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 I was poking around papers citing this paper that showed an association between soy intake and low sperm concentrations. Two reviews popped out. One is by Mark Messina, titled Soybean isoflavone exposure does not have feminizing effects on men: a critical examination of the clinical evidence. It basically says that worries about soy affecting masculinity are nonsense. I looked and looked for the conflict of interest statement that is standard on papers these days, but could not find any. It's no wonder, as Mark, an animal-rights vegan, has received funding from the soy industry. His name appears as the author on many industry publications. Another paper from roughly the same time is a little more skeptical. Soy, phyto-oestrogens and male reproductive function: a review says:

Exposure to endocrine disruptors (e.g. BPA or dioxins) during critical periods of reproductive development increases the incidence of reproductive disorders. Given the popularity of soy-based formula, isoflavone supplements and soy-derived products, a better understanding of the influence of phyto-oestrogens on male development is needed. To date, there has been a lack of consistency in human and animal studies examining the effects of soy and phyto-oestrogens on reproductive parameters. These discrepancies certainly reflect the variety of experimental designs, the differences between the specific endpoints measured but also inadequate descriptions or insufficient sample size to permit confidence in the observed results. In humans for example, it would be important to investigate adult male reproductive and endocrine functions of healthy full-term infant fed soy-based formula compared with breast-fed or cow milk formula-fed infants. These studies should investigate pubertal development and reproductive endpoints such as adult testicular function (testicular volume, spermiogram) and endocrine parameters (testosterone, DHT, oestradiol, LH, FSH, IGF1, INSL3, etc). The cohorts should be large enough to ensure statistical power to detect meaningful differences. Concerning animal studies, the choice of the animal model and nutritional differences in animal diets need to be considered carefully when designing experiment. It would be relevant to assess dose response relationships, mutigenerational studies and evaluation of both reproductive and post-natal endpoints. Finally, most studies are designed to investigate the effects of a single endocrine disrupting chemical. Although straightforward in term of scientific design, this approach fails to appreciate the chemical soup that is more typical of the human or animal environment. Thus further investigation is needed to evaluate the consequences of simultaneous exposure to phyto-oestrogens and other EDCs on fertility and testicular function.

Indeed. So they are two ideas at war: the idea that nutritionists are gods that can pronounce with good faith on the health effects on industrial foods. And then the more precautionary idea that we really need to look deeper and at the long-term effects. You know what camp I'm on. Unfortunately the money is behind the other camp and people like Mark get paid to blog and write for the layman. 

Honestly, I'm not really against soy per-se. I enjoy tamari and miso soup every so often. These are delicious traditional whole foods. I'm much more concerned with soy in infant formulas and industrial soy products that are engineered for high-levels of consumption. Cutting soy milk out of my diet was one of the best decisions I've ever made and cured me from several digestive ailments and some menstrual irregularities. I was drinking it with every meal because I thought it was a healthy whole food...