We are energy and energy does not disappear. We are programmed for answers that are not available for the biggest questions of our existence. Can we accept that we are part of all of it without evidence and without definition?

This song is obviously getting at the somewhat common Bad Religion motifs of the role of religion, man's place in the universe, and the existence of God. It's essentially driven between these two conflicting lines in the chorus, "I know I'm part of something greater than myself" and "I don't know anything when I'm factored out to scale". That first line gets at Brett's reluctance to definitively state that there is no God, and that the "meaning of life" is that there is no meaning besides chemical duplication. And yet that second line contradicts the first line, stating that even if there is something more out there and it's important, on a cosmological scale the narrator's life is so insignificant that it is essentially meaningless.

The verse in the song tries to get at what is driving narrator to have these "Blenderhead"-esque questions. "A monkey with a madding affliction" refers to the Darwinian idea that humans descended from some form of ape (a theme that you'll see come up again in the similar song, Murder). That "madding affliction" I believe is the sense that I suspect almost every human gets that asks that first question proposed by the narrator, that he doesn't know what the meaning of his life is, but he just knows that there is something to it. And yet throughout the rest of the verse, like the second statement proposed in the chorus, address the narrator's worry that science, or "fact checking", is driving him in the opposite direction.