Soybeans (like most beans) are mildly toxic, and also include analogs of animal hormones - part of their defense against animal predation. In Asia, where soybeans have been cultivated for over 5000 years for nitrogen fixation in crop rotation, they have been consumed for only 2200 years. This began after development of fermented forms (soy sauce, tempeh, natto, miso, etc.) or extracted forms (tofu) to detoxify them. The exception is during times of famine. Fermented soy products are considered safe and tofu is considered pretty safe. Even so, some attribute the notable increase in stature of the Japanese since WWII not so much to Western diet as to a reduction in use of soy foods - and others don't.
There are now many non-traditional products being heavily promoted here in North America, many sold as "health foods". These products may or may not be healthy, or even safe. Unfortunately, vast amounts of money are involved, so the truth is hard to know, but it seems pretty certain the public is being deceived, at least to some extent.
Disclaimer: I am not a health professional of any kind, nor
do
I play one on TV, nor even pretend to be one on dates. Nothing here is
to be, nor can be, construed as medical advice. What I have written is
derived from a large pool of publicly available documents by people who
do have those qualifications. Some of these people are considered,
particularly by the soy industry, to be "controversial".
Soybeans were heavily planted in the U.S. to produce soy oil for industrial production, particularly of paints. Paints were reformulated for ecological and economic reasons - leaving the soy industry to find new markets. They chose "health food". This had, after all, worked spectacularly well 100 years before for a failing soap company that decided to sell their cotton seed oil as a "healthy" alternative to lard - in the form of Crisco, partially hydrogenated vegetable shortening - now known as "deadly trans fats".
Since that time the industry has spent hundreds of millions on advertising, public relations, and government lobbying to build a "health food" reputation for their products, but the actual safety of many soy products is still highly questionable due to presence of toxins, estrogen-like hormones, substances which block mineral and protein absorbtion, pesticide residue (Roundup) and bacterial DNA spliced into the genes to make the plants Roundup resistant (well over 80% of the U.S. soybean crop is GM (genetically modified) with bacterial DNA). If you don't know why GM would be a problem, check link S4.
Despite industry efforts, these problems are only partially removed in processing or cooking. In particular, soy based infant formula is suspected of causing abnormal sexual development. This remains unresolved, but some advisors no longer recommend soy formula as broadly as they once did.
The safety of textured soy protein used for veggie burgers and other meat analogs is also questioned, particularly on grounds of substances that block mineral absorption. Also, the high temperatures used in processing result in degraded protein and possibly carcinogens.
Soy products are particularly good at blocking absorption of zinc, a mineral critical to brain and nervous system maintenance. Combine that with vitamin B12 deficiency and it's no wonder vegans seem a bit flaky (they say its from "being on a more spiritual plane").
Traditional fermented soy products (miso, soy sauce, fermented black beans, tempeh, natto) are generally considered safe. The fermentation process degrades the questionable substances. Tofu is considered reasonably safe in moderation but not as a large part of the diet. Eating a few steamed fresh soy beans (edamame) at a sushi bar isn't likely to do you noticeable harm either. These are immature beans low in toxins and are eaten in moderation anyway. Soybean sprouts are much used in Chinese and especially Korean dishes and haven't been implicated as harmful.
Two studies linking brain atrophy to tofu consumption are considered questionable because it could have been aluminum in the processing equipment, not the soybeans that caused brain atrophy - but there is that zinc thing too. Further study is needed on both the soy and aluminum.
It was expected that vegetable estrogens in soy would reduce "hot flashes" and breast cancer in women, particularly since women in regions that eat more soy foods have rather low incidence of breast cancer. These hopes have proven false, but many health food purveyors are still claiming such "benefits". Researchers are now looking at seaweed, also much eaten in the same populations. Once again - research is currently inconclusive.
Under heavy pressure from the grain cartels the FDA granted a health claim for soy: "25 grams of soy protein a day, as part of a diet low in saturated fat and cholesterol, may reduce the risk of heart disease." This claim is pretty much meaningless. It's like saying "This pill, combined with a diet lower in fats and sugars, combined with exercise, may result in weight loss". With a diet lower fat and sugars combined with exercise, the pill doesn't have to do anything at all. Other applications for health claims have been rejected or withdrawn under protest.
Some research has shown evidence that high soy consumption can result in Breast Cancer, Brain Damage, Infant Abnormalities, Thyroid Disorders, Kidney Stones, Immune System Impairment, Severe Food Allergies, and Impaired Fertility. Other research has not shown these effects.
More research of higher quality is needed. A problem is that most research funding comes from affected industries, though often laundered through non-profits. The industry knows how to specify research that is likely to support their marketing, and researchers know what results will assure future grants.
In the mean time, moderation in soy consumption, mostly of the traditional sorts, seems wise. It also seems wise to avoid soy for infants, except where breast feeding and dairy are not possible, but definitely Soy Formula, not straight Soy Milk.
For a lot more on this subject you can read the book "The Whole Soy Story" (Dr. Kaayla T. Daniel) and refer to the articles linked below, and many others on the Internet - but watch out for one-sided tracts designed to create a following of believers - one way or the other.