Ayr Muir ‘00, SM ‘01, spent his student days at MIT experimenting with alloys and polymers, thin films and crystals. Today, he’s set up a different kind of lab: one where the raw materials are organic chickpeas and free-range eggs, Prince Edward Island potatoes and Rhode Island rhubarb. He’ll experiment with just about any food that’s fresh and local–any food, that is, except meat.

Muir, 32, is the founder of Clover Food Labs, a deliciously eccentric, environmentally minded, customer-savvy food business that he started in a Kendall Square lunch truck, not far from the labs he used to call home. The truck, which runs on biodiesel, has served a growing (and largely omnivorous) audience for two years. Clover doesn’t trumpet its meat-free ways, but Muir’s not out to convert unwitting Kendall Square lunchers into vegetarians. What he wants is to shrink the ecological footprint of the food industry by making fresh, local, sustainable vegetarian food as common and convenient as the fare at Burger King or McDonald’s. “My biggest motivation is environmental,” Muir says. “We have all these customers who never thought they’d eat meatless every day at lunch, and they do.”

Muir hails from tiny Bernardston, Massachusetts, a rural town on the Vermont border that’s ringed by the Green Mountains. His parents, both teachers, founded a school there that uses the pine forest, hills, marshes, and brooks to teach students respect for the natural world. (He is a distant cousin of John Muir, the naturalist and activist who started the Sierra Club.) “I grew up in the woods,” says Muir, who now lives in bucolic Lincoln with his wife and two small children.

Though “buy local” is a catch phrase these days, for Muir it was just the way his parents filled the fridge. They got milk from a neighboring dairy and groceries from the food co-op. The owners of the town’s general store, the Streeters, had a sprawling rhubarb plant that produced far more of the mouth-puckering vegetable than the family could eat. Every spring, they would share it with Muir’s family and other customers by the armload. (He’s still a fan: Clover’s spring menu features rhubarb compote, rhubarb muffins, and rhubarb agua fresca.)

Muir’s father was the family chef, his mother the baker. They taught him basic cooking skills that served him well at MIT, where he’d make simple meals in his Bexley suite’s kitchen, buying food from the Harvest Co-op. On nights he didn’t cook, he sampled MIT-area favorites: the falafel-soda-baklava combo from a Mass. Ave. food truck, the ice cream at Toscanini’s, the Mandarin and Szechuan food at Mary Chung.

Muir studied materials science, and like many at MIT, he believed that the right idea could change the world. After graduating, he worked at a startup within Polaroid that had just such an idea, impeccably engineered. But Polaroid’s core business was on shaky footing, and the company came crashing down around them before the new technology (which involved thin films for imaging) made it to market. “I learned it’s not just about having a really good idea,” he says. “I started thinking about the importance of business.”

He ditched plans to apply to law school or go for his PhD, heading to business school instead. He hatched the idea for a business like Clover in 2001, just before he started at Harvard Business School, and he nurtured it after graduation during stints at Patagonia and the consulting firm McKinsey. Muir didn’t grow up wanting to start a restaurant. What he wanted was “to start a company with an impact on environmental issues,” he says. And focusing on food, especially meat production, seemed like a promising way to do that.

Some scientists, Muir notes, believe that the livestock industry is second only to the transportation industry in its carbon impact (and some reports, including one from the Food and Agriculture Organization of the United Nations, see it as even bigger than transportation). Researchers have estimated that raising a kilogram of animal protein uses about 100 times more water and 11 times more energy than growing a kilogram of protein in the form of grain. Scientists at the University of Chicago estimate that switching from a meat-based to a plant-based diet could do as much to shrink a person’s carbon footprint as switching from an SUV to a Camry.

The way Muir sees it, plenty of bright minds are working on reducing the carbon footprint of energy and transportation. But far fewer people are thinking about the environmental implications of the food system, which an individual can influence just “by choosing what foods you eat every day,” he says. The key is to persuade enough people to make a small change–say, from a hamburger to a chickpea fritter at lunch.

An engineer’s approach to food

Like many good inventions, Muir’s business started somewhat by accident. Muir and his culinary partner, chef Rolando Robledo (formerly of the French Laundry in Napa Valley), wanted to test out their concepts for a restaurant serving fresh, meatless fast food, and they thought setting up a food truck for a few weeks would be easier than arranging focus groups. He asked the owner of his favorite Mass. Ave. falafel truck to let him test his food there. Although the proprietor declined for business reasons, he offered to show him the ropes of running a food truck. So Muir and Robledo bought and renovated a used delivery van, tracking their efforts on a blog, and started Clover in the fall of 2008. They anticipated 20 to 30 customers a day, which would have given them enough feedback to close up shop in six weeks. Day one met expectations. On day three, though, roughly double that many customers showed up; by the end of the week, they were overwhelmed. Muir had to call in his sister (graduate student Teasel Muir-Harmony) and his father-in-law to help. By late summer 2010, Clover’s staff had grown to 30 employees.

