An example of nature described through a mechanical metaphor,
"In things without us, ignorance is no wonder; since we cannot profound into the hidden things of nature, nor see the first springs and wheels that set the rest a-going. We view but small pieces of the universal frame, and want phenomena to make entire and secure hypotheses. But if that whereby we know other things, know not itself; if our souls are strangers to things within them, which they have far greater advantages of being acquainted with than matters of external nature; I think then this first instance will be a fair one, for the extorting a confession of that ignorance I would have acknowledged."
Joseph Glanvill (1661) Scepsis Scientifica; or, The Vanity of Dogmatizing
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Many examples of science metaphors are listed in 'Creative comparisons: Making science familiar through language. An illustrative catalogue of figurative comparisons and analogies for science concepts'. Free Download.