A fun find in my research for Bookish Words. Multiple writers speaking of the flood as the defacing of the book of nature. Here's Samuel Clarke in 1642: "As Noah, when the deluge of waters had defaced the great booke of nature, had a coppy of every kind of creature in that famous Library of the Arke, out of which all were reprinted to the world: so he that hath God hath the original coppy of all blessings, out of which if all were perished, all might easily bee restored."
Then there's a 1647 pamphlet titled A Word to Lieut. Gen. Cromwel: "Let not us therefore indeed fear any thing, but this only, least God should be our Enemy; For as Noah, when the deluge of waters had defaced the great Book of Nature, had a Copy of every kind of Creature in that famous Liberary of the Ark, out of which all were reprinted to the world; so we, that have God, have the Original Copy of all blessings, out of which, if by this generation of monsters, I mean those that have put the Army into this distemper, all were perished, all might easily be restored again, for God is the best store house a people can have; The Name of the Lord is a strong tower, and the righteous flie unto it and are safe."
This pamphlet riffs on Clarke's words to make a political claim. It's a bit awkward. Several other writers in the later seventeenth century reuse the same phrasing Clarke uses. I haven't yet tracked down whether Clarke was the first, though he is the earliest I've seen so far. My initial response to this bookish metaphor is that it's a messy one, bibliographically.