Lyric discussion by TLEStupid 

Atomic bombs? Geez, somebody's overthinking it. Here's what the songwriter says (NME via Wikipedia):

In an interview with NME, Francis commented on the meaning of the song: “It's about winos and hobos traveling on the trains, who die in the California Earthquake. Before earthquakes, everything gets very calm–animals stop talking and birds stop chirping and there's no wind. It's very ominous.

I've been through a few earthquakes, actually, 'cause I grew up in California. I was only in one big one, in 1971. I was very young and I slept through it. I've been awake through lots of small ones at school and at home. It's very exciting actually–a very comical thing. It's like the earth is shaking, and what can you do? Nothing.”

The word "boxcar" was apparently a starting point for the song's lyrics, and Francis has suggested that this was in part inspired by the song "Carnival of Sorts (Box Car)" by R.E.M.: "I probably liked the word 'boxcar' because I heard it on the R.E.M. song, from their first record."

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