So I could be wrong. I'll make an attempt here.
If finding a complete and consistent set of axioms for all of mathematics is impossible this implies to me that the hard sciences, physics, chemistry, etc. are also limited by Godel's theorem given their reliance upon that same system of mathematics.
Hello Gnomon
Godel approximately says: In any sufficiently strong formal system there are true arithmetical statements that cant be proved (in the system).
More rigorously: If S is a formal system such that (i) the language of S contains the language of arithmetic, (ii) S includes Peano Arithmetic, and (iii) S is consistent, then the consistency of S, is not provable in S.
Freeman Dyson wrote:
Gödels theorem implies that pure mathematics is inexhaustible. No matter how many problems we solve, there will always be other problems that cannot be solved within the existing rules. because of Gödel's theorem, physics is inexhaustible too. The laws of physics are a finite set of rules, and include the rules for doing mathematics, so that Gödel's theorem applies to them. (NYRB, May 13, 2004).
According to Dysons argument, there cant be a Theory of Everything (TOE). It is also said that after having supported the pursuit of a TOE, Hawking concluded in his Dirac lecture of 2002 that there cant be such a thing on account of Gödels theorem.
(Some thinkers however say that physical laws encapsulated within the System S can be known in completeness, although there are propositions of higher mathematics that are undecidable in S.).
The second problem is Under-determination of Scientific Theory.
http://plato.stanford.edu/entries/scientific-underdetermination/