Lyric discussion by Sekhemnet 

the breakdown 'if there's blood on the roots then there is blood on the branches' I dunno I always assumed it was talking about like the fruits of the spirit, and how if you are not anchored in christ (blood on the roots) then the fruits of your life will be hollow and not of God (blood on the branches) i always took this lyric as sort of a warning on being grounded in the bible and in god.

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