Lyric discussion by purplebluewhite 

This song is in reference to Yahweh, or our God. However the name of the song is a play on words due to the fact that in order to prevent themselves (the Jews) from ever using the Lords personal name in vain they decided not to say it all together (hence the name Ya Hey). The "through the fire and through the flames" portion is in reference to Exodus 3:2 where God calls to Moses from within a bush on fire. The main point of Exodus 3 is that God has seen the suffering of his children in Egypt and has come to rescue them; through sending Moses to bring them out of Egypt and into the promise land. In Exodus 3:13,14 (NIV) Moses said to God “Suppose I go to the Israelites and say to them, ‘The God of your fathers has sent me to you,’ and they ask me, ‘What is his name?’ Then what shall I tell them?” God said to Moses, “I am who I am. This is what you are to say to the Israelites: ‘I am has sent me to you.". Therefore I think that Ezra is saying to God, how can you love them (Israelites/Jerusalem/Zion) and rescue them when they do not love you Lord? He is showing sympathy for God by saying how can you love so much and not get any credit? This song is showing Ezra's adoration for God's unfailing and unconditional love for his children.

He's openly mocking God in the song.

"But you love everything... Oh, you saint"

To be honest, I'm not sure how anyone could read this as "Ezra's adoration for God's unfailing ... love". On this song and elsewhere on the album, his doubts are everywhere. I look at the album as an expression of his inner conflict of believe vs. non-belief, and it certainly seems by the end of the album that he has landed on the side of non-belief.

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