Astronaut Lyrics
Said the preacher to the astronaut
I heard it's kinda lonesome there
Nothing to talk to but a cold, cold air
Tell me, tell me what was it like?
Did meaning fall from that celestial light?
Did it wrap you up in conversation?
Did it leave you like some ineffable nothing?
Are you feeling alright?
In the blink of a flashing, blinding light
Did you ever really feel anything?
Tell me, are you gonna come back?
Do you really think you're one of them?
They're gonna hunt you, they're gonna cut you
They're gonna open up your body and stuff you
'Til you say its written, 'til you make the payments
Leave you heaving in the twigs and the toxic
There's nothing inside
Tell me, are the words still paralyzed?
In the blink of a flashing, blinding light

I think the first verse here is someone religious talking to an atheist, who believes in science. The second verse is the atheist replying to the religious person.

Also the words "Lies, lies, lies" are before the last line, "In the blink of a flashing, blinding light"

This song is obviously a conversation between a preacher and an astronaut, but to me, I think it covers a wider range of people. I think the preacher represents earthly and Godly people, people who are attatched to a specific belief and home. The astronaut represents explorers, people who are constantly searching for more in their life.
The preacher is scared of the astronaut's life, and vice versa, so the preacher asks all kinds of questions regarding how different of a person the astronaut is after his explorations, such as: "Do you still believe in God?" "Did meaning fall from that celestial light?" As for the latter question, I think the preacher is asking whether or not the astronaut found his answers through his new life.
So to summarize it, I think this song is a representation of a conversation between two lifestyles, the pros and cons, how certain things worked out, and so on.

I agree that the first verse is preacher -> astronaut, but I think it's about losing your faith. The preacher has always doubted his religion, and looks to an astronaut (representing science) to confirm his belief that there is no God. Lines like "I heard it's kinda lonesome there" and "Nothing to talk to but a cold, cold air" deal with the preacher's idea that there's nothing out there. The last line, "in the blink of a flashing, blinding light", is a direct reference to the Big Bang.
In the second verse we have the astronaut's perspective. He's been asked by a devout religious man whether or not he believes in God after going to outer space. The astronaut counters with "Are you feeling alright? Did you ever really feel anything?", which is suggesting that the preacher must have never had faith in what he believed if he is asking the astronaut his opinion. The astronaut talks about how after the preacher has come out and said this, he won't be accepted back into his faith "Do you really think that you're one of them? They're going to hunt you, they're going to cut you..." until the preacher 'says it's written, and makes the payments". It ends with a brilliant bit of lyricism where the last syllable of paralyzed is repeated as "lies, lies, lies", referring to the astronaut's indecision.
Oh, and the song is awesome. The drummer is unbelievable on every song this band makes and, just like every other song on the album, the rest of the band is providing haunting instrumentation. Awesome song on my favourite album.