The apocryphal books of the second class [the Gospel of Judas, the Gospel of Thomas, etc.] are therefore not divine, because the church hath never chosen to approve them. Therefore, the whole matter (namely, of receiving and rejecting books) depends upon the authority and judgment of the church.
To this Whitaker issues three responses:
1. Since it has the Holy Spirit, the Church does, indeed, distinguish "the true and genuine books from spurious." But how does it then follow that we "judge by no other criterion than the church's determination"?
(Whitaker also suggests that whatever reasons the Magisterium and/or her apologists produce to refuse something like the Gospel to Thomas into the canon, these reasons are also accessible to the Protestant.)
2. Against heretics, the "authority and consent" of the Church on the matter of the canon is a useful and powerful argument. The Church universal is better able to judge the matter of the canon than any private individual (such as a heretic), so its testimony carries a good deal of weight (although Whitaker suggests in the very same sentence that it does not have binding, ultimate authority). The fathers made this argument often enough, yet how does it therefore follow that an appeal to the Church is the only and/or best argument on the subject of the canon? Even some of the fathers Stapleton quotes use other arguments to support the authenticity of the canon.
3. The fathers appealed not just to the authority of the Church, as if it alone were sufficient, but also to "other proofs which were taken and derived out of the books themselves." (Whitaker cites Eusebius and Augustine to support his position. While this testimony is interesting, for the sake of time, I will not address it here.)
Whitaker's response stands on its own, so I only have a few observations to add:
This is a variation of the other canon arguments we've looked at, but I still find it valuable to analyze given my experience over the years on various discussion boards and sites. The argument that the church determines the canon comes in various forms, and I've encountered the one Stapleton uses here often enough. I recall a Catholic once asking how I would show that the Gospel of Thomas should not be considered Scripture (without, I assume, an appeal to the testimony of the Catholic Church). While I am fortunate enough to have the resources at hand to investigate and respond to this kind of challenge, some Protestants don't have these resources and might have to admit they do not know why the Gospel of Thomas might have to be excluded other than it contradicts other Scripture. While this would be a public concession of sorts, I don't think it gives any sort of significant victory to the Catholic position.
The modern versions of these canon arguments stem from an underlying strategy to create epistemological and theological uncertainty in the mind and heart of the Protestant. Consider their similarity to the "33,000 denominations" argument. The (oft-refuted) "fact" of 33,000 denominations within Protestantism is sometimes cited as a means to demonstrate that no lay Protestant could ever hope to determine which one was correct above all others. Therefore (the argument goes) we need some infallible, authoritative body to settle the matter for us. The same reasoning is applied to the canon. There are possibly dozens of documents claiming to be of the Apostles. How will the Protestant ever hope to know which documents are part of Scripture without the help of some authoritative body to tell them?
It's important to recognize this strategy--to create a need where none exist and to quickly fill it with the Magisterium of Rome before any other possible sources are considered--and to deal with it on its own terms. Is the only answer for these kinds of questions to turn to Rome? No, since as noted in the last two posts of the series (see here and here), the Holy Spirit is a valid means by which we can come to know the true extent of the canon (among other items of knowledge). So the question here is not whether we internally--that which is in our hearts and minds--are unable to know the canon. The Catholic can only cast doubt on our external reasons for what we believe. Just as the witness of a parent stands for a child who does not understand the reasons behind it, the testimony of the Holy Spirit stands even if we cannot always explain to someone else why, according to other principles, it does so.
Of course, in this situation we do have recourse to additional evidence and principles (via historical inquiry) to reject books like the Gospel of Thomas as later novelties and to demonstrate the historical reliability of (for example) the Resurrection and the Gospels (thus creating a standard by which the Gospel of Thomas can be judged as heretical). But even if we didn't, it doesn't logically follow that we must turn to Rome to solve the question for us.