Continuing the discussion regarding organ donation: Previously, I explained that Chazal believed the heart (and kidneys) to be the seat of the mind and soul. As such, the approach of figuring out how to define death based on Chazal's statements about physiology is fundamentally mistaken. But if Chazal did believe that life resides in the heart, would we have to follow them anyway, even if they were mistaken?
In the final chapter of my book Sacred Monsters, I discussed the topic of halachos in the Gemara that are based on mistaken views about the natural world. I favored the approach of Rav Herzog and others, which is that the halachos still hold true, for reasons that I explained in the book. But in this case, there are two crucial differences.
First is that in cases where lives are at stake, nobody follows the Gemara. The classic example of this is that the Gemara says that whereas a baby born in the seventh month of pregnancy can be viable, a baby born in the eighth month is not, and thus one may not violate Shabbos to save its life. Now, people come up with all kinds of explanation as to why the Gemara is not binding - nishtaneh hateva of babies, nishtaneh hateva of medicine - but the bottom line is, pikuach nefesh trumps everything. Nobody is going to let an eight-month old fetus die just because Chazal said it's not viable. So if it is the case that a person's soul is seated in his brain rather than his heart - and I think that is clearly so - then there is no essential halachic problem in pulling the plug, and the pikuach nefesh of saving all the people that can be saved with his organs would supersede the importance of upholding Chazal's authority.
The second difference is that it's not as though the Gemara said "A brain-dead person is still halachically alive." Instead, those who do not hold of brain-death infer this position from various halachos in the Gemara dealing with different aspects of life and death, such determining whether people in a collapsed building are alive. Now, the halachos themselves are perfectly valid, given the medical realities of the period. It is only the inferences, which depend upon Chazal's (and Rashi's) understanding of physiology, which are problematic. Thus, even if the inferences are correct from the point of view of analyzing Chazal, but one ignores them because Chazal had a mistaken view of physiology, one is not contravening any actual halachos in the Gemara.