Information posited in a metaphysical picture does imply subjectivity. It implies an interpretation of a signal that extracts semantic meaning rather than just isolating a natural indication (like the way smoke signals fire). Otherwise, "signal" is just any old result of a process that tells us about its cause. Information in the full sense is anthropocentric and thus a slippery metaphor to apply to metaphysics. It entails something like idealism or theism.
Scientists can use the term if they like, but they probably restrict its definition, even though this is slippery because the word has those anthropocentric connotations. Remember, again, that information theory was first used in the context of human technology. The universe isn't necessarily such a technology that's been built for us. Wheeler's account is an exception because it seems explicitly idealistic or mind-centered. Most naturalists take the mind to be epiphenomenal or a by-product of mindless processes.
Can natural processes be explained, though, without turning them into quasi-living things? We're not so far apart here as it might seem since I toy with the idea that pantheism implies something like an animistic re-enchantment of nature, which is comparable to Aristotle's teleology. I cast this in more postmodern, literary terms rather than metaphysical ones, mind you, since I think metaphysics is closer to art/fiction/myth than science.
Anyway, the key question for me is whether a mindless natural process could fail to seem monstrous in the sense of being only quasi-intelligent.
