There is a lot of psuedo-arguing going on here. I'm a mathematician who specializes in logic and foundations, I think I can settle most of the controversy with the following summary:
1) Second-order logic is a perfectly acceptable way to formalize mathematics-in-general, stronger than Peano Arithmetic but somewhat weaker than ZFC (comparable in proof-theoretic strength to "Type Theory" of "Maclane Set Theory" or "Bounded Zermelo Set Theory", which means sufficient for almost all mainstream mathematical research, though inadequate for results which depend on Frankel's Replacement Axiom).
2) First-order logic has better syntactic properties than Second-order logic, in particular it satisfies Godel's Completeness Theorem which guarantees that the syntax is adequate for the semantics. Second-order logic has better semantic properties than first-order logic, in particular avoiding nonstandard models of the integers and of set-theoretical universes V_k for various ordinals k.
3) The critics of second-order logic say that they don't understand the concept of "finite integer" and "all subsets" and that the people using second-order logic are making meaningless noises, and all we really can be sure about is ZFC and its consequences, and since the ZFC axioms actually allow us to prove more theorems about objects we care about than the usual formalizations of second-order logic (such as, for example, the consistency of full Zermelo set theory), the fans of second-order logic should just quit and use ZFC instead
4) the fans of second-order logic reply that nothing we actually prove and translate into the language of set theory is false and our reasoning is sound by your standards so stop insulting us by claiming that since YOU can't decide what's true about sets, OUR notion of "property" or "subset" is vague and incoherent. We say that CH is either true of false but we don't know which because we don't have a deductive calculus that settles it which we are confident in, you say that CH is vague and meaningless, but this is a pseudo-problem until either you come up with new set-theoretical axioms which decide CH or we come up with a stonger deductive system which decides it. We can still prove "ZF proves Con(Z)", we just think that the theorems we can derive in pure second-order logic are epistemologically better supported than theorems you need the full power of ZFC to prove (because they already follow from "logical" rather than "mathematical" axioms) and you shouldn't mind us making this distinction.
5) The best theories of physics we have need real infinities and finitely many iterations of the Powerset axiom but Second Order Logic or "Type Theory" is completely adequate for them and it is hard to conceive that questions about higher infinites that require infinitely many iterations of the Powerset operation can be relevant to physics.
6) It is also hard to conceive that any form of mathematical finitism is adequate for making actual progress in theoretical physics, even if results that are proved using standard infinitary mathematics can be reformulated as finitary statements about integers and computations, these nominalistic reductions are so cumbersome that the self-imposed avoidance of infinitary ontology cripples physical insight.
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I think philosophers who think that the categoricity of second-order Peano arithmetic allows us to refer to the natural numbers uniquely tend to also reject the causal theory of reference, precisely because the causal theory of reference is usually put as requiring all reference to be causally guided. Among those, lots of people more-or-less think that references can be fixed by some kinds of description, and I think logical descriptions of this kind would be pretty uncontroversial.
OTOH, for some reason everyone in philosophy of maths is allergic to second-order logic (blame Quine), so the categoricity argument doesn't always hold water. For some discussion, there's a section in the SEP entry on Philosophy of Mathematics.
(To give one of the reasons why people don't like SOL: to interpret it fully you seem to need set theory. Properties basically behave like sets, and so you can make SOL statements that are valid iff the Continuum Hypothesis is true, for example. It seems wrong that logic should depend on set theory in this way.)
This is a facepalm "Duh" moment, I hear this criticism all the time but it does not mean that "logic" depends on "set theory". There is a confusion here between what can be STATED and what can be KNOWN. The criticism only has any force if you think that all "logical truths" ought to be recognizable so that they can be effectively enumerated. But the critics don't mind that for any effective enumeration of theorems of arithmetic, there are true statements about integers that won't be included -- we can't KNOW all the true facts about integers, so the criticism of second-order logic boils down to saying that you don't like using the word "logic" to be applied to any system powerful enough to EXPRESS quantified statements about the integers, but only to systems weak enough that all their consequences can be enumerated.
This demand is unreasonable. Even if logic is only about "correct reasoning", the usual framework given by SOL does not presume any dubious principles of reasoning and ZF proves its consistency. The existence of propositions which are not deductively settled by that framework but which can be given mathematical interpretations means nothing more than that our repertoire of "techniques of correct reasoning", which has grown over the centuries, isn't necessarily finalized.