"Is there an underlying message for atheism in your book or did you simply want to write a fantasy story,
like Tolkien? Kim Mapstead, Friday Harbor, Wash.
What I was mainly doing, I hope, was telling a story, but not a story like Tolkien’s. (To be honest I don’t much care for “The Lord of the Rings.”) As for the atheism, it doesn’t matter to me whether people believe in God or not, so I’m not promoting anything of that sort. What I do care about is whether people are cruel or whether they’re kind, whether they act for democracy or for tyranny, whether they believe in open-minded enquiry or in shutting the freedom of thought and expression. Good things have been done in the name of religion, and so have bad things; and both good things and bad things have been done with no religion at all. What I care about is the good, wherever it comes from."
"...when asked by the Washington Post what famously Christian author C.S. Lewis would think of his books?
'I'm trying to undermine the basis of Christian belief,' says Pullman. 'Mr. Lewis would think I was doing the Devil's work.'"
"And what did he tell the Sydney Morning Hearld in 2003?
'I'm a great fan of J.K. Rowling, but the people - mainly from America's Bible Belt - who complain that Harry Potter promotes Satanism or witchcraft obviously haven't got enough in their lives. Meanwhile, I've been flying under the radar, saying things that are far more subversive than anything poor old Harry has said. My books are about killing God.'"
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The truth of the matter is that an author's work will always reflect his/her belief(s) in some way. Pullman is an atheist and it is okay for us to understand that what he has done is write a series of books in the same style as C.S. Lewis' "Narnia" series. Both series were written with specific agendas in mind. There is nothing wrong with letting us know this.
Here's my take on the whole situation. I don't mind Pullman being open and honest. The very fact that he is back peddling tells me he has another agenda in mind. Could it be that since his first book has been made into a movie, with the others to follow, he wants as many people to read them as possible in hopes that it would destroy their faith or help them see clearly? Frankly, I've read all three books. Though they are decent stories they are not faith destroying in any way. In fact, I would say to parents that they should read the books and let their kids read them as well. During the reading of them, or after, parents and children should sit down and talk about how Pullman portrays the church and God. Pullman does do a good job of showing how any religious (or political) institution can become corrupt when a sovereign God is not a part of it.
Don't let Pullman pull your leg. On the other hand, don't be afraid of Pullman's weak attempt to sway people from God. He tried to be a master of allegory like Lewis but fell short.