In fact, products marketed to gluten-avoiders are often packed (into multiple layers of plastic) with sugar and questionable additives. After the initial wave of media-generated hype died down and copies of Wheat Belly and similar books began showing up in secondhand stores, some scientists and nutritionists decided to take a closer look at wheat.

Why try to save wheat? For some, it’s the simple love of good bread, in all its traditional forms. Dr. Stephen Jones, of The Bread Lab at Washington State University, is on a mission to rediscover the nutritional possibilities and complex flavors of heritage wheat, starting with the seeds a farmer sows. His curiosity explores each step of wheat’s life cycle. From the art of hand-breeding grain, to sustainable agriculture practices in which wheat can enrich the soil as a rotational crop, to the baker’s craft of mixing, rising, and shaping. Jones wants to bring back good bread: a loaf that nourishes the belly, delights the senses, and enriches our lives.

We reached Dr. Jones in what may be the world’s only artisanal bakery fully enclosed in a state-of-the-art scientific facility. It makes a strange sort of sense — after all, don’t bakers and lab techs both wear white?

Breeding: wheat has genes too.

Wheat, it turns out, is not just wheat. Since agriculture began, first farmers and then agribusinesses have been experimenting with wheat varieties in hopes of manipulating its yield, taste, or culinary properties. Now biotech companies like Monsanto bring wheat into the genetic engineering (GE) lab to increase resistance to herbicides, pathogens, drought, and salinity. No GE wheat is yet approved for production, but field tests have been made. Some GE contamination has already been discovered in shipments of supposedly non-GE wheat. The debate rages on about the safety and sustainability of GE crops; Monsanto protests that its mission involves fighting hunger and increasing crop yield to feed a growing population. Dr. Jones reframes the question: “To me [genetic engineering] is about ownership, who owns the seed? It is not about production. There is plenty of food on the planet today, yet people are going hungry.”

Old-school plant breeding serves the interests of the collective, like open-source software. How is breeding different from engineering? Breeding is an ancient, low-tech agricultural method that simulates the way plants naturally interbreed, though pollination. Selective breeding created the foods we now take for granted: apples, corn, tomatoes, and virtually all other produce originated as marginally edible wild plants we would scarcely recognize. Michael Pollan’s The Botany of Desire offers a fascinating introduction into the strange hidden histories of a few familiar species.

Yes, you can cross-breed your own grains at home, if you’ve got the space to grow a little grain. All it takes is a few simple tools, such as tweezers and scissors, and a basic understanding of plant reproduction. “Make some crosses and develop new varieties,” says Dr. Jones. “It’s fun, easy and important.” Making your own crosses demystifies the process, and makes a great science experiment for kids — or adults tired of feeling powerless and alienated from our food supply.

Why let the big seed companies have all the fun — especially when their priorities are so different from the home gardener’s? The new seed-saving movement is the first step to reclaiming control over our homegrown food supply. Ordering seeds can feel like a gamble, with no choice but to trust the catalogue’s claims while guessing which varieties you might prefer, and which might thrive in your unique conditions. When we select and save seeds at home, we gain awareness of the entire lifecycle. Instead of pulling out all the bean vines after the green bean salads, casseroles, and pickles of August have passed, we notice which plants produced our favorites, and let a few pods remain to come to maturity. Bolting spinach isn’t just the end of this season’s efforts, but an opportunity to jump-start next year’s crop. Grains are no different, though few of us grow them at home anymore. Deliberately crossing two distinct strains, in hopes of gaining some of the best qualities of each, takes seed-saving a step further.

Winter wheat makes sense in home gardens of any size. It is an excellent cover crop, aerating the soil, suppressing weeds, and controlling erosion. It can be tilled under in spring as a rich green manure, or harvested as a grain for those interested in producing their own cereal crops.

It’s the massive, monoculture farms that are in trouble. Stephen Jones wants his wheat to be more than delicious: he hopes better grain can have a positive impact on a troubling agricultural system. He explained to me that “Grains are an important rotational crop. They have a fit in most systems, even very diverse vegetable systems. They are low input (require few chemical inputs) and are relatively easy to grow organically. They also offer a local feed source for integrated animal systems.” What if we don’t need all those endless corn fields covering huge swaths of the central states, with their devastating environmental impact (water supplies poisoned with herbicides, a huge Gulf of Mexico “dead zone” from fertilizer run-off, massive bee-killing neonicotinoid dependence)? What if there is an economically viable route for farms to transition to diversified sustainable production? If the good-bread revolution helps us return to a saner farming model, let’s start kneading.

Nutrition: what's in a grain?

When bakers at The Bread Lab pull an aromatic, crusty loaf from the wood-fired oven, it’s the result of a series of patient, traditional processes one would expect to find in a medieval French village rather than a state-of-the-art modern laboratory. And yet the investigations made by Jones and his team of researchers is decidedly technical and scientific. After all, they are taking on a bread industry built by a science that puts efficiency and cost-cutting first. Only a rigorous, evidence-based approach can systematically challenge the methods and products we’ve come to accept as standard.

