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I agree with you on the most important line, but I disagree with your interpretation. The story of the animals is true but Pi understands that most people are not willing to believe what they don't understand. Out of frustration he retells the same story in a more gruesome but more believable form. His "so it is with God" comment address people who refuse to believe in God because they can't understand how a God could exist. Interesting how different our takes are on the story.