(Web posted: http://users.erols.com/igoddard/soy.htm)
IS THERE REASON TO BELIEVE TOFU MAY CAUSE BRAIN ATROPHY?
The recent study suggesting a link between tofu and brain atrophy  calls to attention animal research showing that the soy-phytochemical genistein reduces DNA synthesis in the brain and inhibits the proliferation of brain cells.  That research tends to support the tofu study, for, since cell replication requires DNA synthesis, genistein-induced synthesis reduction leading to fewer new cells could manifest as atrophy.
The only counter I've seen is that cell-proliferation physiology does not apply to adult brain cells, since they don't replicate. That claim, however, has been invalidated, for it has been shown that neurogenesis--the replication of new brain cells--appears to occur in the brain throughout life. As Dr. David Amaral told The Washington Post (11/21/99): "A decade ago, we still had the notion that you acquired all the neurons you would ever have by the sixth month of pregnancy... It turns out that nothing could be further from the truth." The Washington Post continued:
"Last month, biologists at Princeton University demonstrated that monkey brains constantly produce thousands of new neurons which travel to the cerebral cortex, the center of higher intellectual functions. Earlier studies had documented other examples of neurogensis... The same process occurs in humans. ...researchers at the Salk Institute for Biological Studies in La Jolla, Calif., found evidence of recent cell division in a part of the brain called the hippocampus in every person studied." 
Research in animals shows neurogenesis occurs in several areas
of the adult brain.  Research also shows that reduced
DNA synthesis decreases the number of new brain cells produced.
 Based on the available data, I would dare to posit that IF
in fact genistein inhibits DNA synthesis in the adult human brain as it has been shown to in developing rat brains  (and based on human/animal/soy studies, I see no reason to believe the rat/soy-to-human/soy extrapolation is unfounded), it stands to reason that soy products would reduce neurogensis and/or initiate apoptosis (programmed cell death) in the human brain, which could manifest itself as brain atrophy. In short, there's reason to believe the tofu study  may be accurate.
But Asians Are Smarter
A counter argument to the findings in the tofu study  is that Chinese and Japanese consume more soy products than other people, and yet they have very-high IQs, and thus don't appear to suffering from a chemically induced diminution of cerebral capacity. Sounds plausible on its face, but it should be considered that if Asians have higher IQs, due to nature or nurture, this does not mean they could not suffer decrements of IQ that would go unnoticed if, despite the decrement, they still exceed the average IQ of non-Asians. In short, a 500-lb man would still be very large even after losing 200 pounds.
Another point to consider is that if Asian families care for grandparents more often than in the West, where they may be sent to retirement/nursing homes, such family care might tend to "conceal" the rate of cognitive decline in Asian countries.
Another factor to consider is if Asians have been consuming soy for centuries (while it's relatively new to Westerners), then Asians may have inherited immunities to any toxic agents in the foods they consume, since those who food x happens to harm least tend to survive more, passing on their immunities to food-x-toxins to their offspring. In short, Westerners may be more vulnerable to toxins in Asian foods, although I'm not aware of the races of those in the tofu study. 
Of course I hope what I argue above isn't true, and that soy products ARE the healthy panacea I've always assumed! I've been a vegetarian since I was 13-years old because I believe we need to advance beyond the systematic mass murder sentient beings simply for pleasurable taste sensations. With my refrigerator full of soy stuff, I wish I could be sure now, but until the soy picture gets clearer, the evidence is enough for me to be inclined to err on the side of caution. However, it should be noted that the research indicating an anticancer potential for soy is consistent, and research shows that the cytotoxic properties of soy products are strongly specific, but apparently not entirely exclusive, to cancer cells. If I had terminal cancer, I would consider using soy products!
 Exp Neurol 1999 Sep;159(1):164-76.
Early effects of protein kinase modulators on DNA synthesis in rat cerebral cortex.
 Brain Research, 1998 Jan 19;781(1-2):159-66.
Transmural compression-induced proliferation and DNA synthesis through activation of a tyrosine kinase pathway in rat astrocytoma RCR-1 cells.
 About glial cells: NeuroNews: Modulation of
neuronal activity by glial cells. June 15, 1998
 The Washington Post: The Brain's Power to Heal.
D. Hales and R. Hales, Parade section, 11/21/99, page 10.
 Science 1999 Oct 15;286(5439):548-52.
Neurogenesis in the neocortex of adult primates.
 Proc Natl Acad Sci 1999 Sep 28;96(20):11619-24.
Regeneration of a germinal layer in the adult mammalian brain.
 J Comp Neurol 1999 Aug 30;411(3):495-502.
Neurogenesis in the adult rat dentate gyrus is enhanced by vitamin E deficiency.
 Brain Res Dev Brain Res 1998 Jun 15;108(1-2):39-45.
Developmental neurotoxicity of chlorpyrifos: delayed targeting of DNA synthesis after repeated administration.