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(This is pretty much a logic question.) such as in ⋀y . Py seems to be a kind of placeholder. It occurs after using apply (rule allI) or apply (erule exE. At first I thought it was like a pretend ∀, because of the rule allI which is (!!x. Px) => ∀x. Px (I believe that !! is used to represent in the place I got this from). But I didn't seem to be able to apply allI in certain scenarios which appeared to match this rule. What does really mean? I'm wondering if can mean different things in different situations.

IIM
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is an universal quantifier, yes, but it's the metalogical one. I.e. the one which you use to describe the logic you work in, including . Similarly, is the metalogical implication operator. And these are the only two primitives of Isabelle's metalogic; there is no negation, so it's much weaker than classical logic. See http://isabelle.in.tum.de/coursematerial/PSV2009-1/session2/document.pdf or https://www.cl.cam.ac.uk/teaching/1011/L21/5%20-%20Logic.pdf for more.

Alexey Romanov
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