I said more about this in the longer version of the article, but regarding your analogy, that's related to the distinction between the known-cipher and unknown-cipher case. Your analogy, to the extent that only you understand what remains after applying the standardized decryption, actually has one more cipher at the end that the attackers don't know, which puts it into the "unknown cipher" case. (EDIT: Yikes! That previously said "unknown cipher-text" and has since been corrected.)
And this indeed is a harder kind of cryptanalysis, and I expect cryptanalytic methods to be less productive in the corresponding areas of science -- to the extent that the attacker must first learn the cipher, they have a lot more work to do. But if it's a simple cipher that, say, falls prey to simple frequency analysis, then even that can be broken.
For a further explanation, here's an excerpt of what I was had in the longer-longer version:
Now, there are two kinds of cryptanalysis I'll focus on, and for which I'll give the mapping to a problem in science:
Known-cipher cryptanalysis: Cryptographers usually focus on this kind of attack, because it's usually assumed that "the enemy knows the cipher" (but not the key), or at least, they must make the system safe even in the case where the enemy does know the cipher. This is very much like the problem of parameter estimation. ...
Unknown-cipher cryptanalysis: This is, of course, tougher than the known cipher kind, although (for reasons I won't go into here), cryptographers advice against choosing a cipher based on "the enemy doesn't know of it!" However, over the history of codes and codebreaking, more general methods were developed that allow you to find regularities in the ciphertext from which you can infer the plaintext, even if you didn't originally know what cipher was being used.
[end excerpt]With that in mind, I don't think your analogy carries over as an explanation for why cryptanalysis would fail on scientific problems. Remember, the plaintext being sought is in the form of observations. To the extent that we can infer the plaintext, where the plaintext is yet-to-be-observed data, then we have cryptanalytically solved a scientific problem because we can predict the data, even if we can't ascribe any deeper meaning to it.
In short:
1) The plaintext refers to the meaningful plaintext, and so your example implicitly adds one more unknown cipher, a case generally ignored by cryptographers because of Kerchoff's law.
2) In science, once you can consistently predict future data, you have the (analog of the) plaintext.
Your analogy, to the extent that only you understand what remains after applying the standardized decryption, actually has one more cipher at the end that the attackers don't know, which puts it into the "unknown cipher-text" case.
Maybe. But I don't know that at that point it's a question about what cipher was used... just how to make the resultant data useful for, as you said, predict future data.
You seem to be specifically asking about how to "crack the code" -- I'm saying that even if you "cracked the code", you would st...
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.