Lyric discussion by shanak 

It's not a direct slap a Bush, but rather a general disgust at religious war. Peter and Paul's words (the Bible) are the rules, but the Bible's teachings are the first things lost in war.

I see the "rocking harder" as a reference to how when someone is very, very upset, they'll curl into a ball and rock back and forth. All he can do is sit and wait and hope she makes it home.

He loves her, and he thinks she's being unjustly sacrificed for nothing, and there isn't a damn thing he can do about it. Not even prayer can help.

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