Let's say that I wanted to send a message to you that I didn't want others to understand, such as top secret information. One obvious method of doing so is encoding my message and then providing you with some kind of encryption key by which to decrypt the message. If I wanted to make certain that clever people couldn't figure out the key (or steal the key), I might get clever and embed the key in the message, and only you knew how to extract the key from the message.
Still, if others were looking for a key, they would try to find the key in the message, and see if what they found could decode the message into something meaningful. To get around this difficulty, I might be a little tricky in how I encode the key into the message, such as embed the key such that it only looks like you can encode the message, but with a little research, you would soon see that some parts of the message are not understood. To understand those parts of the message, you would need to re-examine the key and find clues as to another key - like a second tier of encryption - that opened up more understanding of the message that the others originally thought they understood. In a sense, I could even communicate with you at certain levels of your understanding of the overall key. The more understanding of the key you possessed, the more I could know where you were based on your understanding of the key. For example, what if I wanted to communicate to you classified information, but I wasn't certain how much to communicate to you because I wasn't certain of your level of clearance. If I were real clever, I could encode information in the message based on classification levels. That is, if you had key A, then you would be able to decode the portion of my message that had a classification unique only to A. However, if you had key B, then I would want you to not only decode the contents of my message that is unique to key A, but I also want you to be able to see the portions of my message that are unique to having the key B. I could do this repeatedly, assuming I was a real genius at encoding a message, and it wouldn't require for me to know who I was talking to, only that the person I am talking to possesses a certain key, and with that key they can decode a certain high or low portion of my message.
Now, look at the universe and some of this looks somewhat familiar. We haven't been given any key from what we can tell from science, but what we have been given is a certain amount of reasoning abilities, and with those reasoning abilities we seem to encounter 'keys' or theories along the way of our evolution. Each new successful theory appears to decode the universe (coded message), and where we are in our understanding of the universe is based on where we are in terms of what key (theory) we hold to be our best current set of theories. We assume that later we will have a different set of theories we hold in high esteem, and with that, we believe we'll have a better understanding of the universe.
So, I ask again my opening question. Is the universe a code? Are we merely decoding the universe and at each step in the way we have the 'key' that is unique to our current predicament in the universe (e.g., allows us to read very specific classified documents, and none other)? I'm sure that scientists aren't accustomed to think that they are reading classified information about the world with their current classification rating, but I think the analogy bears some thought.
What does it mean if it is true? Why would we be limited to understanding only a certain portion of the universe as a coded message, and not allowed to read more at this time? Well, extending the analogy further with coded messages, the reasons could be numerous. Some kids code messages as a game, and that is just as much a reason for coded messages as any other. However, there is a clue as to what this 'game' could be about. In the case where I disclose my coded message to unknown decoders with certain keys (e.g., key A, key B, etc), I do so in this manner because I don't know who they are or, at least, what level of classification they possess. However, another reason besides my lack of knowledge, is that I do it because I don't want them (the decoders) to know who I am. That is, if I wanted the decoders to have a certain level of classified knowledge, then I either have to encode my messages like this, or I have to communicate directly with them, and do so with them knowing that they are talking to Someone who possesses highly classified information. By encoding my messages without communicating with my decoders, I can then communicate indirectly with them without them being aware of my presence. The question "who wrote the code?" might be one the decoders will ask throughout their generations, but I don't have to answer that question.
So, this brings up the whole issue on whether the universe is encoded intentionally as a means to allow us to progress without any direct interference from the Encoder. There is only us (the decoders) trying to make sense of the world, using various keys, such as our scientific theories, and then trying to understand as much of the universe as possible. The question "who wrote the code?" may never go away since the whole way in which this universe is 'written' implies that it was written this way intentionally as a means to hide the Encoder as we decode the universe.
One can only hope that at some point the classified information we obtain will provide enough clues as to who wrote the message, but for right now we have to depend on faith that the Encoder is what will give meaning to the message of the universe.