Soundgarden keeps posting previews online of songs on King Animal. They explain the song too. Here's what Cornell has to say about "Bones By Birds." 

“[The song] is a little dark,” says Chris Cornell. “It was sort of lyrically kind of inspired by being a father and having children and having that stress. You know, that stress about you don’t want to see them lose their innocence; in a way that when children lose their innocence and sort of learn about the real world it’s never a good thing - it’s always because of loss, something bad happens, something they weren’t expecting.”