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 violent changes in the church. His signature is appended to a suggestion for an amendment of Archbishop Ussher's scheme ‘for the reduction of episcopacy into the synodical form of government’ (, Reliquiæ Baxterianæ, pt. i. p. 240). But he soon saw that this scheme was impracticable, and when he grasped the meaning of the issue he became a fervent royalist. He first came into collision with parliament upon an academic question. The original statutes of the founder of Emmanuel provided that a fellow should vacate his fellowship within a year of taking his doctor's degree. The fellows had succeeded in obtaining the king's permission to rescind this rule, but the representatives of the founder in 1640 brought the matter before parliament, which showed a decided willingness to interfere, and annulled an election to a fellowship (, Annals of Cambridge, iii. 307, note 1). Holdsworth joined with his fellows in making representations to parliament (Baker MS. Cambridge Univ. Libr., Mm. 2, 23, 95–6), and probably resented its action. He was vice-chancellor, and very influential in the university; it is clear that he was reckoned a formidable person from the care with which parliament watched his proceedings. In a formal speech delivered as vice-chancellor he deplored the prospects of religion and learning, praised the existing state of the church, and extolled the completeness of the reformation settlement (Oratio in Vesperiis Comitiorum, at the end of his Prælectiones). Parliament at once took notice of these sentiments, and on 23 July referred the matter to a committee (, Hist. Coll. vol. i. pt. iii. p. 335). Charles I meanwhile appointed Holdsworth one of his chaplains, and offered him the bishopric of Bristol, which he refused, probably because he thought he could do better service where he was. In March 1642 he entertained the king and the Prince of Wales in Cambridge (, Annals, iii. 321–2), and strangely enough was soon afterwards nominated by the House of Lords as one of the members of the Westminster Assembly of Divines. It does not appear that he ever attended any of the meetings of this body. Indeed he was too much engaged at Cambridge, where he continued to hold the office of vice-chancellor during 1642 and 1643. In this capacity he was instrumental in raising money and plate from the colleges for the king's use. But Cromwell was in August 1642 commissioned by parliament to take charge of the county of Cambridge. When the university printer at the end of 1642 published a royalist pamphlet, ‘The Resolving of Conscience,’ by Henry Ferne [q. v.], parliament on 2 Feb. 1643 ordered that Holdsworth, as vice-chancellor, should be brought before the bar in custody (Commons' Journals, ii. 900, 951). Holdsworth was not deterred, and when in the following month a demand was made by parliament for pecuniary aid from the university, he presided at a meeting of the heads, where it was resolved that ‘it was against their religion and conscience to contribute’ (Mercurius Aulicus, 22 April). In May Holdsworth was taken as a prisoner to London on the charge of having authorised the publication in Cambridge of the king's declaration printed at York (Querela Cantabr. p. 7).

Holdsworth was next asked to take oath to the solemn league and covenant; on his refusal his mastership and his rectory of St. Peter's were sequestrated. He was confined first in Ely House, and afterwards in the Tower. It did not help him that he was elected by his friends in Cambridge to the Lady Margaret professorship of divinity, and by a private patron was presented with a living in Rutland. He remained in confinement till 31 Oct. 1645, when he was released on bail, on condition that he did not go further than twenty miles from London (Commons' Journals, iv. 328). Perhaps it was some consolation to him to know that at Cambridge his library was spared by Manchester, on the ground that he intended to leave part of it to the college, and in his confinement he was anxious about the safety of the college plate, which was in his possession. He never seems to have returned to Cambridge, where Anthony Tuckney took his place as master of Emmanuel. His only interest seems to have been to cheer the king among his troubles. He applied for leave to visit him at Holmby House, but was refused. In September 1647 he was allowed to see him at Hampton Court, when Charles conferred on him the deanery of Worcester. It was an empty honour, for Holdsworth died of jaundice on 22 Aug. 1649. As he lay on his deathbed his friends consoled him that he was being taken from the evil to come. ‘No,’ said the dying man, ‘from the good to come,’ and in later days his hopefulness was regarded as a prophecy. He was buried in his former church of St. Peter-le-Poer, where his friend Bishop Brownrigg wrote an elaborate epitaph in his honour (see, Survey of London (ed. 1720), bk. ii. p. 114).

Holdsworth shrank from literary fame. The only work published in his lifetime was ‘The People's Happinesse; a Sermon preached in Marie's, Cambridge, upon Sunday, May 27,’ Cambridge, 1642, and this was published only in consequence of a thrice-repeated request