The fact that the Church, as led first by John Knox and afterwards by Andrew Melville, claimed an inherent right to exercise a spiritual jurisdiction is notorious. More apt to be overlooked is the comparative freedom with which that right was actually used by the church irrespective of state recognition. That recognition was not given until after the queen's resignation in 1567;[2] but, for several years before it came, the church had been holding her Assemblies and settling all questions of discipline, worship, and administration as they arose, in accordance with the first book of polity or discipline which had been drawn up in 1560. Further, in 1581 she, of her own motion, adopted a second book of a similar character, in which she expressly claimed an independent and exclusive jurisdiction or power in all matters ecclesiastical, "which flows directly from God and the Mediator Jesus Christ, and is spiritual, not having a temporal head on earth, but only Christ, the only king and governor of his church"; and this claim, though directly negatived in 1584 by the "Black Acts," which included an Act of Supremacy over estates spiritual and temporal, continued to be asserted by the Assemblies, until at last it also was practically allowed in the act of 1592.[3] This legislation of 1592, however, did not long remain in force. An act of parliament in 1606, which "reponed, restored and reintegrated" the estate of bishops to their ancient dignities, prerogatives and privileges, was followed by several acts of various subservient assemblies, which, culminating in that of 1618, practically amounted to a complete surrender of jurisdiction by the church itself. For twenty years no Assemblies whatever were held. This interval must necessarily be regarded from the Presbyterian point of view as having been one of very deep depression. But a second reformation, characterized by great energy and vigour, began in 1638. The proceedings of the Assembly of that year, afterwards tardily and reluctantly acquiesced in by the state, finally issued in the acts of parliament of 1649, by which the Westminster standards were ratified, lay-patronage was abolished, and the coronation oath itself framed in accordance with the principles of Presbyterian church government. Another period of intense reaction soon set in. No Assemblies were permitted by Cromwell after 1653; and, soon after the Restoration, Presbytery was temporarily overthrown by a series of rescissory acts. Nor was the Revolution Settlement of 1690 so entirely favourable to the freedom of the church as the legislation of 1649 had been. Prelacy was abolished, and various obnoxious statutes were repealed, but the acts rescissory were not cancelled; presbyterianism was re-established, but the statutory recognition of the Confession of Faith took no notice of certain qualifications under which that document had originally been approved by the Assembly of 1647;[4] the old rights of patrons were