First of all, I should inform everyone that I am not a mathematician and my question might sound not at all rigorous or maybe even absurd to many of you. But I have been thinking about this problem for some time and I decided to ask it here.
I am an engineer and use math, mostly calculus and differential equations, to model physical systems.
The problem is this: What if nature is "discrete" and the underlying continuity assumption of calculus renders it (or will render it in the future) impossible to model physical systems accurately?
Not getting into what a physical system is, I think it would be possible to solve this problem purely mathematically if one can prove (or disprove) that a discrete mathematical system has inherent properties that a continuous mathematical system cannot map or vice versa. So, is that possible? Does this question even have a rigorous meaning?
PS: I asked my mathematical friend this question and although he was very uncomfortable with my "non-rigorous" sequence of arguments, he did give a very interesting comment. He said that the essence of continuous mathematics, the only thing that sets it apart from discrete mathematics, is the "completeness axiom" which states that a bounded set must have a supremum. [For expample, the set $ (X: X^2 < 2)$ does not have a supremum if we stick to rational (discrete) numbers.] Is that true?
It was this same friend that mentioned the word "isomorphism" to me which I interpreted to mean something along the lines of "functionally similar". Just as complex numbers are similar to 2-d vectors on a plane. So I took the audacity to put that word up on the question.
Please be gentle in your criticism!


Interesting post.
I think it's natural to regard nature as a "continuous system", but I'm not a physicist myself, so I'm not sure about deep concerns about this matter. What I would like to point out is that even though we use continuous models, we can perform computations using discrete approximations as precise as we need them, so I really doubt that using continuous models can blur our understanding of physical systems.
Addressing your question about proving fundamental differences between discrete and continuous systems, I can give you at least some intuition for a very specific "systems". Consider for example the set of integer numbers and the set of real numbers. You have a good intuition about what an isomorphism is: two "structures" are isomorphic if they are "in escence" the same, under some clear definitions and where the "escence" depends on the context. If we go back to our example with $\Bbb R$ and $\Bbb Z$, an "isomorphism" between them should preserve some properties that these two sets do not share! for example, an "isomorphism" should preserve cardinality, but it is the case that (despite the fact that both sets have an infinite number of elements) these sets have different cardinality.
The property that your friend mentioned is another example, but I'm not sure I'd regard the rational numbers as a "discrete" structure since, in the usual definition of a discrete set, we require that the "elements have enough space between them", which is not the case with $\Bbb Q$.