Samuel Johnson's refutation of Bishop Berkeley's immaterialism, which says that matter does not exist, is one of those slightly famous moments in the history of philosophy. As the story goes, Johnson and his friends stood outside a church and complained about "Bishop Berkeley's ingenious sophistry to prove the non-existence of matter." They did not believe the idea but did not see a way to refute it. As James Boswell reports it, Johnson answered with great enthusiasm. He kicked or stomped a large stone and declared, "I refute it thus." As see it, such a demonstration only shows that Johnson did not understand the substance of the matter.
What matters about matter is that it's a certain kind of substance, which is to say that matter is refutable and problematic because it is taken as something underlying or standing below (sub-stance) the outward appearances, such as the hardness and heaviness of Johnson's rock. In other words, "substance" is a metaphysical reality, not an empirical or phenomenal reality. Johnson only confirmed the latter, which was not in dispute in the first place. The point is not to defend Berkeley or Idealism but rather to simply unpack this stuff called substance. Pragmatists like William James and Robert Pirsig both reject what the latter called "the metaphysics of substance" - and not just physical substance but also mental substance - so I'll rely on them to help unpack this notion. Let's start with Charles Sanders Peirce's "canonical statement," as the Stanford Encyclopedia describes it, from his essay titled ‘How to Make our Ideas Clear’. (James approvingly quoted this pithy formula):
Consider what effects, which might conceivably have practical bearings, we conceive the object of our conception to have. Then, our conception of those effects is the whole of our conception of the object.
As the SEP article explains, this was the central proposition of Pragmatism and it was meant to be used, among other things, "as a tool for criticism, demonstrating the emptiness of a priori "ontological metaphysics" and "to undermine spurious metaphysical ideas." Oddly, perhaps, Pierce deployed this pragmatic principle to show "that the Catholic understanding of transubstantiation was empty and incoherent." Just as it is with Johnson's rock, the bread and the wine is identified by a certain set of distinctive features found in experience, by a particular set of effects on the senses so, Pierce says, "to talk of something as having all the sensible characters of wine, yet being in reality blood, is senseless jargon". The doctrine of transubstantiation (please notice the root word "substance") says that the bread and wine still look and taste exactly like bread and wine but its underlying substance, which can never be experienced or sensed, has been transformed into the body and blood of Christ. The point is not to dispute theological doctrines but to fully illustrate the difference between empirically knowable rocks and the unknowable material substance that supposedly lurks beneath.
Physicalism or scientific realism is often taken as non-metaphysical or even as anti-metaphysical but it certainly counts as metaphysics, as a metaphysics of substance. And to the extent that empirical science is predicated on metaphysical substances, it's going beyond the empirical world and beyond the proper domain of science. The pragmatists weren't rejecting religion or science as such. Far from it. But they do have very strong reservations about metaphysical claims, claims about essences, or about the things-in-themselves. In the application of the scientific method, Pierce, who was as hard-nosed as a Positivist, said that...
Almost every proposition of ontological metaphysics is either meaningless gibberish--one word being defined by other words, and they by still others, without any real conception ever being reached--or else is downright absurd; so that all such rubbish being swept away, what will remain of philosophy will be a series of problems capable of investigation by the observational methods of the true sciences.
Illustration by James Asher at There Are Real Things.