The other day I overheard two people talking about the health dangers of pizza. While one person was going on about gluten, the other countered with the dangers of saturated fat. It occurred to me, how many of us can truly answer, “Just how big a health threat does pizza pose?”

The answer eludes us mostly because the science of nutrition is dismal. Consider the sheer quantity of research: 44,000 on obesity and diabetes last year alone, according toThe New York Times science writer Gary Taubes. Plus a lot of the science is just plain bad.

So where do you turn for an answer? Unfortunately, most of us doctors have no idea what to tell you about food. What’s worse, when you come to us with concerns about, say, tomatoes, we’re confined by standard-of-care to tell you: “It’s not in the evidence base.” Then, more likely than not, we order a test or a medicine we’re constrained to request but that you don’t need. But some top-notch researchers, alternative practitioners, fitness experts, and frustrated patients are gathering good data about the health effects of food. Here’s what they tell us.

Gluten and Wheat. It’s really a problem. For people who are slim and who love bread, it’s easy to wave off concerns about gluten as ridiculous. On the other hand, some health bloggers barely consider grains to be a food—perhaps for good reason. First of all, almost 1 percent of us have Celiac disease—a disorder that destroys the gut lining in the presence of the wheat protein gluten. At least another 6 percent of us have non-allergic reactions to gluten that show up as symptoms as diverse as abdominal pain, eczema, headache, foggy brain, fatigue, diarrhea, depression, anemia, numbness in legs, and joint pain.

Cheese and Dairy. By now perhaps everybody has heard the news that dairy is getting a second look as a possible source of good fats. But even so, many people do poorly on dairy. The symptoms can show up as a wide array of intractable health problems. Indeed, The New York Times food writer Mark Bittman describes fruitlessly attempting to stop taking antacids for seven years (seven years!) only to find that his chronic heartburn resolved immediately after quitting dairy. Besides an improvement in stomach pain, many people find that without dairy their sinuses open and their energy levels rise. Even acne clears up, no matter what some smart conventional physicians may say about not being any evidence.

The toppings: Mushrooms and Onions. Doing yeoman’s work as low calorie treats packed with anticancer phytonutrients—both mushrooms and onions contain poorly absorbed substances that can cause real digestive problems. They’re called FODMAPS—which stands for Fermentable Oligosaccharides-Disaccharides-Monosaccharides and Polyols. Because they are poorly absorbed, these FODMAPs feed our gut bacteria, which then cause bloating and cramps. FODMAP foods can worsen irritable bowel symptoms for many of the 15 percent of Americans that suffer from the condition. The low FODMAP diet was first identified by an Australian dietitian Dr. Sue Shepherd and has been proven to be highly effective for people suffering with irritable bowel.

Anchovies. A lot of people have fish allergies, but anchovies also have a lot of amines—a breakdown product of proteins. And, while we’re at it, tomatoes have salicylates, a compound related to aspirin. Both amines and salicylates are naturally occurring chemicals that can trigger behavior problems and ADHD. Many parents get huge improvements in their children’s behavior simply by cutting out dietary sources of salicylates and amines. More than 20 years ago, a provocative study showed that behavior improved on a diet that removed many naturally occurring substances as well as food additives. And while the medical establishment has been slow to acknowledge the psychological effects of food, over the last two decades, Sue Dengate, an Australian parent of two children with food sensitivities, has worked with thousands of parents to create an extensive database of the physical and behavioral effects of foods and food additives.

Tomatoes. Again? Can you believe it? While being praised for its antioxidant content and its low calorie deliciousness, tomatoes are getting a second look as a possible key to a wide variety of conditions. Tomatoes are nightshades, a plant family whose other members include tobacco, potatoes, pimentos, peppers, eggplant and paprika. Nightshades have been associated with arthritis, fibromyalgia, autoimmune conditions and headaches. There are a number of interesting theories as to why, but most conventional physicians will point to the fact there aren’t any good studies. This is exactly the problem: nutrition studies are difficult and expensive. Think about it: Exactly who is going to pony up the money to study the downsides of eating eggplants? So, no matter what the research says, if you suffer from intractable migraines or inexplicably achy joints, instead of popping a pill, you might consider French fries and ketchup off the menu.

If all of this is true—or even any of it—then most complaints that bring people to the doctor may be caused by common foods. Perhaps we doctors have been needlessly ordering antacids for milk problems, anti-depressants for gluten reactions, rheumatology consults for nightshade sensitivities and colonoscopies for FODMAP intolerances. Luckily, patients no longer have to depend solely on us. As the scientist-health blogger Paul Jaminet wrote about their work on cholesterol, “It takes medical researchers years—often decades—to track down the causes of simple phenomena…we’re on pace to figure out the essentials in a year.”

So while dogged citizen-scientists and alternative practitioners move forward, conventional medicine will be left behind—because the medical establishment is totally broken. So, please, go on without us. In fact, next time, before you go to the doctor—before we prescribe you something toxic and dangerous—ask yourself one simple question, “Could it have been the pizza?”