We went over this in our english class, and while everyone thought there was some overly complicated theme about nature and humans somewhere in the story, turns out the theme is basically just Mark Twain making fun of humanity. Think about it, Mark Twain was best known for his sense of humor and use of sattire, and so with this story he tries to show the extent of human's idiocy. It begins with the narrator being ever so gullible as to just believe some man's account of his encounter with blue jays, then some crazy man (Jim Baker) in the mountains believing he can truly communicate with animals, Jim then says blue jays have the best grammar while he's using horrific grammar, and then blue jays crowding around a hole trying to put acorns into it, finding a door and seeing their stupidity with the matter of the acorn and the hole, and then laughing at their own stupidity. One might even go to the extent of saying Twain is trying to poke fun at the reader who might interperet the story's theme as to be dealing with nature. So however you wish to word the theme, it's basically Mark Twain using his way of sattire to say how stupid humanity is, (though you could put it in a nicer tone ;) Hope this helps!