The patent on the Shopping Cart Metaphor is extremely concerning to me as a designer and programmer.

The digital "Shopping Cart" is nothing more than a metaphor, similar to digital "pointing" is a metaphor. These metaphors are the basis by which we design computer interactions. There's nothing technically unique or special about the term or interaction design of a shopping cart, yet it seems the patent has held.

Can a metaphor really be "patented" in this way? How can a metaphor not be "Prior Art"?

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This is a legal question, and perhaps not on-topic for a skeptics site. That being said, this may be helpful to bear in mind: patents are awarded only for ideas deemed to be novel, non-obvious and useful. Whether the idea is a metaphor is not a relevant consideration except insofar as being a metaphor affects the three criteria. As you point out, there may be prior art, which in turn may go to the novelty of the idea. However if the patent was awarded, clearly the prior art was not persuasive to the examiner. – Brian M. Hunt Feb 4 at 21:30
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Agreed: there seem to be no claim here to investigate. It seems a "let's chat about this interesting topic" question. – Sklivvz Feb 4 at 22:15
"patents are awarded only for ideas deemed to be novel, non-obvious and useful". Unless you are in the US. – DJClayworth Feb 6 at 14:35
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closed as off topic by Sklivvz Feb 4 at 22:15

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