Certainly I agree with you that "every aspect of the Universe is sending intelligible messages." The Universe is an intelligible structure, and humans are intelligent beings. As such, the Universe is the "sender," and humans the "receivers." My earlier point was only that "meaning" is only possible for intelligent, self-reflective, conscious beings capable of making judgments. Most of the "information processing" that goes on in Nature is done by entities that do not appear to have this form of consciousness. But the business of Nature gets done notwithstanding.
Please forgive me for belaboring the point, but that is why the Shannon model is so critically important IMHO. It does not deny messages have meaning; it simply avers that "successful communication" is independent of meaning; that is, it doesn't focus on the particular meaning of the message, but rather on the mechanism of its successful communication. Or as George Gilder puts it, Shannon's model concerns itself, not with the "content" of the message, but with its "conduit"; or more simply, its concern is with the medium, not with the message per se. The message could be something richly meaningful — say, Shakespeare's Hamlet — or it could be something utterly mundane (i.e., "blow your nose"). The Shannon model handles all messages in the same way because successful communications of every kind have exactly the same structure. Thus, the model has universal applicability.
You wrote that "the main job of science is to decipher the meaning of those messages." Well, it seems that you and I and TXnMA are all agreed about this. Aristotle would have agreed with this. But how do the vast majority of scientists understand their role today? I hazard the opinion that most aren't concerned with the meaning of Nature, but with how Nature can be instrumentalized and harnessed to human goals.
For Aristotle, meaning was the essential thing. He proposed that we could never meaningfully understand a phenomenon of nature if we could not describe it in terms of four causes — material, formal, efficient, and final — with the description given in natural language.
But a couple of things happened early in the history of science of the most momentous importance. Beginning with the pre-Socratics, the foundations of mathematics and geometry were laid. From that point on, the natural sciences gradually began to speak of their discoveries in the language of mathematics, not natural human languages; and eventually to formulate it as a predictive tool. (Evidently Aristotle tried to resist this mathematizing tendency.) And this represented a tremendous advance for the natural sciences; for mathematics seems to have an uncanny ability to model nature. It is "unreasonably effective," as Eugene Wigner put it. None of this would have come as a surprise to Pythagoras, I feel pretty sure.
A second great revolution was Sir Francis Bacon's expulsion of final causes from the scientific method in the late 16th century.
A final cause refers to purposes and goals — to teleology. Now I don't know how to find meaning in a phenomenon if I don't know what it's for. But evidently, scientists do not worry much about such matters nowadays.
You wrote that "the statistics of the message is interesting, but the meaning of those messages is crucial." Probability theory is the sine qua non of the increasing mathematization of the natural sciences. Hillel Furstenberg (Department of Mathematics, Hebrew University of Jerusalem) has remarked that the great beauty of statistical mathematics is that "probability theory uses human ignorance systematically to create a useful scientific discipline. This in itself is something of a miracle."
However, the efficacy of probability theory depends on the "Law of Large Numbers," which basically states that when there is a sufficiently large number of chance events, there is a very high probability, practically a guarantee, that certain outcomes will occur. But this circumstance does not obtain in macroevolutionary theory, focusing as it does on unique events, not the law of large numbers. Except to note that Darwinism also vigorously eschews teleology, the ramifications of this situation go beyond the scope of the present writing....
Must close for now by saying I'm a Christian, a lower-case "c" creationist, a student of science with a background in philosophy, culture, and history. I'm no academic or working scientist; but I hear what many, if not most of them are saying nowadays.
My conclusion is that if the natural sciences want to "reduce" Nature to a method which is agnostic with regard to either purpose or meaning in Nature, then that just leaves a whole lot for philosophy/theology to do.
In the end, the two great knowledge domains, though seemingly "separate" according to their methods and "mutually exclusive," are finally necessarily complementary for human beings wanting to understand the Universe and their place in it in a meaningful way.
Thank you so much for writing, GGG!