Newton was then living in Trinity College, Cambridge. The autographs of his four letters in reply to Bentley's inquiries are preserved in the library of the college. The first is dated 10 Dec. 1692, the last 25 Feb. 1693. 'When I wrote my treatise about our system,' Newton says to Bentley, 'I had an eye upon such principles as might work with considering men for the belief of a Deity, and nothing can rejoice me more than to find it useful for that purpose. But if I have done the public any service this way, it is due to nothing but industry and patient thought.' He confirms nearly all Bentley's arguments, but demurs to his concession that gravity may be essential and inherent to matter. 'Pray,' Newton writes, 'do not ascribe that notion to me; for the cause of gravity is what I do not pretend to know.' In a later letter Newton speaks more positively, and declares that the notion of gravity being inherent to matter seems to him an 'absurdity.' 'Gravity must be caused by an agent acting constantly according to certain laws; but whether this agent be material or immaterial I have left to the consideration of my readers.' Taken as a whole, Bentley's 'Boyle Lectures' afford a signal proof of his vigorous ability in grasping a complex subject, and of his originality in treating it. The eagerly combative style of many passages reminds us that, in Bentley's view, 'atheism' was no abstract danger, but a foe everywhere present in 'taverns and coffee-houses, nay, Westminster Hall and the very churches.' The opponent against whom Bentley's arguments are more especially levelled is Hobbes, whom he regarded as an atheist in the disguise of a deist. In power of close and lively reasoning, in readiness of retort, and in aptness of illustration, the lectures exhibit Bentley as a master of controversy. Evelyn, who heard the second lecture, writes of it in his 'Diary' (4 April 1692), 'one of the most learned and convincing discourses I had ever heard.' The lectures were published in a Latin version at Berlin, and afterwards in a Dutch version at Utrecht.

In 1692 (the year of his Boyle lectureship) Bentley was appointed to a prebendal stall at Worcester; in 1694 he received his patent as keeper of the royal libraries, and was also elected a fellow of the Royal Society; and in 1695 he became a chaplain in ordinary to the king. Hitherto, since 1682, he had resided with Bishop Stillingfleet. It was early in 1696 that he took possession of the lodgings in St. James's Palace which were assigned to him as royal librarian. Here—as appears from a letter dated 21 Oct. 1697—a small group of friends were in the habit of meeting once or twice a week: John Evelyn, Sir Christopher Wren, John Locke, Isaac Newton, and Bentley. During these prosperous years Bentley accomplished at least one considerable task. He made a collection of the 'Fragments of Callimachus,' for an edition of the Greek poet which was published at Utrecht by John George Graevius in 1697. This collection may be regarded as the earliest example of a really critical method applied to such a work, Bentley was also active in procuring subscriptions for the renovation of the Cambridge University Press, and received authority to order new founts of type from Holland. Evelyn's 'Diary' (17 Aug. 1696) alludes to 'that noble presse which my worthy and most learned friend…is with greate charge and industrie erecting now at Cambridge.'

The famous controversy on the 'Letters of Phalaris' arose out of the discussion, so popular in the latter part of the seventeenth century, on the relative merits of ancients and moderns. Sir William Temple, in his essay on 'Ancient and Modern Learning' (1692), had maintained that the ancients surpassed the moderns in every branch of literature, science, and art. The 'Letters of Phalaris,' for instance, he said, 'have more race, more spirit, more force of wit and genius,' than any other letters in existence. 'I know several learned men (or that usually pass for such, under the name of critics) have not esteemed them genuine;' but genuine, Sir William added, they must be; 'such diversity of passions…could never be represented but by him that possessed them.' Such a panegyric, from a man of Temple's repute, drew attention to the 'Letters,' and in January 1695 an edition of them was published by a young Oxford man, the Hon. Charles Boyle, whom Dr. Aldrich, dean of Christ Church, had induced to undertake it. In the course of preparing his edition Boyle had desired to consult a manuscript which was in the king's library at St. James's, and had written to a bookseller in London to get it collated for him. Bentley, as soon as he was in charge of the library (May 1694), granted the loan of the manuscript for that purpose, and allowed ample time for the collation. The person employed as collator failed, however, to complete his task before the time appointed for returning the manuscript to the library, and the bookseller most unjustly represented to Boyle that Bentley had behaved churlishly in the matter. On the strength of the bookseller's story, and without inquiring from Bentley whether it was true, Boyle wrote in the preface to his book: 'I have