I follow Dr. Mercola and have studied some research regarding soy as a product and as a toxin in the body. First of all, most soy is Genetically Modified, which is a whole eco issue unto itself, but secondly I do believe that unfermented soy is actually damaging to the thyroid and causes imbalance in the hormonal system. I'm excited about fermented soy products, like natto, miso, and tempeh, but I feel it's a serious issue for vegans/vegetarians if you have studied the harmful effects of soy.
As a caveat, Dr. Mercola does tout the benefits of eating small amounts of animal protein for various reasons, but aside from that I feel his research and opinions on food are valid and important, and usually not mainstream, which is why I appreciate him. He also touts eating raw as much as possible. From what I've found my body performs the best and feels the best with mostly vegetable and some kind of protein per meal, not much fruit, and no dairy or gluten. I try to steer clear of unfermented soy but I am wondering: if you eat a lot of soy product, have you noticed any negative effects?