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What is the difference between the meaning of ‘confession’ and ‘doctrine’ in this context, and what their ‘unity’ is supposed to mean. I know based on my searches that ‘confession’ might mean something like belief or system of beliefs, and ‘doctrine’ might mean principles or teaching. But I want the meanings in the context of Christianity.

It is important to note that Kant did not deny ‘the preeminent importance of its [theology’s] subject’, but that his problems with this discipline were twofold. First, in his view theology falls outside the scope of what can be established by means of human rationality alone. As we have seen, this principal argument was not new, since late medieval nominalists like Ockham had already claimed that the principles of theology cannot be supported by natural reason.30 Second, what was new was Kant’s political argument against the way in which theological orthodoxy was used by the state for its own interests. In fact, such (mis)use had become widespread ever since the Peace of Augsburg in 1555 with its famous maxim cuius regio cuius religio, which had turned religion into a means to bolster the identity of the newly emerging nation states. From now on unity of confession and doctrine often came to be enforced by the state, and it was in this context that the notion of theology as queen of the sciences got its most articulate meaning (one should note that a queen was, first of all, a political figure). Apparently, it was this political constellation that, quite understandably, sparked Kant’s deep dissatisfaction with the academic status quo in general and the role of theology in particular.

How Theology Stopped Being Regina Scientiarum—and How Its Story Continues
Gijsbert van den Brink
Studies in Christian Ethics 13 August 2019

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"Doctrine" is the set of religious beliefs held by someone, usually a church. "Confession" is the statement of those beliefs, usually in the form of a public declaration. Obviously they are closely related but not identical. A church may hold to a doctrine, but it may be implicit rather than openly stated.

"Unity" here has no special theological meaning. What the sentence means is that the state enforced on religious believers that they all held to the same beliefs, made the same public statements about those beliefs, and enforced what those beliefs should be.

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I believe the proper reading is slightly different. It should be understood in the sense of "The state now enforces the unity of doctrine, as well as the unity of confession" rather than "the union of doctrine and confession".

The wikipedia article on the Peace of Augsburg seems to confirm this

It officially ended the religious struggle between the two groups and made the legal division of Christianity permanent within the Holy Roman Empire, allowing rulers to choose either Lutheranism or Roman Catholicism as the official confession of their state

Thus, the political situation the author is speaking of, is that the state itself determines the official religion, and outlaws deviation. Preventing any kind of internal religious division.

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Purpose of the article

The purpose of the article is to propose a new, more productive, role for the faculty of theology in modern universities:

... if we want to re-present theology as a public and rational quest, we should be able to explain in which form and under which conditions it deserves a proper place at contemporary universities and other academic institutions. It is this twofold ambition that forms the agenda of this article. (page 443, end of 2nd paragraph)

What is theology

In Christianity, theology is the study about God and what He is doing with His creation. How do we know the truth about God? Distinct from philosophy whose data is only from what reason and our bodily senses perceive, theology also uses the data that comes from what God reveals about himself. In Christianity this revelation comes from 2 main sources:

  • Bible
  • Tradition, represented either in a church authority (like the Catholic Church Magisterium) or in a confession such as the Augsburg Confession.

When the data from "confession" predominates, this type of theology is called confessional theology (appears in page 448). Christian groups that have a lower view of confession will call their theologies biblical theology.

There is also another kind of theology called natural theology, but this kind of theology does not use data coming from revelation, but only from reason and bodily senses, just like philosophy. This is the kind of theology that Kant approves of.

Meaning of "doctrine" in the article

First, the article mentions doctrine as a shorthand of "sacred doctrine", the way Aquinas understood it, which was identical to theology itself, as the queen of sciences with philosophy as her handmaiden, representing how the medieval university views the place of the faculty of theology.

... the "Queen of the Sciences" (Regina scientiarum) ... is often attributed to Aquinas ... first question of Summa theologiae. Indeed, Thomas Aquinas argues that theology — or, rather, 'sacred doctrine' — not only is a science, but 'from every standpoint ... is nobler than other sciences'.3 (page 443)

But then the article also uses the term doctrine to mean a teaching within a theology, such as "doctrine of the unmoved mover", "doctrines of God" (page 444), "doctrines of Holy Scripture and Christianity" (page 447).

