas in, say, California might taste different from those in Florida — a discrepancy that would make many chains cringe. Although Jones and his community celebrate Chipotle’s openness to such diversity, they have also been unnerved by its interest. When Jones started working with wheat farmers in the Skagit Valley, he hoped to ‘‘keep value where it was produced,’’ not to partner with a company that has more than 1,900 venues and serves 1.4 million customers each day. What if satisfying Chipotle deprives others?

Edison wheat grows primarily in one location: 500 acres of Oregon farmland managed by Jones’s collaborators Tom and Sue Hunton and their family. A few months ago, nearly all of that wheat had been reserved for Chipotle, which irked some of the Huntons’ customers, like Mel Darbyshire of Grand Central Bakery in Seattle and Nan Kohler, who owns Grist & Toll, the only stone mill in greater Los Angeles. ‘‘Businesses like mine and local bakers need to be baking with that Edison,’’ Kohler said at the time. ‘‘If Chipotle walks away, then what? We haven’t created something sustainable.’’

Since then, thanks to a bountiful harvest and a decreased quota from Chipotle, the Huntons have been able to sell Edison to Darbyshire and Kohler. Tom Hunton is still waiting on an official contract from Chipotle. Yet he is optimistic that the partnership will work out. He also sees this as an opportunity to extend the benefits of re­gional grain economies beyond their geographic borders. ‘‘In this case, even over distance, the connection between grower, baker and miller is much more cemented and transparent than other instances in a closer radius,’’ he says. ‘‘There’s a void out there that needs to be filled with something other than the industrial-mill model. This is one way to do it.’’

Despite the Bread Lab’s growing influence, it is still quite sealed off from most of American society. For those of us who are not ardent home bakers buying fresh whole-grain flour from one of the few recently resurrected stone mills, who do not regularly queue up at Tartine or dine at the likes of Blue Hill, the kinds of wheat and bread the lab extols are still largely inaccessible. That is the power of industrial agriculture: It has so thoroughly expunged genuine whole-wheat flour from our diet that most of us do not even notice its absence. And here is where the partnership with Chipotle just might make sense: If it succeeds, it will bring real whole wheat to more American plates than any other Bread Lab collaboration so far.

Of course, that all depends on how faithful Chipotle remains to Jones’s grand vision. If the final tortillas are less than 50 percent Edison, aren’t they just the restaurant equivalent of the imitation whole wheat from the grocery store? A month or so after touring the Bread Lab, I asked Jones one last time whether he was worried about compromising, now that his dream was giving way to an ambiguous reality. After all, this was a man who practiced daily communion with his wheat plants. His swift response surprised me: ‘‘Our job at the Bread Lab is not to get all religious on 100-percent whole wheat.’’ Then he caught himself. ‘‘Although,’’ he continued in a quieter voice, ‘‘I guess we do.’’