The distinguishing mark of a man is the hand,the instrument with which he does all his mischief. This is from the book Animal Farm.

No.
A metaphor would have man be something else, or his hands something else. 'Instrument' in the broad sense is just a descriptive noun that can mean anything that can do something, whether it's a tuba or a pencil or a tool or even a piece of paper with certain writing on it.

That sentence is a concept, based probably on the fact that we humans have this prehensile thumb and can build, create, ravage and destroy with our hands.

Joy is correct. No metaphor.

distinguishing mark (subject) = hand (predicate nominative) = instrument (appositive)

Oh OK I get it. Thanks!