Lyric discussion by curious1 

Cover art for Three Seed lyrics by Silversun Pickups

like mostermouthattacks i think this is about the death or suicide of a son. Not so much an abortion though. "i can see the pictures on the floor sketches of what was there before" here he is looking at old pictures of him with his partner or wife and his son, and what used to be. "three came from one little seed the last one is all i need" and here, i think, he is explaining his son came from the "seed" of his partner, and the three of them exist because his son was concieved. Also i think he is saying since his son was the latest addition to his family, he's the only thing he needs for everything to be right again. "i can hear the bottle on the ground we turned the corner safe and sound no thought of him as it was done a clean execution" here he is describing the way his son died. he hears the bottle (either a perscription bottle that he may have overdoised on or some kind of posion in a glass bottle) hit the ground. Then him and his partner turn the corner to their sons room, alive and well("safe and sound"), to find him dead or unconcious. and since it was an overdoise or poisoning there really isnt a mess just him body ("a clean execution). the next verse, like descendent said, is a stuggle with religion. When drastic things ,such as the death of a son, heppen to people they often question their religion to help them through tough times. But even though he quetions it he still "signs right in again." I know that sounds very emo, but its just my opinion i could be way off.