Protestant apologist Jason Engwer, in his online article, “You Ought To Believe In A Real Absence,” wrote:

Biblical precedent gives us reason to conclude that no physical transformation has occurred if there’s an absence of physical evidence of such a transformation. For example, in John 2, Jesus didn’t change the water into wine under the appearance of remaining water. He didn’t heal lepers and blind men under the appearance of their remaining leprous and blind. Physical miracles produced the sort of corresponding physical evidence you’d expect. The absence of such evidence in the context of the eucharist is most reasonably taken as implying the absence of such a physical transformation.

This is untrue. Jesus had a body after his resurrection (and he encouraged his disciples to touch him, including his wounds, to establish this fact), but it was a glorified body. He could, for example, pass through walls in a way that we normally deem to be physically impossible (yet which modern quantum physics actually claims is entirely possible): 

• John 20:19 (RSV) On the evening of that day, the first day of the week, the doors being shut where the disciples were, for fear of the Jews, Jesus came and stood among them and said to them, “Peace be with you.”
• John 19:26 Eight days later, his disciples were again in the house, and Thomas was with them. The doors were shut, but Jesus came and stood among them, and said, “Peace be with you.”

Ellicott’s Commentary for English Readers (1905) explained these passages:

The obvious intention is to point out that the appearance was preternatural. The body of the risen Lord was indeed the body of his human life, but it was not subject to the ordinary conditions of human life. The power that had upheld it as he walked upon the Sea of Galilee (John 6:16-21) made it during those forty days independent of laws of gravitation and of material resistance.

Likewise, Meyer’s New Testament Commentary (1880):

It points to a miraculous appearance, which did not require open doors, and which took place while they were closed. The how does not and cannot appear ... the constitution of his body, changed, brought nearer to the glorified state, although not immaterial, is the condition for such a liberation of the Risen One from the limitations of space that apply to ordinary corporeity.

Now, one could say that the “physical evidence” (I suppose) was his passing through the wall of the house, but how is that “physical” in an empirical sense? As far as the disciples were concerned, Jesus still had a normal physical body. He even ate with them. 

For that matter, how would someone “physically” prove that Jesus was God, even before he was resurrected? By looking at his cells in a microscope? There was no way to do that. The Incarnation has to be received with faith as a supernatural miracle. So why does Jason demand so much more of the Eucharist?

Therefore, “Biblical precedent” indeed “gives us reason to conclude” that a “physical transformation has occurred” in the “absence of physical evidence of such a transformation.” The truth is the opposite of what Jason claims. And it is an analogy to transubstantiation. Moreover, this is not the only biblical example:

• Exodus 13:21 And the LORD went before them by day in a pillar of cloud to lead them along the way, and by night in a pillar of fire to give them light, that they might travel by day and by night; (cf. 14:24; Num 14:14; Neh 9:12, 19)

Note what is happening here. We’re talking about actual clouds (a form of water) and fire, which “consist[s] primarily of carbon dioxide, water vapor, oxygen and nitrogen” (Wikipedia, “Fire”). Yet God is somehow “in” both of them (so much so that the ancient Hebrews would worship God facing this cloud: Exodus 33:10). How? How could one tell the difference between a regular old cloud or a fire and the ones that God was “in”?

They couldn’t (by scientific/empirical criteria). And no one could today, either, if God did that again. The only difference is that God said he was in both, in particular circumstances when both formed a “pillar.” But that’s not physical proof. It’s revelation. And it is exactly the same, analogously, as what we have in the Eucharist (substance changing without the accidents or appearances changing).

With regard to fire with God specially “in” it, we also have the burning bush (Exodus 3:2-6), which is not only fire, but also called an “angel of the Lord” (Exodus 3:2), yet also “God” (3:4, 6, 11, 13-16, 18; 4:5, 7-8) and “the LORD” (3:7, 16, 18; 4:2, 4-6, 10-11, 14) interchangeably. Also, the Bible states: “Mount Sinai was wrapped in smoke, because the LORD descended upon it in fire” (Exodus 19:18).

One could arguably make similar points about many other miracles, too. God all of a sudden made a donkey talk to Balaam (Numbers 22:21-31: “the LORD opened the mouth of the ass”: 22:28). Now, how would one go about demonstrating a physical change in the donkey, which now enabled it to speak (whereas we normally assume that animals do not speak, and not in the language we understand)? 

Would a neurologist be able to examine the brain of the animal and figure out how it could speak; what change was in the brain compared to those of non-speaking donkeys? I doubt it. But Bible-believing Christians think this actually happened and that we can’t hyper-analyze and explain it through the usual scientific means of verification. 

Thus, here again there was no outward change (the “accidents” perceived by our senses remained the same), but a miracle occurred in which a donkey talked. In other words, it is analogous to the Eucharist. In both instances, change occurs that we can’t examine under a microscope, but believe in faith because Our Lord or the Bible told us to so believe.