This is a RUSH transcript from "The O'Reilly Factor," October 9, 2009. This copy may not be in its final form and may be updated.

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BILL O'REILLY, HOST: In the "Personal Story" segment tonight, author Richard Dawkins is a committed atheist. His new book says evolution should be taught to every child and faith-based beliefs like intelligent design are hooey. His book is called "The Greatest Show on Earth: The Evidence for Evolution." I spoke with Mr. Dawkins a few days ago.

(BEGIN VIDEO TAPE)

O'REILLY: Now, when we last left you, Mr. Dawkins, you were selling your book "The God Delusion," big best-seller, based on atheism is good and those of us who believe are kind of sappy. Now, I want to show the audience the key part of that interview, and then we'll get to your new book. Roll the tape.

(BEGIN VIDEO CLIP)

O'REILLY: I'm throwing in with Jesus rather than be thrown in with you guys, because you guys can't tell me how it all got here. You guys don't know.

Click here to watch the debate!

RICHARD DAWKINS, AUTHOR, "THE GOD DELUSION": We're working on it. Physicists...

O'REILLY: When you get it, then maybe I'll listen.

DAWKINS: Well, if you look at the history of science over the centuries, the amount that's gained in knowledge each century is stupendous. In the beginning of the 21st century, we don't know everything.

O'REILLY: All right. When you guys figure it out, then you come back here and tell me, because until that time I'm sticking with Judeo-Christian philosophy.

(END VIDEO CLIP)

O'REILLY: Tell me where I'm going wrong here. I believe in creative design. I believe in evolution, but I think it was overseen by a higher power, because as we just stated and you acknowledged, you guys still haven't figured out how it all began.

RICHARD DAWKINS, AUTHOR, "THE GREATEST SHOW ON EARTH": There's a great deal that science hasn't worked out, and we don't know how it all began. But it's the most extraordinary piece of warped logic to say that because science can't answer a particular question, you're going to throw in your lot with Jesus. And there's no evidence that he did it either. You would never get any evidence with either of them. Throw in your lot with science which at least is working on the problem.

O'REILLY: Well, here's the problem that I have with throwing in my lot with science. Science doesn't advance the human condition in any moralistic way, and Jesus did. See, my thesis is that if everybody followed the teachings of Jesus Christ, that we'd have peace on earth, love your brother, everybody would love one another, and we'd almost be an idyllic civilization. Now, am I 100 percent sure that Jesus is God? No. But I choose to believe that, because the man was so extraordinary in what he did in his 33 years on earth, still resonates to this day. That, I think, is more powerful than your belief that, "Hey, some day we might figure it all out but, in the meantime, we're not going to believe in any deity."

DAWKINS: Why would you muddle up the question of giving you a moral compass for life, which is important, with the other question, which is explaining the nature of the world, the nature of life, the nature of the universe? That's what science is about.

O'REILLY: OK. And I understand that, but I don't think that my belief system contradicts science. And I believe there is a higher power and, in my life, I can point to it. I see it. But what disturbs me about you guys — and I'm putting you into this category, perhaps unjustly — is that you seem to look down on believers.

DAWKINS: Well, there is a problem when you guys, if I could turn it back on you, try to say that, because you believe what you do, because of a holy book and because of the way you've been brought up, therefore that entitles you to go into science classes and tell teachers what they can or cannot teach. You may think that God oversaw evolution, and that's a point of view that you could probably defend, but leave it out of the science class.

O'REILLY: It's not fair to leave it out of the science class if the science class is incomplete. And you, by your own admission, say we don't know how it all began. So if the science class is going to say evolution only, but I really don't know how it started, that gap has got to be explored.