The doctrine of transubstantiation has two primary components:
- The real presence of Christ's body and blood
- The real absence of bread and wine.
Some objections center on the Real Absence. After all, it looks like bread and wine are present—why would God make our senses deceitful?…(Quick answers: Senses give prima facie reasons to believe, but in the context of the liturgy as a whole there is no deceit as it is explicitly stated that this is Christ's body and blood.
i) To my knowledge, most contemporary Catholic intellectuals espouse theistic evolution. And at least some, if not many, Catholic intellectuals have contempt for young-earth creationism. They think young-earth creationism is intellectually dishonest. Rides roughshod over the evidence. Indulges in special pleading.
ii) However, let's compare that to faith in transubstantiation. If true, then transubstantiation is at least as skeptical as mature creation, if not more so. In mature creation, artifacts of fiat creation appear to be older than would normally be the case given conventional natural processes. However, if you see an instant tree, it's still a tree. So even though it looks older than it would if it was produced by the usual process, there's a truthful correlation between what you perceive it to be and what it is. A tree appears in your field of vision. You interpret the image to be a tree. And, in fact, that's what it is.
Moreover, it's not as if natural objects have an intrinsic appearance of age. Rather, that's relative to the usual rate at which they occur and endure.
The closest thing to illusion in mature creation would be, say, supernova, where the effect exists even though there was no stellar explosion to produce that effect.
iii) Compare that transubstantiation. If true, all five of our senses systematically deceive us. And not just our unaided senses. If we subject the consecrated bread and wine to chemical analysis, it still appears to be bread and wine. So it's sensory deception all the way down. And undetectable illusion. There's no correspondence between what we perceive and what it really is. In principle, the consecrated bread could be an elephant, or Mt. Fuji, or a velvet Elvis painting. The relation between appearance and reality is entirely arbitrary. It's more radical (i.e. scientific antirealism) than mature creation.
Let's assume for the sake of argument that the empirical evidence for evolution (i.e. macroevolution, universal common descent) is absolutely overwhelming. All the evidence points in that direct. There's no counterevidence. Yet given the principle of transubstantiation, that could be a Matrix-like illusion.
The justification is that the dogma of transubstantiation corrects or overrides our misinterpretation of the sense data. But, of course, young-earth creationists lodge a parallel appeal: mature creation is a revealed truth. God has explicitly told us how he made the world–appearances to the contrary notwithstanding.