"She'eilat chacham chatzi tshuvah" - if you don't start with the right question, odds are you are not going to get the correct answer. In reacting to the previous post some of the comments suggested that Chazal in Pesachim 94 must be interpreted as being in conflict with science because in the historical context in which they wrote that is the more plausible meaning of the sugya. Putting aside whether this is in fact the case, the central problem with this argument is that it asks the wrong question. When confronted with a text that requires explanation, one can try to: 1) figure out historically what the original meaning of the text was, or 2) figure out what meaning text has to the reader in his/her present day context. The former is how a historian reads a text; the latter is how a halachist reads it. Even if it were theoretically possible to determine which reading of a Talmudic text is closer to its original meaning (answering question #1), that determination has absolutely no bearing on the meaning constructed and assigned to a text by its present day community of readers (question #2). We are halachists, not historians, and our interpretation is needs to be taken on those terms.
For example, I sincerely doubt (with all due forgiveness to Briskers) that the Rambam had in mind notions of tzvei dinim and gavra/chaftza when he wrote the Yad. Historically speaking, R' Chaim imposed his own system of thought on the Rambam; he did not uncover original meaning or authorial intent. Does that make his interpretation false? Only if you are a historian, but not if you are a halachist.
A halachist's concern is for the meaning of the Rambam's conclusion as an abstract philosophical or legal idea for himself and his community. The halachist acknowledges that this meaning is a construct and not a discovery of original meaning, but that does not matter, because Torah interpretation is validated and measured by communal consensus regarding those conclusions and not by degree of historical fidelity to some unknowable original intent.
Roland Barthes essay entitled "The Death of The Author" (thanks to my wife for her help with Barthes) makes the point that a text does not exist as a means to uncover or convey its author's meaning and voice -- "a text’s unity lies not in its origin but in its destination" -- that destination being the reader and the meaning s/he constructs. The difference between lit crit and the reading of Torah is that in the world of lit crit it is up to the individual to construct his/her own meaning; in the world of Torah scholarship meaning is constructed by consensus of the chachamei hador. As that consensus changes over time, meaning changes and Torah evolves ("u'kmo she'hanefashos mishtanos m'dor l'dor *kein haTorah*, v'haynu hatorah sheba'al peh shemischadesh b'chol dor chadashos *al y'dei* chachamei yisrael" -- Tzidkas haTzadik #90).
When we have a halachic conflict between Rashi and Tosfos as to how to read a gemara, the fact that we pasken like Tosfos does not necessarily mean that the Amoraim had Tosfos' interpretation in mind when they wrote the gemara! What it does mean is that the consensus of talmidei chachamim looking at the issue in their own historical context have preferred Tosfos' reading.
As the overwhelming consensus of talmidei chachamim is to accept the idea of pnimiyus haTorah as a means of interpreting Talmudic text, that agreed upon communal consensus becomes the accepted meaning of the text vis a vis the halachic system, irrespective of whether it is historically more or less valid. It is subscribing to that consensus of interpretation which makes for identification with the Torah community.