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Top 100 Atheist Challenges

The Bible says that God’s eyes are too pure to look upon sin. So then how can the Holy Spirit be present at all times with people (even believers, who still commit sins)?

Interestingly enough, the Bible does not actually say that God's eyes are too pure to look upon sin.  The passage in question is Habakkuk 1:13, which is a prayer in which Habakkuk says this in reference to God.  He is expressing his confusion as to the presence of evil in the world: If God cannot look upon sin (which Habakkuk took as an assumption), why is he allowing all of the pain and suffering that he allows? Obviously, then, “looking upon” has reference to tolerating, or allowing, rather than any kind of vision or knowledge as such.  Habakkuk’s question will be taken up in later questions.