Regarding chemistry and this subject: The doctrine of transubstantiation predates modern chemistry. In fact, I seem to recall some resistance to modern chemistry by the Catholic church precisely because of the doctrine of transubstantiation. Now, they seem content with nonsensical pronouncements about it, instead of denying chemistry.
"A wise man ... proportions his belief to the evidence."
— David Hume, An Enquiry Concerning Human Understanding, Section X, Part I.