Context of your quote

Shortly before your quote (starting with page 448), the article says that in the first section of his book The Conflict of the Faculties Kant argued 3 things:

  1. The government should not support conservative theology (as had been the case in Prussia).
  2. The Enlightenment values of rationality and freedom from external tutelage should reign in the university.
  3. The faculty of philosophy is the prime guardian of these values, since, unlike confessional theology with its external authorities (such as the Bible and the Augsburg Confession), it follows reason wherever it leads.

Therefore, philosophy should no longer be regarded the handmaiden of theology but rather have a watchdog-function over the other faculties from the standpoint of rationality, critiquing them whenever they transgressed its universal canons. Philosophy had to take over final control in the university from theology. ...

Although Kant does not continue to use this metaphor, it is clear that in his view philosophy has now become the queen of the sciences, leading the way also in religious matters.

What is the problem?

In Kant's view, a university that doesn't have Rationality as watchdog cannot be relevant anymore in producing modern knowledge, especially if the university sees itself as beholden to confessional theology whose result is not amenable to be validated / watched-over by philosophy. This kind of university will eventually become stale, defunct, "rigid, pedagogically retrogade, socially useless" (page 449), etc.

Your quote mentions how the problem is compounded when a confessional theology is being used as "a means to bolster the identity of the newly emerging nation states". If confessional theology remains the queen, then through the theology faculty the nation state becomes the "queen of the university", and therefore, how can there be progress if the university cannot "follow reason wherever it leads" (point #3 above)?

The article then talks about the solution in the next section: The Berlin Settlement (1810).

Meaning of "unity of confession and doctrine"

Now we are in a good position to understand what the author means by:

From now on unity of confession and doctrine often came to be enforced by the state

As described above, "doctrine" here means a teaching about a subject within theology, such as a teaching about God, about salvation, etc. Kant still acknowledges theology's subject's preeminence (God) and how theology can still be a "queen" in this sense (since God is greater than the world). But this "queen" should only exercises its "queenship" when contributing as natural theology, contributing its view on other sciences as metaphysics does to other types of philosophy. So "doctrine" here means a teaching about God based on reason. In other words we have "unity of philosophy and doctrine enforced by rationality".

Is there a room for confessional theology to become queen? Yes, but it can only happen if the teaching (doctrine) and the confession it is based on ("unity of confession and doctrine") is "enforced by the state" who adopts a confession to be the reason for the state's power as in the maxim cuius regio cuius religio since the religio here is defined by a particular confession adopted by a particular ruler.

CONCLUSION: "Unity" here means alignment between the teaching ("doctrine") and its supporting data ("confession"). This is in contrast with how Kant envisions theology to work in the modern university, where the alignment (unity) is a happy working together between natural theology and other disciplines within the university, enforced by rationality.

Postscript

Since the past 200 years, confessional theology has been kicked out from the theology faculties of modern universities (like Princeton, Harvard, etc). That is why churches that have a high view of the Bible and Tradition set up their own seminaries outside modern universities. These are the only institutions that generate confessional and biblical theologies, and they are the queen of their own domain, but unfortunately don't have other departments to rule over.

confessional theology are still being studied in modern universities though, but they become data points in the department of Religious Studies that treat Christianity as just one other religion, whose queen is Rationality as Kant envisioned it 200 years ago.

Even most modern universities that profess to be a Christian university like Notre Dame, Trinity Western University, Biola University, etc. the theology faculty tends to be isolated from the rest, as the various non-theology faculties like Psychology, Literature, Philosophy, etc. follow the same methods and curriculum like in other secular universities, although they tend to be more friendly to Christianity.

Only a handful of Christian universities have given more role to the theology faculty to exercise her medieval role as "queen of the sciences" such as in Wheaton College in Illinois (for Evangelicals) or Thomas Aquinas College in Santa Paula, California (for Catholics).

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