What passes for “bread” in today’s supermarkets, Jones argues, hardly deserves the name. A host of chemical bleaches, dough-conditioners, and shelf-stabilizers are added to a wheat flour engineered for blandness and industrial mass-production. The result: a nutritionally bankrupt, flavor-neutral ageless “sandwich bread” which has rightly become the target of wide-ranging criticisms. Americans have gotten used to it, as the decline of home-baking accompanied the increasing out-sourcing of formerly common domestic skills.

If not Wonder Bread, then what? It turns out even store-bought bread yeast is a modern shortcut, with a hidden cost. Traditionally fermented wholegrain sourdough contains a broad range of vitamins and proteins made significantly more digestible by the naturally-forming lactic acid produced in the long-rising process. Another benefit of slow-fermented bread: its effect on your blood sugar is much gentler. That mass-produced shrink-wrapped loaf can give your body a nasty sugar-spike, making it a restricted food for diabetics and anyone struggling to control weight-gain or pre-diabetic tendencies. Short-cut (quick rise) bread products also leave a burden of undigested gluten in your body, which may explain some non-celiac wheat-triggered discomfort. Carbohydrates from slow-rising sourdough have a gentler effect. To lower the glycemic load of your bread even further, eat it at the end, rather than the beginning of your meal, or make sure to combine it with low-glycemic foods like healthy fats and proteins. No surprise: bread is better with butter (or olive oil).

Peter H. R. Green, the director of the celiac-disease center at the Columbia University medical school, warns that “Often, gluten-free versions of traditional wheat-based foods are actually junk food.” He and other researchers caution that pop-culture diet trends are often misguided: take the fat-free product craze, or the substitution of margarine for butter, both of which were later judged to cause more harm than good. The most uncontroversial diet advice almost all medical professionals agree upon: buy and cook whole ingredients which our ancestors would have recognized as food.

Dr. Jones says “I personally look for foods that support a vibrant regional agriculture.” When we know both where and how our food was produced, eating starts to feel good again. When you know your farmer, anxieties about genetic engineering and industrial farming no longer hover over the dinner table.

Baking: good dough takes time.

If you don’t have time to bake your own, artisan “slow bread” bakeries are popping up in many urban and even some small-town settings. Their loaves may cost more, but can’t be compared with a mass-produced product: even that “fresh baked” supermarket loaf is factory-formed with an arsenal of dough conditioners and preservatives, and merely finished off in the store’s oven. Buyer beware!

The recent popularity of “no knead” breads has made home bakers out of many too-busy people. Our relationship with bread changes when we engage all our senses in its many textures and smells during fermentation, baking, and cooling — strangely, as we become intimate with the process, it becomes more mysterious. Most of the work is done not by human hands, but by an unseen universe of yeasts and bacteria. When a neighbor hands you a mason jar containing a cup or two of murky sourdough starter, treat it like a witch’s potion. Handle with care, this stuff makes things happen! This kind of bread becomes a companion in your kitchen, a force of its own.

But if wheat is so variable, which flour should I use? There’s no definitive answer, but keeping it simple and fresh (nutrients and oils in whole grain flour oxidize rapidly) makes sense. Ask around at your local whole food market, or find out which flour Dr. Jones recommends. If you want to take it a step further, take a look at the home grain-grinding equipment on the same page. Whole, unground wheat berries retain freshness and nutrients many times longer than flour, with good storage practices.

It’s a perspective shift.

Want to reclaim grain? It starts with tilling the soil. For centuries, wheat and similar grains have provided the staple carbohydrate for many of the world’s cuisines. For 8000 years, civilizations in North Africa, West Asia, and Europe have depended upon domesticated wheat baked into many forms. The unleavened roti from India. Pita, first baked in ancient Mesopotamia and now integrated throughout the Middle Eastern, Balkan, and Mediterranean countries. Braided, raised challah familiar to Jewish communities throughout the world, essential for celebrations and ritual. Yet in the melting pot of North America, modern bread has evolved into a controversial product of technology, bound to no culture save convenience.

Eat bread or don’t — it’s up to you. But if you love your morning toast or lunchtime sandwich, start with a deserving bread. Cheap processed food makes us treat eating as incidental and compulsive: we don’t feel great about what we’re putting in our bodies, so we munch automatically while distracting ourselves with multitasking (websurfing, driving, working, TV, etc). When you bake with your own hands, or make a pilgrimage to the baker whose craft and integrity you trust, each bite can be consciously savored.

For all our fretting about which diet to choose — vegan or paleo, gluten-free or locavore — it’s mindfulness that transforms our relationship with food. Our information age puts everything under the microscope of science, but in our homes we have a simpler relationship with what’s on our plate. Where did it come from? Does it nourish me? The Bread Lab’s work gives us the opportunity to slow down and consider our bread.