Previously, I discussed the advantages of academic methodology in ascertaining historical realities. In this post, I want to focus on one limitation (there are others) of academic methodology. It is my belief that, in most cases, academic methodology should not be relevant to halachah.
In my book Sacred Monsters, I explained why according to some opinions, even though based on the academic/ rationalist approach we see that Chazal were mistaken in believing that lice spontaneously generate, this should not affect the halachah that it is permissible to kill them on Shabbos. I discussed the case of Tanur Shel Achnai and showed that the Torah has its own protocols which can sometimes diverge from objective reality.
There is a much more common case, which ironically was brought up in the comments to the previous post by someone opposing my viewpoint. I am referring to the prohibition of bishul, cooking, on Shabbos.
It is very clear that from a scientific perspective, whether or not a food becomes cooked depends on factors such as the temperature, the duration for which that temperature is maintained, the specific heat capacity of the food, and so on. Yet the halachos of bishul are based on concepts such as kli rishon, kli sheni etc. To my mind it is obvious that there is no need to change the halachic parameters of bishul, and I don't believe that anyone would ever suggest otherwise. Aside from the fact that the parameters of kli rishon/ sheni have been canonized, they make for a much more useful application of the melachah than temperature and specific heat capacity. The physical reality is used as a rough basis for the halachic concept, but the halachic concept then takes on its own reality which does not change by virture of it not being precisely matched by the physical reality.
In the same way that scientific realities generally do not affect canonized halachah, the discovery of new or more correct manuscripts of ancient halachic authorities should also not affect it. The Chazon Ish's views on this matter are well known; there is a fascinating article in an old issue of Tradition (I think) which discusses it, and notes that if an ancient sefer Torah - even that of Moshe Rabbeinu - were discovered, we would not change our contemporary sifrei Torah to match it! Similarly R. Shlomo Zalman Auerbach was opposed to using the botanical findings of Prof. Yehudah Feliks with regard to changing certain halachos of Pesach, even though he was apparently not opposed to the scientific method per se.
I am sure that some readers will be shocked by this; I recommend that you read (or re-read) the final chapter in Sacred Monsters to appreciate this point of view. (If anyone can provide the precise reference for the Tradition article, I would appreciate it.)