I love the lapping water and seagulls in the background of the opening. I'm less fond of the reverb on the vocal line, but hey, it was 1979 and these things happened. Then at 1:56 the real power of the song makes itself felt. As I tried to break it down, I was surprised to realize that musically, the band plays more traditional rock roles than usual. Alex has the wheel firmly in hand, Geddy plays something a little more deliberate, and Neil drums with some serious urgency. If you took out the drum part this section might seem slow, but Neil's rapid-fire ticking makes it feel fast. Is that a metaphor for the way that the pace of change in modern life sneaks up on us? It is if I say so. Which I don't.
At 2:18 we get a little synth bit that calls all hands to rocking stations. The band plays super tight, almost in unison in time if not in melody. Geddy also detonates some serious chops here, but does so in an almost subtle fashion. Around 3 minutes he begins to step out a bit, and then suddenly at 3:15 it evolves into one of those "damn!" moments. It's not that I can't imagine playing it (which was the case for, say, "Freewill"), it's that it's so smooth I could almost overlook it if I wasn't listening for it. There are alternating bits of lyrics punctuated by serious rock until about 5:08.
At that time they change gears and trot out some reggae influence. If you didn't already know, that would make it clear that this was Permanent Waves. Ged throws in some more very smooth play under his singing, as if to remind us that being a real master means making it look easy. I hadn't consciously noticed all the synth sounds in the background at the six minute mark. I'm not sure but I think there may be a frog in there somewhere.
At 6:33 Alex starts his guitar solo, and damn, that's a beautiful tone. I like the way he starts it slow, builds it, goes nuts, and finishes it off in the space of about 20 seconds. It shows off his chops without disrupting the song, since the band already established the pattern of long interludes between lyrical passages.
That pattern ends around 7:20, and by 7:30 we're firmly into the climax of the song, with a new sense of drive in Neil's drumming. Geddy's vocals also get stereo delay, an effect I only appreciate when I'm wearing headphones.
I don't want to get into a detailed examination of Neil's lyrics. I do want to call attention to the way the end of "Natural Science" harkens back to "The Spirit of Radio." Ayn Rand once wrote that the true facts of her life were just a postscript to her fiction, and the postscript would read "and I mean it." I happen to think she fell well short of that ideal, but anyway... in "Spirit" Neil talks about the importance of honesty in making music, not just turning a quick buck with an instrument. In "Natural Science" I think he widens that idea to include everything else as well. If we couple science with integrity, it will "serve us well". The honest man "will still survive annihilation", which implies that the dishonest man may well be devoured by his inability to understand or control the world he creates and inhabits. It's been 31 years and I think that idea holds up pretty well.