A lot of people who've gone far into shamanism are insistent that trees have a certain spirit and thought (despite lack of what we would call a brain). I can't say I've ever had experiences leading me to feel I can verify the claim, but I do believe I've had experiences suggesting animals might be more conscious than we give them credit for. And I'm willing to generally grant the idea that consciousness may be a pervasive universal quality.
(One person espousing this idea is Peter Russell, in this video on the primacy of consciousness).
Recently I was describing how when humans behave very predictably they start to lose their importance as free agents and might better be modeled as a force of nature. For instance, I remember an instance in which a Christian man linked to an article on The Onion which was a "humorous" opinion column. The Onion joke was written from the point of view of a girl raving about how much she was looking forward to getting an abortion. On his website the Christian railed against it, saying it was an outrage that someone would be so brazen and sick as to think it was fun to kill their unborn child. Hundreds of mocking atheist bloggers linked to his rant, saying it proved that Christians were stupid and couldn't recognize humor. But after a critical link mass had been reached, he changed the page so that instead of being the critique, it was graphic photography of aborted fetuses.
So who turned out to be stupid? Kind of like Jujitsu, he redirected the energy of his opponents to get his message linked... raising his Google rank and possibly bringing those who were eager to click-and-mock closer to confronting the harsh reality of abortion. These human beings acting very predictably can be manipulated, and when that happens the inner consciousness can become ignored and people can be studied as a kind of science. A sufficiently high-level entity might not bother to learn our language, but just start harnessing us based on our predictable behavior...using it to create a desired resource. (I think the Matrix movie went a bit too far in proposing that machines would actually harvest humans for electricity, but metaphorically it makes sense to say it is "energy".)
Thus it wouldn't surprise me if atoms had an internal consciousness, but we are only able to know them (at the moment) for their emergent properties. Perhaps if I took enough LSD I'd be talking to trees like Timothy Leary and listening to their treeish wisdom, yet I don't think that's where I'm going to be doing my investigation. ("If trees could scream, would we be so cavalier about cutting them down? Maybe. If they screamed all the time. For no good reason."--Jack Handey)