An example of a historical scientific idea (now considered an alternative conception) explained by an analogy
"Both Fitzgerald and Lorentz, however, imagined that there was some absolute 'frame of reference', defined by a hypothetical substance known as 'the ether', through which the Earth was thought to move. Light was imagined as a wave in the ether analogous to waves on the sea, and it was thought to be motion relative to the ether which caused the Fitzgerald contraction."
John Gribbin (1996) Companion to the Cosmos. (Ed., Mary Gribbin) Weidenfeld & Nicolson.
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Many examples of science analogies are listed in 'Creative comparisons: Making science familiar through language. An illustrative catalogue of figurative comparisons and analogies for science concepts'. Free Download.