I found the history of soy section pretty fascinating. The takeaway message is that soy based foods are a relatively recent innovation in Asia. Soy was used as a cover crop and fertilizer for millenia, but only in the last few centuries did it start to play a significant role in the food supply. Fermented soy products, like miso and tempeh, have a longer history. Soy oil was a lamp fuel in China! Even now unfermented soy foods like tofu are a small component of the diet, used in conjuction with eggs, fish, poultry and meat. As a population biologist I find it pretty interesting that soy foods increased in importance with increased population size.
Daniel is pretty clear throughout the book: traditional soy foods are not the target. The fermentation processes used to make miso, tempeh and many others greatly reduce or eliminate "antinutrients" in raw soybeans. Tofu is borderline because the relatively mild processing it receives does not reduce antinutrients to the same extent as fermentation.
The vitriol is focused primarily on industrial uses of soy in processed foods. If you want to get completely turned off of a product, just read her chapter on first generation soy products. There's clearly a profit motive to using soy everywhere possible, and you won't find me promoting processed foods as healthy. I confess, if you look in our refrigerator you'll find soy dogs with an ingredient list that goes: "Water, Soy based protein Isolate, Soybean Oil, Evaporated cane syrup ..." ugh. Non GMO soybeans though! Nowadays I buy them because they are easy for a teenager to heat and eat, and boy, do teenagers eat.
The steady introgression of soy products into nearly everything processed is problematic because of the many anti-nutrients associated with soy, and Daniel devotes a substantial amount of the book to detailing these. The trouble with these industrial processes is that they do not reduce antinutrients like phytates and trypsin inhibitors. What about these things in real food, like tofu*? This turns out to be a really good example of how risk tolerance influences the interpretation of data. According to the research Daniel cites, tofu retains 2.5 to 7.9% of the Trypsin inhibitors in the raw soybean. Compare that to 0.3 % retention in Miso and you can see why fermentation is a good thing. Reductions of this magnitude eliminate growth deficits in rats caused by trypsin inhibition. And most of the trypsin in our guts exists in cationic form which is resistant to these inhibitors. So I look at that and say, "well, seems like there's nothing to worry about from tofu." Daniel on the other hand says (I'm paraphrasing) "but it's not ALL gone, and there's SOME effect, and we don't know EVERYTHING."
But, but, I hear you sputtering, soy is GOOD for us! It's true that these same trypsin inhibitors are being investigated as treatments for cancer. However, the devil is in the details. If you chemically isolate Bowman-Birk inhibitors from soy, treat them to change the relative rates of inhibition of chymotrypsin to trypsin, then feed that chemical product to rats predisposed to get cancer, the rats get less cancer. But that's a long ways from what you're getting in soy food, real or processed. Daniel comes back to the claims that soy protein or isoflavones reduce cancer risk in a later chapter, and similarly, the evidence is equivocal at best, and absolutely in the opposite direction at worst.
The section that got my attention was the one on phytoestrogens. Soy has a lot, and if you eat a lot of tofu like I do you're getting a pretty hefty dose. The primary negative effect here seems to be on the thyroid gland. Well that's OK, because I had mine removed in 2000 because of Hashimoto's Thyroiditis. What's that? Oh, Hashimoto's has the highest incidence in Japan (hence the name ...), which also has the highest consumption of soy products. Hmmm. Well, correlation doesn't equal causation.
Overall, I call this one a draw. Processed food is bad, yep. I'm with you on that. Infant formula bad, yep, soy infant formula really bad, got it. Breastfeed as long as you can stand it, and then keep going for a few more months please! Easy for me to say, I'm not the one producing the milk. Hey, I tried to do my part by getting up and carting the little devils around after feeding in the middle of the night.
Am I going to stop eating tofu? Not yet.
*Yes, I know, tofu is actually processed. However, if I could make it on my kitchen counter then I'm going to call it real food. Like Beer and Wine. :)