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Soy is a bean. That much we know.

But is soy a miracle worker that protects us from cancer, heart disease, bone loss and hot flashes? Or is it an overrated and menacing little legume that affects the thyroid and raises certain cancer risk and is found in nearly every processed food?

Massive public confusion over the beans from those green fuzzy pods began in 1999, just after the Food and Drug Administration allowed food labels to advertise that coronary heart disease could be reduced by eating 25 grams of soy protein daily along with a diet low in saturated fat and cholesterol.

The health claim, however, covered only soy protein, because there was a lack of evidence that soy isoflavones, which are plant compounds with estrogen-like properties, were involved in cholesterol reduction.

Isoflavones, in fact, are at the center of the uncertainty about soy. On one hand, they can reduce the effects of estrogen on breast and prostate tissue. Estrogen is thought to stimulate cancer growth in genetically susceptible people.

But some animal research has shown that processed soy can aggravate existing hormone-dependent cancers and that isoflavones don’t prevent further development once cancer has been established.

Regardless, soy, a versatile and nutritious plant-based protein, soared to superstar status, with sales rising 24 percent since 2001, a market valued at $4 billion in 2005, according to the market-research firm Soyatech.

Suddenly, mainstream Americans began discovering a well-kept vegetarian secret: Soy protein contains nine essential amino acids found in animal protein but is much lower in saturated fat and has no cholesterol. It’s also a source of fatty acids (including some omega 3s) and supplies B vitamins, potassium, zinc and other minerals.

And soy’s two main isoflavones, genistein and daidzein, were said to benefit heart health and blood pressure and to offer cancer protection.

Today soy, a staple in hog fodder, has landed in every aisle of the grocery store. In addition to traditional fermented forms such as tempeh and miso, and whole-soy foods such as tofu and soy milk, consumers now can buy soy pasta, soy jerky, soy-nut butter, soy mayonnaise, soy ice cream, soy sour cream, soy yogurt and soy grits.

Textured and genetically modified vegetable proteins, including soy isolates, are used in cereals, energy bars, sports-performance drinks, smoothie powders and processed foods.

Critics say that’s part of the problem: We’re getting too much of it. It’s present in nearly every packaged food, and for some populations, such as those at high risk of breast cancer, this might be dangerous. But soy researcher Mark Messina, an adjunct professor in the department of nutrition at Loma Linda University, says the amount of soy protein added to foods is very low in isoflavones. The average American eats 70 to 80 grams of protein a day, and only 1 to 2 grams of that is soy protein, said Messina, who often serves as a consultant to the soy industry.

PR in overdrive

Others say that soy isn’t dangerous but that its benefits have been overhyped and oversold. At worst, soy is simply ineffective. Still, what’s difficult for consumers is that for every negative charge, there’s a possible positive benefit to soy consumption.

Consider:

– Last August, the federal Agency for Healthcare Research and Quality found unclear or insufficient evidence that soy can prevent heart disease, menopausal symptoms or osteoporosis, largely because more than half the studies were poorly designed. It did, however, find that soy may decrease the weekly frequency of hot flashes by as much as 40 percent.

– This year, the American Heart Association concluded that soy doesn’t cut the bad cholesterol as much as experts thought. “Taking soy or isoflavone supplements is unlikely to reduce your risk of heart disease,” the AHA said in the journal Circulation. But just to keep consumers befuddled, it added: But “eating foods that contain soy protein to replace food high in animal fats may prove beneficial to heart health.”

– A review of studies using animal tests demonstrates minimal effects in prevention of breast, prostate and colon cancer, and results are inconsistent when it comes to soy’s ability to relieve symptoms of osteoporosis and menopause, according research in the Journal of the Association of Official Analytical Chemists International.

But when it comes to osteoporosis and menopause, animal tests might not accurately reflect what is happening with humans. And isoflavones in moderation are “probably not dangerous” and might even be able to delay Alzheimer’s disease, according to Gerard Cooke of the University of Ottawa, the lead author of the study review.

So although soy is an excellent complete protein that could potentially provide hormonal benefits for some people, “we’re not quite sure for who and whether it’s consistent all the time,” said Lisa Dorfman, a spokeswoman for the American Dietetic Association.

“Just because Asian women include soy in their diet and don’t have as high of a risk of breast cancer doesn’t mean that isoflavones have that kind of impact for everyone. It’s not consistent,” she said. “The good news is when it comes to cholesterol for some people, there are incremental improvements.”

One problem is that isoflavones are thought to be the key active substance in soy, but even this isn’t certain.

When researchers investigate the health effects of food, they also must deal with a variety of variables, “including the complex interaction between the substances within the foods and other foods,” according to the Agency for Healthcare Research and Quality.

A sensible approach

The bottom line, most researchers and nutritionists say, is to eat soy like anything else: in moderation. Also consider what stage of life you’re at–mounting evidence shows high soy intake during adolescence can lower the incidence of breast cancer–and what type of soy you’re sticking in your mouth. The closer it is to its original state, the better.

“Soy beans are great and so is tempeh [fermented whole beans],” said Christopher Gardner, an assistant professor at the Stanford Prevention Research Center, who just wrapped up a six-year study on the effects of soy isoflavones on prostates, breasts and bones.

“Tofu and soy milk involve processing the soy, which means the loss of folic acid and fiber,” Gardner said. “By the time you get to soy ice cream and soy hot dogs, you have lost even more of the natural soy, and the product is mostly non-soy.”

So even though soy might not be the miracle cure that prevents or treats breast, endometrial or prostate cancer, and results are mixed on postmenopausal bone loss, it’s too early to call it a “has bean.” Many soy products can benefit cardiovascular and overall health because of their high content of polyunsaturated fats, fiber, vitamins and minerals and low content of saturated fat.

“The key to soy is that it is a healthy food if you’re eating it in place of another [lesser] protein,” said Pauline Maki, associate professor of psychiatry and psychology at the Center for Cognitive Medicine at the University of Illinois at Chicago, who specializes in testing hormones in the brain. “That message from a public health point of view needs to be considered.”