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 language in his public discourses, but his sympathy with the puritan party continued undiminished, and, according to Bancroft (Daungerous Positions, ed. 1593, p. 92), he was one of the members of a ‘synod’ which in 1589 assembled at St. John's College to revise the treatise ‘Of Discipline’ (afterwards ‘The Directory’), an embodiment of puritan doctrine which those present pledged themselves to support. In the same year he was one of the petitioners to the authorities of the university on behalf of Francis Johnson [q. v.], a fellow of Christ's, who had been committed to prison on account of his advocacy of a presbyterian form of church government (, Annals, iv. 134; Lansdowne MSS. lxi. 19–57). His sense of the severity with which his party was treated by Whitgift, both in the university and elsewhere, is probably indicated in the preface to his ‘Armilla Aurea’ (editions of 1590 and 1592), it being dated ‘in the year of the last sufferings of the Saints.’ In the same preface he refers to the attacks to which he was himself at that time exposed, but says that he holds it better to encounter calumny, however unscrupulous, than be silent when duty towards ‘Mater Academia’ calls for his testimony to the truth. He also took occasion to express in the warmest terms his gratitude for the benefits he had derived from his academic education. The ‘Armilla’ excited, however, vehement opposition owing to its unflinching Calvinism, and, according to Heylin (Aerius Redivivus, p. 341), was the occasion of William Barret's violent attack on the calvinistic tenets from the pulpit of St. Mary's [see, fl. 1595]; but the work more especially singled out by the preacher for invective was Perkins's ‘Exposition of the Apostles' Creed,’ just issued (April 1595) from the university press, in which the writer ventured to impugn the doctrine of the descent into hell (, Whitgift, ed. 1718, p. 439).

Against the distinctive tenets of the Roman church, Perkins bore uniformly emphatic testimony; and the publication of his ‘Reformed Catholike’ in 1597 was an important event in relation to the whole controversy. He here sought to draw the boundary-line indicating the essential points of difference between the protestant and the Roman belief, beyond which it appeared to him impossible for concession and conciliation on the part of the reformed churches to go. The ability and candid spirit of this treatise were recognised by the most competent judges of both parties, and William Bishop [q. v.], the catholic writer, although he assailed the book in his ‘Catholic Deformed,’ was fain to admit that he had ‘not seene any book of like quantity, published by a Protestant, to contain either more matter, or delivered in better method;’ while Robert Abbot [q. v.], afterwards bishop of Salisbury, in his reply to Bishop, praises Perkins's ‘great trauell and paines for the furtherance of true religion and edifying of the Church.’

Perkins's tenure of his fellowship at Christ's continued until Michaelmas 1594, when it was probably vacated by his marriage. He died in 1602, having long been a martyr to the stone. He was interred in St. Andrew's church at the expense of his college, which honoured his memory by a stately funeral. The sermon on the occasion was preached by James Montagu (1568?–1618) [q. v.], master of Sidney-Sussex College, who had been a fellow-commoner at Christ's, and one of Perkins's warmest defenders against the attack of Peter Baro [q. v.] His will was proved, 12 Jan. 1602–3, by his widow, whose name was Timothie, in the court of the vice-chancellor. To her he bequeathed his small estate in Cambridge, and appointed his former tutor, Laurence Chaderton, Edward Barwell, James Montagu, Richard Foxcroft, and Nathaniel Cradocke (his brother-in-law) his executors. To his father and mother, ‘brethren and sisters,’ he left a legacy of ten shillings each. Of his brother, Thomas Perkins of Marston, descendants in a direct line are still living.

Perkins's reputation as a teacher during the closing years of his life was unrivalled in the university, and few students of theology quitted Cambridge without having sought to profit in some measure by his instruction; while as a writer he continued to be studied throughout the seventeenth century as an authority but little inferior to Hooker or Calvin. William Ames [q. v.] was perhaps his most eminent disciple; but John Robinson [q. v.], the founder of congregationalism at Leyden, who republished Perkins's catechism in that city, diffused his influence probably over a wider area; while Phineas Fletcher [q. v.], who may have heard him lecture in the last year of his life, refers to him in his ‘Miscellanies’ thirty years later as ‘our wonder,’ ‘living, though long dead.’ Joseph Mead or Mede [q. v.], Bishop Richard Montagu [q. v.], Ussher, Bramhall (in his controversy with the bishop of Chalcedon, William Bishop), Herbert Thorndike, Benjamin Calamy, and not a few other distinguished ornaments of both parties in the church, all cite, with more or less frequency, his dicta as authoritative. By Arminius he was assailed in his ‘Examen’