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Bathurst considerable eminence in his profession, and in spite of being a royalist was employed by the state as physician to the sick and wounded in the navy, in which capacity he is said to have given great satisfaction ‘both to the sea commanders and the admiralty.’ He did not, however, forget his clerical calling, one branch of which he exercised with imminent risk to himself. Robert Skinner, the ejected bishop of Oxford, was allowed to hold the rectory of Launton near Bicester, where, notwithstanding the danger of so doing, he was wont to confer holy orders. On these occasions Dr. Bathurst used to act as his archdeacon, the proximity of Oxford enabling him to visit Launton under the pretence of attending his patients. It is said that the ordinations were sometimes held in the chapel of Trinity College, where Dr. Bathurst still retained his fellowship, having submitted to a temporary compliance with the conditions of the parliamentary visitation of 1648. As fellow of Trinity he was able to do good service to an old friend; for after the death of Cromwell he persuaded a majority of the fellows to elect Dr. Seth Ward as president, though disqualified for the office by the college statutes. Dr. Bathurst took a prominent part during the rebellion in the formation of that little band of scientific men at Oxford which was the germ of the Royal Society. Bishop Sprat mentions him among ‘the principal and most constant of those who met in Dr. Wilkins his lodgings in Wadham College, which was then the place of resort for vertuous and learned men.’ In 1650 he prefixed a recommendatory copy of Latin iambics to Hobbes's ‘Treatise of Human Nature;’ but it is clear that at this time (1650) Hobbes was not regarded by churchmen as a dangerous writer, for Seth Ward also wrote a commendation of Hobbes. These iambics recommended Bathurst to the notice of the Duke of Devonshire, eldest son of that Earl of Devonshire who was Hobbes's patron, and it was through the duke's interest that he subsequently obtained the deanery of Wells.

Upon the Restoration he abandoned medicine and openly resumed his clerical character. In 1663 he was made chaplain to the king, and in 1664 president of Trinity; in the same year he married Mary, widow of Dr. J. Palmer, warden of All Souls. He was elected fellow of the Royal Society in 1663, and in 1688 president of the branch of it established at Oxford. In 1670 he was made dean of Wells, still retaining his presidentship; from 1673 to 1676 he was vice-chancellor of Oxford, and in 1691 he refused the offer of the bishopric of Bristol, with license to keep the deanery and headship in commendam, because he thought it would interfere with his work in college. The work referred to was ‘the repairing, adding to, and beautifying of the college buildings.’ Trinity is deeply indebted to him both for his pecuniary and his personal help in this matter. The college chapel, which had been injured in the civil war, was rebuilt through his means; he completed the shell entirely at his own cost (2,000l.), while the furniture and internal decorations were supplied through collections which he made. The architect was probably his friend, Dean Aldrich, but the original plan received some improvements from Sir Christopher Wren. It is supposed that this chapel was built in imitation of the chapel at Chatsworth erected by Bathurst's patron. The new quadrangle facing the fellows' garden was also built through his exertions. Wren was the architect, and it was finished in 1668. Nor were these the only college buildings which were due to his liberality and energy; he is said to have spent nearly 3,000l. of his own money, besides purchasing for 400l. the rectory of Oddington in Otmoor, near Oxford, for the Trinity fellows. He lived on terms of intimacy with all the great Oxford churchmen of his time—Skinner, Fell, Aldrich, South, Allestree, and, above all, Seth Ward, who calls him ‘one of the worthiest men his time affords.’ Hence it is not probable that there is any truth in the report that he was unsettled in his religious views, a report which perhaps arose from the fact of his having written favourably of Hobbes. He had evidently, however, wide sympathies, for Calamy tells us of an ejected nonconformist who resided at Oxford, and ‘was very great with Dr. Bathurst, whom he would often speak of as a very polite catholic-spirited person, and of great generosity.’ There is reason to believe that Bathurst helped this good man pecuniarily.

Bathurst was an eminently successful president of Trinity, raising the college both intellectually and socially. No doubt the fact of his being connected with the aristocracy attracted young aristocrats to Trinity. Among others was his own nephew, the well-known Earl Bathurst, Pope's friend, who has given us an amusing account of his uncle's rule. Though the nephew was only fifteen when he entered at Trinity, while the uncle was beyond eighty, the earl told Bathurst's biographer that ‘he well remembered being charmed with his uncle's conversation;’ and he adds, ‘although he maintained the most exact discipline in his college, his method of instruction chiefly consisted in turning the faults of the delinquent scholars into ridicule; all the young students admired and loved him.’ The fact is, he was fond of the society of young