I believe this song is centered around government oppression.
"You know there's no free lunch" sounds like it's referring to the Welfare (Social Assistance) system. "My mind feels like a sieve" seems about the endless lies and false promises that politicians feed us. There's so many that it's confusing.
The part about "I need room breathe", is about Capitalist values and mindsets taking over the country. Everything else sounds like karma (what goes around always comes around).

First, in the beginning of the song Graffin refers to a "plastic trend" which (if taken literally) would mean easily formed or influenced in reference to Christian doctrine.

As the song goes on he describes human instinct to need to have structure in life and that the Christian belief was merely a convenient set of rules and laws that both explains and establishes a fear factor that keeps people in line. The emphasis on human nature is apparent when Graffin sings, "what goes around always comes around." The "protected walls" in which all Christians dwell is merely dogma, which is considered unquestionable (look back on Galileo). Sure a "clarion call" might be taken as a positive thing in the eyes of many, however, if you look the word up the definition is "Shrill and clear" the key word being shrill.

Skip down a little and Graffin refers to "countless shadows." An interpretation of shadow would be an imperfect copy of something else. After this he goes on to say "all suffering in the notion of better things to come." This basically says that all Christians do is give up luxuries for an unseen voice.

And, of course, the infamous last couple of lines in which Graffin basically says that, scientifically, heaven and especially hell couldn't possibly hold the population of the earth up until now.

So, clearly, this song has nothing to do with the big bang theory (its just a metaphor of a big explosion of something) and has everything to do with religion.

I think this song is kind of a prediction of things to come with overpopulation and people heeding 'clarion calls.' (i.e. the protesters that have no clue what they're protesting) and of course, thinking that following or resisting certain things is going to change the world (i.e. all the movements that are around today, calling for arms, to create a 'better place') when he knows nothing will change the world.