Seconded, I've wondered the same thing myself and voiced similar concerns here.
It has always perplexed me how WWII US cryptographers managed to get anything done, when the plaintext still looks like gibberish -- further complicated by a novel encoding betweeen a non-western script and EM signals.
My partial answer is this: you would not be able to accomplish anything unless you know something about the real-world referents of the code. So you'll have to do something like a known-plaintext attack. For example:
Send 3 planes to Island A, listen to enemy's chatter.
Send 5 planes to Island A, listen to enemy's chatter.
Send 3 planes to island B, listen ... .
Send 3 boats to island B, listen...
From the differences between the chatter at those times, you can figure out the symbols for island a, island B, plane, boat, 3, and 5.
(Incidentally, I remember you comparing foreign language learning to English lit in that everything's arbitrary and not model based. But it helps to think of learning a foreign language as cryptanalysis through a "known plaintext" attack and differential analysis. Given a bunch of phrases and their foreign translations, find the differences and infer how the language works.)
It has always perplexed me how WWII US cryptographers managed to get anything done, when the plaintext still looks like gibberish -- further complicated by a novel encoding betweeen a non-western script and EM signals.
I believe the Germans had a policy of starting every message with some standard boilerplate, so Allied cryptographers were usually able to perform known-plaintext attacks with only passive monitoring as long as they observed any one message while it was still unencrypted.
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.