Dear Flavio and Chiara,
Unless I have misunderstood your essay, it seems to me that what you are proposing is that the methodology followed by us in science determines that which is fundamental in science.
However, where does one draw the line between methodology and theory? Would not some portion of the methodology followed (determinism, etc.) be part of the scientific theory? Certainly to assert,say, determinism to be true feels not much unlike asserting a new theory to be true.
One cannot fall back onto the defense that methodology is not based on empirical knowledge which theories are, for we know that methodologies can be refuted by the appropriate empirical data, which directly implies that methodologies must be based on certain empirical data-if they go that way, they must have arrived that way.
I have not read Karl Popper, and so I must ask you to forgive me if I am ending up blatantly ignoring some evident line of thought contradicting my position.
Essentially, then, my query is this: Can one ever differentiate what you refer to as "philosophical prejudices" from the remaining statements of the theory? Determinism need not be a philosophical prejudice but merely an implication of classical mechanics.
If one cannot, then there need to be found other grounds for giving, say, determinism a higher status than other propositions of the theory. I have suggested in my own essay one such ground.