John Henry Newman suggested that one could accept the doctrine of transubstantiation—that the bread and wine become the body and blood of Christ—because human understanding of matter and substance is limited. While it is true that philosophy and science do not fully explain the nature of substance, Newman’s reasoning is problematic. To claim that something is true simply because it is mysterious or difficult to understand is logically unsound. A lack of knowledge about matter does not provide justification for redefining it; it only highlights the limits of our comprehension. Methodologically, we must label and understand things according to observable properties: bread is bread, wine is wine. Accepting that bread is “really a man” based solely on epistemic uncertainty conflates belief with empirical reality and ignores the importance of clear, consistent categorization. Therefore, Newman’s argument fails as a method of reasoning, as it substitutes mystery for evidence and undermines the very principles of logical and empirical inquiry.
Newman was thinking of the bare philosophy of matter, substance etc.
But Catholic doctrine adds to the lack of clarity.
An eye exists to see. If an eye were somehow turned into a marble, it would no longer be an eye because it could no longer perform its essential function of seeing. Similarly, if a marble were said to become an eye without gaining the ability to see, it would still be a marble. The essential powers of a thing define what it is. Applied to the Eucharist, if the bread is said to become Jesus but retains none of the properties of a human being, it cannot truly be Jesus in any meaningful sense. In practice, worshiping the wafer is worshiping bread, because the physical and functional reality of Jesus is not present.