latest volume of Techumin has a terrific article by Rav Shlomo Dichovsky entitled "Halachic Reality vis-a-vis Empirical Reality" (מציאות של הלכה בצד מציאות עובדתית). I was pleased to see that he follows the approach of Rav Moshe Shmuel Glasner and Rav Yitzchak Herzog, recently ignored by Rav Bleich. That is to say, he openly admits that Chazal's rulings are occasionally based on beliefs that are refuted by modern science, but argues that this is irrelevant for halachic purposes. Thus, lice may be killed on Shabbos, and worms in fish may be eaten, even though Chazal based these rulings on the mistaken belief in spontaneous generation.
Rav Dichovsky's way of presenting his case uses an interesting strategy that had not occurred to me before. He points out that even within halachah (i.e. regardless of science), there are times when there are conflicting realities. For example, if a man is lost at sea, he is presumed to be alive vis-a-vis his wife (who thus may not marry someone else), but presumed to be dead vis-a-vis his heirs. An even more potent example is from a case in the Gemara regarding two pathways, one of which contains tum'ah, but we don't know which one. If two people walk on the two pathways, and separately inquire if they have become tamei, we reply to each that they are tahor - even though one of them certainly walked on the tamei pathway. Halachic reality is sometimes independent from empirical reality.
It's an excellent article. Note that as well as buying the book on Techumin's website, it is also possible to purchase the individual article as a download for 15 NIS.