Ask Muir about food and flavor, and he can give you a dissertation on just about any part of Clover’s pantry. A mildly basic solution helps soften chickpeas enough to make a creamy hummus but doesn’t overpower them with a bitter baking-soda taste. Squeezing the freshest lemons means Clover can use one-sixth the sugar in competitors’ lemonades (the lemons have a natural sweetness that disappears after a day in the fridge).

Muir believes his MIT degrees helped prepare him for being a food entrepreneur. If he’d studied something more focused than materials science, like chemical engineering, he wouldn’t have gotten such broad exposure to practical matters like surface science, mixtures, and thermal changes. “For food, you need to know all of that,” he says.

People looking at Clover for evidence of his MIT experience sometimes focus on the more obvious techie trappings–the iPod Touch devices that employees use to take orders and track sales, the laboratory-style whiteboard on which they hand-write the menu, the blog and the Twitter feed. The real lineage, though, may be found in Muir’s relentless spirit of experimentation, underscored by Clover’s optimistic tagline: “Everything will be different tomorrow.”

This spirit was evident during a breakfast shift in late July that found Muir telling a couple of customers, “You guys are experiencing an entirely new way to make iced coffee!” Clover’s original cold-brewing process, which gave the grounds an overnight soak, produced a smooth and delicious cup, but one that Muir believes was “absurdly” high in caffeine. He tinkered over a summer weekend and decided to try using a paper filter and cone to brew fresh coffee directly over ice, one cup at a time. For Muir, it seems that every problem is just an opportunity to find a creative fix. He even punched holes in the truck floors so that his crew can scrub and disinfect them, hose them down, and let the water drain out–an ingenious way to mop with less mess.

Crafting a brand and scaling it big

Turn the corner from Main Street onto Carleton by the Kendall Square T station at quarter to noon on a typical summer day and you’ll see lunch trucks lined up along the curb. There’s Jerusalem Falafel and Olives Kitchen (falafel), José’s (Mexican), and Goosebeary’s (Thai-Vietnamese). Kendall Square doesn’t offer many cheap, tasty restaurants, so the trucks play a central role in its culinary ecosystem. Clover’s truck stands out in the lineup, and not just for the crowds it attracts. There’s no splashy art, no cartoon characters–just a white truck with a black-and-white hand-lettered logo and menu. “The only color is from the people and the food,” Muir says. “Natural things.”

Clover’s customers are a mix of MIT students, staff, and professors (Yet-Ming Chiang ‘80, ScD ‘85, materials science and engineering professor and cofounder of the upstart battery company A123 Systems, is a regular), as well as area workers and the stray outsider who’s read about Clover on a food blog. Clover’s order takers stand on the sidewalk, where they often greet customers by name. Sandwiches and drinks are passed hand to hand instead of getting placed on a counter or a tray. That’s deliberate, Muir says, to maximize interaction and build relationships. “It’s important to have as much face-to-face contact as possible,” he says.

The background music is an ever-­changing bluesy mix. The menu includes lavender lemonade, hibiscus iced tea, fresh-cut rosemary French fries made with potatoes from Prince Edward Island (600 miles from Boston, but a lot closer than Idaho), and a special summer sandwich that features basil spread slathered on Havarti cheese and thick-sliced local cukes. A sidewalk board promises a tasty afternoon snack: “Sweet plantains, thick cut and fried, Aleppo pepper and sugar = fried plantains, our 3 p.m. special.” The prices are low, considering the quality: $5.00 for a sandwich, $3.00 for soup or an inventive side salad.

Customers say that besides the prices, the cool factor is definitely part of Clover’s appeal. But the flavor is what keeps them coming back. Mike Norman, a recent Sloan School grad and founder of SoChange, a startup that encourages consumers to use their economic power to do good, was queuing up for the popular “egg and egg” sandwich–slices of hard-boiled egg from Chip-in Farm in Bedford, Massachusetts, served in a whole-wheat pita with roasted eggplant, cucumber-tomato salad, hummus, and tahini. Norman, a Clover regular, is a self-described meat eater, and he never expected this combination of ingredients to be so delicious. “Who knew?” he says. Students of marketing can learn from Muir’s approach, Norman says: “Ayr stays very close to his customers and asks for a lot of feedback. He can experiment fast with the food truck.”

Muir himself has dreams that stretch far beyond Kendall Square. He’s got a second truck at South Station, and he was slated to open his first sit-down restaurant in Harvard Square, at Holyoke Center, this fall. He expects his staff to double with the opening of the restaurant. Ultimately, he envisions thousands of locations worldwide–all with an ecological footprint much smaller than what’s typical for fast food.

Other companies have managed to preserve their distinctiveness as they grew far and wide, Muir says–Apple, Trader Joe’s, and In-N-Out Burger, to name a few. Yet it remains to be seen whether a style of eating that’s become so popular in Cambridge will play as well in Peoria or Prague. Can vegetarian fast food that’s fresh, local, and sustainable scale across the country and around the world? “I think it can as long as we don’t call it that,” Muir says, “because no one will eat it if we do.”