Short version: Why can't cryptanalysis methods be carried over to science, which looks like a trivial problem by comparison, since nature doesn't intelligently remove patterns from our observations? Or are these methods already carried over?
Long version: Okay, I was going to spell this all out with a lot of text, but it started ballooning, so I'm just going to put it in chart form.
Here is what I see as the mapping from cryptography to science (or epistemology in general). I want to know what goes in the "???" spot, and why it hasn't been used for any natural phenomenon less complex than the most complex broken cipher. (Sorry, couldn't figure out how to center it.)
EDIT: Removed "(cipher known)" requirement on 2nd- and 3rd-to-last rows because the scientific analog can be searching for either natural laws or constants.
Arguably, the entire history of classical astronomy is one big case of frequency analysis: people noticed the repeating patterns in the observable cosmos (ciphertext) to infer future positions of celestial bodies (the plaintext) and the relative period lengths to determine the relative positions of them all and our position/view direction within it (private key).
First, they noticed that light and dark cycle, and called those days. They noticed that moon phases and seasons cycle and came up with years and moon charts. They noticed "wanderers" like mars and venus, and the cycling of those observations led them to postulate future appearances and the kind of cosmos that would lead to our observations. And so on.