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Okay here’s my full transcript of what he said on this.

“This is fascinating stuff. It also opens up a huge debate. People say ‘how can something this complex come to be out of nothing?’ Well, the logic goes like this. If this motor system is composed of complex individual parts and al these parts work together to perform the overall function of rotating, then how did the individual parts come to be?”

“Did it all have to happen at the same time? Or is there some evolutionary advantage to the cell for every intermediate stage of development? Is 15% of this motor advantageous to the cell? What function would 50% of the structure perform? What were the steps these components took to assemble into such a complex molecular machine in the first place?”

“Scientists are trying to figure this out, and I encourage you to read their papers. Many seem to be focusing on the type 3 secretion system which works like a hypodermic needle that a cell can use to inject other things. This device looks similar but it’s quite different in its protein structure. The complexity and origin of the bacterial flagellar motor is a really interesting conundrum.”

“As I was a younger man and I would read things on the internet and find people saying ‘hey, you gotta believe all this over here.’ People say ‘hey, you gotta believe all this over here.’ There’s a big war going on between science and faith and you’re either in one camp or the other. Get your flag and figure out where you’re going to put your flag.”

“And the more I have matured and started to not really care about defending where my flag is, the more I’ve been able to learn from people no matter where they are. I’m still working on this.”

“There’s a really interesting book I’m reading. I can’t speak for everything in the book, I’m not done with it. It’s called Where the Conflict Reall Lies. And it talks about this interplay between science, religion, naturalism. It’s very interesting. It goes into more into the areas of philosophy and I love it because it challenges me and it’s fantastic. And this is what I would encourage you. If you have your flag in a camp somewhere, I would encourage you not to defend your flag. I would encourage you to look at a flagellar motor and just think about it. Think about how it is and what it be. It’s a fantastic thing to think about. How did this get here? You have intelligence and you get to make up your mind. And I love that about consciousness and I love that about life.”

“And so for me, the flagellar motor makes me happy. I feel joy. You know how when you go outside at night and you look up at the stars and you see all these stars and you feel small and you feel wonder. Thats what this makes me feel like, even though it is small. I feel awe and reverence toward this thing.”

(Okay so far so good, really. I mean it depends a lot on if that book really is just a defense of creationism. But there’s nothing here I can disagree with. And then…)

“And as a Christian, this makes me want to thank God that it exists. I feel compelled with gratitude that this thing is so awesome. So that’s just where I’m at. But what I would encourage you to do is just think critically. You have a brain. Don’t defend a flag. Just think about how things are. And I hope you are happy and experience the same joy I feel about this no matter what you think about it. So anyway, enough about that.”

Okay you’re right. He absolutely turns it to god at the end. It was a really intricately balanced little speech he was making there, and for 90% of it I thought he might be talking to Christians and helping them open their minds to possibilities. He talked about not getting dogmatic. And then he proclaimed “I’m a Christian and I thank god for this!” Which was a pretty idiotic 180 after everything he had just said about not planting flags. And that made me flip and think he was talking to atheists and trying to tickle us into being open to possibilities.

It makes me sad because he’s clearly very intelligent, but if you’re raised on religion it can be extremely hard to ever shed. It’s like getting someone to forget the language they used until they were 10. You can teach them any number of new languages but it’s unlikely they will forget that one.