Soy is far from a health food and actually contains dangerous toxins and anti-nutrients that have severe and harmful effects on our bodies.
Soy is the major ingredient in many vegetarian meat substitutes like tofu and is also present in a plethora of common foods including cereal, chocolate, peanut butter, and even some nutritional supplements, just to mention a few. In fact soy products go by more aliases than a seasoned criminal and good rule of thumb is that if it comes in a package, it probably contains soy.
I have a number vegetarian friends who seem to think soy is an excellent and healthy food option. It worries me to see my friends consuming soy in levels that science has so clearly determined to be pernicious in nature. Many of these same friends tend to propagate common myths about soy including that it is a good source of protein, it prevents osteoporosis, and that asian cultures consume it in large amounts and achieve health benefits as a result.
The chemical makeup of soy actually blocks the absorption of vital minerals and disrupts hormone function in the human body. Additionally the heavy processing needed to remove anti-nutrients such as phytoestrogens from soy beans destroy its proteins and create even further toxins in the final product. On top of all of this manufacturer's add MSG and artificial flavoring to some soy products to mask the unpleasant taste of the heavily processed soy.
The only soy products proven to have any nutritional value at all are fermented soy foods such as miso, tempeh, natto and soy sauce. Most of these foods found on the commercial market have undergone processes which create toxins in them and great caution should be practiced when attempting to identify good sources of fermented soy. Unfermented soy should be avoided at all costs and quite unbelievably is not even “generally recognized as safe” by the FDA. In no particular order here are the top 10 reasons to go into your kitchen right now and throw everything containing soy into the garbage.
Soy Blocks the Absorption of Vital Minerals.
Soy contains a substance called phytic acid which prevents the absorption of vital minerals such as Iron, Zinc and Calcium. Zinc is required for the normal functioning of over 300 different enzymes. Without proper levels of Iron the body cannot form hemoglobin which is required to transport oxygen to cells. Calcium is important for bone formation and a calcium deficiency can result in osteoporosis. Substances like phytic acid are known as anti-nutrients because they block absorption of nutrients.   
Soy Goes Through Heavy Industrial Processing Which Create Toxins.
In order to inactivate the phytic acid and other anti-nutrients in soy manufacturers have to do a lot of processing to the soybean. These processes do inactive some of these anti-nutrients but not all of them. Part of the process involves submitting the beans to acid washing in aluminum tanks which leaches high levels of toxic aluminum into the final product. The spray drying process undergone by the soybeans also forms nitrates, which are toxic carcinogens. Additionally the beans are treated with an alkaline solution which causes the formation of a substance called lysinoalanine and this toxin may have the effect of killing healthy gut bacteria and destroying proteins.  
Manufactured Soy products are not a Good Source of Protein.
Proponents of soy as a health food claim that soy is an excellent source of protein because the soybean contains all nine essential amino acids, which is true. Amino acids are the building blocks of proteins and our bodies are entirely comprised of proteins. Essential amino acids cannot be made by the body and must be obtained from the diet. The problem with manufactured soy is that these essential amino acids undergo chemical changes by the intense manufacturing process of soy–including exposure to high temperatures–which denatures and destroys the amino acids. Only soy which has not undergone these processes would contain these amino acids in absorbable forms. 
Soy Products Likely Contain MSG
Soy has a strong “beany” flavor even after all of the industrial processing it undergoes to reduce this taste. To combat this food companies may add MSG (Monosodium L-glutamate) and artificial flavorings. MSG has the effect of increasing the taste sensitivity of food and in this case it makes the artificial flavors overpower the nasty aftertaste of the soybean. MSG is completely toxic and has been linked to brain lesions and obesity–in just one study–among a host of other scientific studies proving its toxicity.  
Phytoestrogens in soy can Cause Breast Cancer.
Phytoestrogens are substances which disturb essential hormone functions in humans. It is hypothesized that plants produce these substances to depress the reproductive hormones of the animals which are overgrazing on them. A specific phytoestrogen found in soybeans called genistein mimics the essential reproductive hormone estrogen in humans. It binds to estrogen receptors in cells–meaning estrogen is blocked from these cells–and and disrupts the normal functioning of the cell in this way. Animal studies have shown that these phytoestrogens and their effects promote the growth of breast cancer cells.  
Soy Contains Goitrogens Which Depress Thyroid Function.
Goitrogens are substances that block the uptake of iodine in the thyroid gland and without proper levels of Iodine the Thyroid becomes dysfunctional. These substances are found in many different foods and drugs and can promote the formation of goiters due to an improperly functioning thyroid. This gland plays a critical role in the body because every cell in the body depends on the hormones produced by the thyroid gland to regulate cellular metabolism. 
Soy Does not Even Have GRAS Status (Generally Recognized as Safe).
