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The question of man's co-operation in his conversion gave rise to what was known as the /Synergist/ controversy. Luther had laid it down as a first principle that man contributed nothing to the work of his own conversion, but though Melanchthon agreed with this view in the beginning, he was disposed at a later period to attribute some activity to the human will, at least in the sense that it must struggle against its own weakness. This view was strengthened and developed by John Pfeffinger, a professor at Leipzig, who taught publicly the necessity of man's co-operation (1550), and published a treatise in defence of this position (1555). Pfeffinger's doctrine aroused the opposition of Amsdorf, Flacius, and the other leaders of the orthodox Lutheran party. Leipzig and Wittenberg joined hands to support the doctrine of co-operation, while the majority of the professors at Jena took the opposite side. One of the latter however, Strigel, supported Pfeffinger, and a public disputation was held at Gotha under the presidency of Duke John Frederick. The Lutheran party demanded the punishment of Strigel and his supporters so vigorously that the Duke was obliged to arrest them, but, annoyed by the attempt of the Lutherans to set up a religious dictatorship to the detriment of the supremacy of the civil ruler, he established a consistory composed of lawyers and officials whose duty it was to superintend the religious teaching in his territory. The anti-Synergists, having protested against this measure as an infringement of the rights of the spiritual authority, were expelled, and Jena entered into line with Wittenberg and Leipzig for the defence of Synergism. With the change of rulers came once more a change of doctrine. The princes, alarmed by the violence of the controversy, assembled a conference at Alternburg in 1568 which lasted four months without arriving at any agreement. On the accession of the Elector August the leading opponents of the Synergists, including a large number of the superintendents and preachers, were deprived of their offices.

By his lectures and teaching at the University of Hemstadt George Calixt[4] gave rise to a new and prolonged discussion known as the /Syncretist/ controversy. The Duke of Brunswick having refused to accept the /Formula of Concord/, the professors at the university which he had founded felt themselves much more free in their teaching than those in other centres of Lutheranism. Calixt denied the ubiquity of Christ's body and the attribution of divine qualities to Christ's human nature. Though a strong opponent of several distinctly Catholic or Calvinist beliefs he saw much that was good in both, and he longed for a reunion of Christendom on the basis of an acceptance of the beliefs and practices of the first six centuries. He was charged with aiming at a confusion of all religions, and in proof of this charge it was alleged that he rejected the Lutheran teaching on Original Sin and on man's natural powers of doing good even before justification, that he defended the meritorious character of good works, the supremacy of the Pope, at least /de jure ecclesiastico/, and the sacrifice of the Mass (1639). In 1643 a disputation was held, in which Hornejus, a colleague of Calixt, supported his doctrine especially on the meritoriousness of good works. The appearance of Calixt at the conference summoned by the King of Poland in Thorn (1645) to promote a reunion with Rome, and the friendly attitude which he had adopted towards the Catholics and the Calvinists helped to increase the suspicions of his adversaries. Calixt died in 1656, but for years after his death the spirit of toleration, that he had done so much to foster, was one of the distinguishing features of the University of Helmstadt. It was during this controversy that the Branch Theory, namely, that Catholicism, Lutheranism, and Calvinism formed three divisions of the one true Church, was formulated clearly for the first time.

Amongst the Calvinists the extremely crude doctrine on Predestination taught by Calvin soon proved too much for the faith of many of his followers. Several of them, holding fast by Calvin's teaching, contended that regardless of Original Sin God had created some for glory and others for damnation, that Christ had died only to save the elect, and that to these alone is given the grace necessary for salvation (Supralapsarians). Others, horrified by the cruelty of such a doctrine, maintained that the decree predestining some to hell followed the prevision of Original Sin (Infralapsarians). This view had been put forward by Theodore Koonhort, and had found considerable support, but it was attacked by the majority of the Calvinist ministers, and a bitter controversy ensued. The orthodox party summoned to their assistance Arminius[5] (Hermanzoon), a distinguished young Calvinist preacher, who had attended the lectures of Beza in Geneva, but whose strict views were modified considerably by a sojourn in Italy. Instead of supporting the Supralapsarians, his sympathies were entirely on the side of the milder doctrine, and after his appointment to a professorship at Leyden (1603) he became the recognised head of the Infralapsarians. His chief opponent was Gomar, also a professor at Leyden, who accused Arminius of Semi-Pelagianism.

Arminius, while repudiating such a charge as groundless, rejoined by pointing out that according to his adversaries God was the author of sin. Both appeared before an Assembly of the States in 1608 to defend their views, and though the majority were inclined to favour Arminius, silence was imposed upon the two principals and upon their followers.