Dear Luigi,
You have written a nice essay, much of which I am in agreement. However, I believe that you have made a mistake in the definition of your premise. You wrote:
"The two pillars of any language are syntax and semantics. The former deals with the basic formal structure of the language, while the latter refers to the meaning of the signs and symbols of the language."
which I agree is a correct and meaningful statement, but then you write:
"Nevertheless, in physical sciences, we can identify the theory with the syntax and the experiment/observation with the semantics (e.g. [8])."*
which is a statement of which I cannot agree. If semantics (meaning) can be identified with experiments/observations (data) alone, then we would have no need for syntax (theory). Experiments/observations can only be the basis and support for a particular theory. The meaning derived from any theory then comes from its interpretation. Meaning can never be derived from data alone, which I believe that you fully agree, since your examples show how meaning changes as the theory changes. But one theory can have several differing interpretations.
IMO the meaning behind of the quantum mechanical description of nature is not yet fully understood. This is due to the fact that, even though QM gives a correct mathematical description of experimental results and observations, it still has several different interpretations, none of which is quite satisfactory to give us full understanding of the microscopic nature of reality. It may be that a deeper understanding will never be achieved, and this is a consequence of the true nature of microscopic reality. It is my hope that this is not true.
If I have misunderstood your statement * above, please let me know.
BTW, you wrote:
"Para-phrasing Augustus de Morgan(7 ), I could say that today the two eyes of the knowledge are philosophy and science: scientists remove the philosophical eye, while philosophers remove the scientific eye, each believing that it sees better with one eye than with two."
This statement is a true gem. IMO philosophy is where theory meets interpretation!
Best Regards,
Dan