This one sounds a little hard to believe considering how many of our foods contain soy, but it’s true! Actually two soybean products–soy protein isolate and soybean oil–do have GRAS status, but only under the category listed by the FDA as, “substances migrating to food from paper and paperboard products”. Soy was considered an industrial product in 1913 and never used widely as a food source in The United States until the 1950s when marketing efforts were able to convince the public of soy’s potential health benefits. So in other words soy was recognized as safe for cardboard boxes but never as an actual food. 
The Farming Practices Used to Cultivate Soybeans Kill Marine Life.
Soybeans are usually grown as a mono-crop, which means that one species is being cultivated on one tract of land. This practice destroys topsoil. Monocropping completely goes against nature as in nature we see incredibly biodiverse environments which are called perennial polycultures. An example of a perennial polyculture is a forest where there exist myriads of symbiotic relationships between plants, animals and microorganisms which actually regenerate topsoil. Because of the destruction of the topsoil by soybean farming we have to add fertilizers back into the soil which have an even further negative impact.
In addition to this soybeans are also heavily sprayed with pesticides and herbicides. In The United States the runoff from these chemicals and fertilizers in the grain belt has led to what is now called a dead zone in the Gulf of Mexico. These chemicals make their way through interconnected waterways, eventually reaching the Mississippi who opens her mouth into the ocean. A dead zone means that dolphins, whales or whatever other marine life is living in the area is killed or forced to move. Recent estimates place the size of the Gulf of Mexico dead zone at around 30,000 square kilometers (12,000 square miles) which is the size of the entire Country of Belgium. 
Most Soy is Genetically Modified (GMO).
99% of soy comes from genetically modified soybeans meaning that they are resistant to herbicides. Some people think GMO crops are a good thing because they eliminate the spraying of herbicides and this is a common myth. The genetic changes allow farmers to spray as much and as many toxic chemicals on the soybeans as they want without killing the plants. These herbicides have been linked to a number of intense and severe health conditions in humans. 
It’s interesting that humans have begun to modify the genes of other organisms. In nature there is another entity that modifies gene expression and it is called a virus. Viruses invade healthy cells and basically take over. Imagine you were sitting at your desk at work and all of a sudden some crazy guy came in and started assigning everyone new tasks and assignments. The problem is that inside the human body when this happens our cells actually listen to that crazy guy. Our cells begin to produce the proteins that the virus tells it to instead of proteins needed for the cell to properly function.
In a strange way humans are changing the genes of plants in a similar way to how a virus changes gene expression in the human cell. Instead of trying to control nature–and force her to act how we think she should–we should try to work alongside nature and create symbiotic relationships with her that will benefit our species in the long term. A virus eventually destroys its host cell and without a host a virus cannot survive and replicate. Humans are the same in that our host is the earth. If we continue on this path of destruction–characterized by genetically modifying plants–we will destroy our host planet and destroy ourselves.
It is a Myth that Asian Cultures Consume a lot of soy and Achieve Health Benefits.
Some people propose the argument that asian people consume a lot of soy and live longer lives as a result. This is a myth and actually soy was never utilized as a food source until sometime during the Chou Dynasty in China (1134-246 BC) when the Chinese discovered that they could ferment the soybean and remove it’s toxic anti-nutrients. These people also understood that by consuming soy with meat or fish the effects of the anti-nutrients are lessened to an even further degree. In these cultures today soy is consumed in very small amounts–mostly as a condiment–and not as a staple food.
Only Fermented soy Products Should be Consumed as Health Foods.
Fermented soy foods like miso, tempeh, natto and soy sauce–also the most common soy foods in asian cultures–have health benefits primarily because they contain vitamin K2. This vitamin has a number of benefits including being proven to prevent and treat osteoporosis. This could potentially be the source of the myth that all soy products lead to strong bone formation. 
The problem with these products is that most of them–while they have been fermented which does decreases anti-nutrient content–were probably also subject to other toxic manufacturing processes. Store bought soy sauce especially is usually packed full of preservatives and other dangerous food additives. Unless there is absolute certainty that these products are non-GMO and have not been subject to intense manufacturing–specifically high heat, which denatures proteins–it’s best to avoid these fermented soy products.
The science relating to the nutritional merits of soy makes it pretty clear that this stuff is completely toxic. Epidemiological studies and soy-industry funded pseudo science combined with effective marketing tactics have given rise to soy as a common ingredient in the American diet. We should be avoiding soy if at all possible unless it is fermented and well sourced. If we’re concerned about getting enough protein from our diet we should turn to animal products instead of those derived from soy. Meat, fish and eggs are all great protein sources as well as the only good, natural dietary sources of Vitamin A, Vitamin D and vitamin B12.