The "pale blue dot" is the Earth. The phrase comes from a photograph taken in 1990 by the Voyager 1 space probe showing Planet Earth as a tiny speck. The astronomer Carl Sagan found the image quite profound, and in 1994 he published a book called Pale Blue Dot: A Vision Of The Human Future In Space where he discussed our place in the Universe.
The song was inspired by Sagan's work. Dream Theater guitarist John Petrucci wrote the lyric, which deals with our responsibility to care for The Earth and also to treat each other kindly, as we're all on this little planet together.
Running 8:26, this opens with a soundscape that integrates audio from various space missions. It then launches into the trademark interplay between Petrucci's guitar, Mike Mangini's drums and Jordan Rudess' keyboards. James LaBrie doesn't come in with his vocal until 2:18.
Some of the lyrics, including the "spineless cowards, fearless warriors" line, come from Carl Sagan's writing. Sagan noted that "every hero and coward" inhabited Earth, making the point that all of human history is but the tiniest mote in the scope of the Universe.
This is a great example of Dream Theater's progressive metal sound. "When Dream Theater came on the scene, 'progressive metal' wasn't even a term," James LaBrie said in a Songfacts interview. "But because we incorporated the metal influence and the progressive, more technical aspects of music, that became a new thing, a new direction musically. It inspired a lot of other bands and still does today. So, when going into Distance Over Time, it was a conscious effort that we wanted to very much incorporate both those elements into this album."
John Petrucci told Billboard several things came together in his life that made him want to write about the Voyager mission and Carl Sagan's famous pale blue dot quote. He added: "It was very specifically about a certain reflection I was doing at that particular point."