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This is the famous ecclesiastical section of Calvin's Institutes (Book 4, Chapter 2, Beveridge edition), so often referred to in debates concerning the nature of the visible church.
It includes, in section 12, the indispensable distinction made by Calvin regarding the two ways in which the church is visible (i.e. as seen in those professing the truth [with their children] and also as corporately constituted). Calvin here recognizes the visible church at Rome in that the elect are present at Rome, but goes on to call for separation from Rome in that she, as a corporate entity (being a harlot and not Christ's chaste bride), is not duly (or lawfully) constituted.
The Battles edition of the Institutes (section twelve in this chapter, "The sound elements do not make the corrupted church a true church"), beautifully translates Calvin's summary of this Scripturally faithful argument, "However, when we categorically deny to the papists the title of the church, we do not for this reason impugn the existence of churches among them. Rather, we are only contending about the true and lawful constitution of the church, required in the communion not only of the sacraments (which are the signs of profession) but also especially of doctrine.
Daniel [Dan. 9:27] and Paul [II Thess. 2:4] foretold that Antichrist would sit in the Temple of God. With us, it is the Roman pontiff we make the leader and standard bearer of that wicked and abominable kingdom. The fact that his seat is placed in the Temple of God signifies that his reign was not to be such as to wipe out either the name of Christ or of the church.
From this it therefore is evident that we by no means deny that the churches under his tyranny remain churches. But these he has profaned by his sacrilegious impiety, afflicted by his inhuman domination, corrupted and well-nigh killed by his evil and deadly doctrines, which are like poisoned drinks. In them Christ lies hidden, half buried, the gospel overthrown, piety scattered, the worship of God nearly wiped out. In them, briefly, everything is so confused that there we see the face of Babylon rather than that of the Holy City of God.
To sum up, I call them churches to the extent that the Lord wonderfully preserves in them a remnant of his people, however woefully dispersed and scattered, and to the extent that some marks of the church remain--especially those marks whose effectiveness neither the devil's wiles nor human depravity can destroy (note: this is why the Reformers accepted Roman Catholic baptisms as valid, though not lawful--RB).
But on the other hand, because in them those marks have been erased to which we should pay particular regard in this discourse, I say that every one of their congregations and their whole body lack the lawful form of the church." Without the understanding of Calvin's (and the bulk of other major Reformers) ecclesiology on this point, it is impossible to fully appreciate the Reformer's position regarding separation, schism, the sacraments, the ministry, eschatology, etc.
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