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Do prototypes necessarily use a sort of ""prototyping"" material? Aren't models made of a different material called a mockup or something of the sort? In that case, the chef example above doesn't work - the new creations are prototypes. 
As for the others, the newspaper industry does use prototypes. That is, the first version referred to above. The first version is the definition of prototype - the prototype is the first version.
The coal industry could benefit greatly from prototypes, and I'm sure they use them already. There are immense safety concerns, to name one only area in which a model, perhaps not full-sized, of a coal mine would work. Additionally, the coal mines themselves are not the only asset of the coal industry - you have countless types of vehicles, mining equipment, and support equipment.
Milking cows - there would of course be no cow prototypes, as cows are not the product of the dairy industry. Instead, milk is. And I would hope there is prototype milk - a sample of the milk throughout its development cycle to make sure it is safe and clean.
As for pet stores, it is right that they would doubtless have a need for a prototype. However, a prototype is used for a product. A pet store has no ""products"", instead they offer a service. They do not produce pets, they recieve and sell them. Even pet breeders do not produce the pets, they just reap the benefits of reproduction.
 03:41, 5 February 2007"