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"In the following excerpt from an interview included with the official screenplay, Anderson explains his logic."
Q: Of all things, why frogs?
A: It truly came from a slightly gimmicky and exciting place. I'd read about rains of frogs in the works of Charles Fort, who was a turn of the century writer who wrote mainly about odd phenomena. (...) So I just started writing it in to the script. It wasn't until after I got through with the writing that I began to discover what it might mean, which is this: you get to a point in your life, and shit is happening, and everything's out of your control, and suddenly, a rain of frogs just makes sense. You're staring at a doctor who is telling you something is wrong, and while we know what it is, we have no way of fixing it [Earlier in the interview the subject of cancer came up]. And you just go: "So what you're telling me, basically, is that it's raining frogs from the sky." I'm not someone who's ever had a special fascination with UFO's or supernatural phenomena or anything but I guess I just found myself at a point in my life where I was going through some shitty stuff, and I was ready for some sort of weird religious experience, or as close as I could get to one. So then I began to decipher things about frogs and history things like this notion that as far back as the Romans, people have been able to judge the health of a society by the health of its frogs: the health of a frog, the vibe of a frog, the texture of the frog, its looks, how much wetness is on it, everything. The frogs are a barometer for who we are as a people. We're pollutting ourselves, we're killing ourselves, and the frogs are telling us so, because they're all getting sick and deformed. And I didn't even know it was in the bible until Henry Gibson gave me a copy of it, bookmarked to the appropriate frog passage.