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Barlow years later, 1680, while the madness was still at its height, James had been presented by Shaftesbury and others as a 'popish recusant,' he took the opportunity of lashing the nation to further fury by the republication, under the title of 'Brutum Fulmen,' of the bulls of Popes Pius V and Paul III pronouncing the excommunication and deposition of Queen Elizabeth and of Henry VIII, with inflammatory animadversions thereon, and learned proofs that 'the pope is the great Antichrist, the man of sin, and the son of perdition.' In 1682 appeared Barlow's answer to the inquiry 'whether the Turk or pope be the greater Antichrist,' giving the palm to the latter (Gen. Rem. 228), and in 1684 his letter to the Earl of Anglesey proving that 'the pope is Antichrist' (ibid. 190). When, 'on Mr. St. John's having been unfortunately convicted for the unhappy death of Sir William Estcourt,' Charles II, fast becoming absolute, interposed the royal prerogative for his pardon, Bishop Barlow published an elaborate tract, 1684-5, in support of the regal power to dispense with the penal laws. This tract was succeeded by 'a case of conscience,' proving that kings and supreme powers have the authority to dispense with the positive precept condemning murderers to death. In the same year (1684) when the persecutions against the nonconformists increased in violence, the quarter sessions of Bedford having published 'a sharp order,' enforcing strict conformity, Barlow, ever discreetly following the tide, issued a letter to the clergy of his diocese, requiring them to publish the order in their churches (Gen. Rem. pp. 641-3). A 'free answer' was written to this letter by John Howe ('s Memoir of Howe, pp. 104-112).

A dispute arising in the parish of Moulton in South Lincolnshire, celebrated in the courts as the case of the 'Moulton images,' gave Barlow an occasion to display his strong anti-popish bias. The churchwardens and leading parishioners, desirous to make their church more decent and comely, obtained a faculty from the deputy-chancellor of the diocese to place the communion table at the east end of the chancel and to fence it in with rails, and at the same time to adorn the walls of the church with paintings of the apostles and other sacred emblems. When done, the pictures proved very obnoxious to the puritanically disposed vicar, Mr. Tallents, and on his protest the bishop's chancellor, Dr. Foster, annulled his deputy's decree. Barlow, being appealed to, sided with the remonstrants, and wrote an elaborate 'Breviate of the Case,' setting forth with great learning the illegality of the whole proceeding. The parishioners, however, appealed to the court of Arches, and the dean Sir Richard Lloyd, gave sentence, 7 Jan. 1685, in their favour, and condemned the vicar and his abettors in costs. Barlow's 'Breviate' was printed after his death in his 'Cases of Conscience' (No. vi.), in the preface to which, by a complete misconception of the editor, it is represented as being called forth by the prosecution of the bishop in the court of Arches for allowing the so-called 'images' to be defaced, and to have been the means of stopping the whole proceedings.

The death of Charles II at once caused a complete reversal of Barlow's policy. He was one of the first to declare his loyal affection for his new sovereign. When James issued his first declaration for liberty of conscience, he was one of the four bishops who, 'gained by the court,' carried 'their compliance to so shameful a pitch' as to send up an address of thanks to the sovereign for his promise to allow the bishops and clergy and their congregations the free exercise of their religion and quiet enjoyment of their possessions, and caused it to be signed by six hundred of his clergy, issuing a letter in defence of his conduct (Gen. Rem. p. 340;, Hist. of Engl. iii. 821). He was much vexed at the refusal of Dr. Gardiner, then sub-dean and afterwards bishop of Lincoln, to sign the address (Tanner MSS.). On the appearance of the second declaration, 1688, Barlow, apparently awake to the probable turn in public affairs, addressed to his clergy a characteristic letter. The caution with which the trimming prelate seeks to avoid committing himself either way, that he may not be compromised whatever course events might take, would be amusing were it less despicable (, Complete History, iii. 512, note i;, Church of the Restoration, iv. 147). This characteristic letter was dated 29 May 1688, a month previous to the famous acquittal of his seven episcopal brethren. A few months later we find Barlow voting among the bishops that James had abdicated, and calmly taking the oaths to his successors. Nor was any bishop, if Wood is to be believed, 'more ready than he to put in and supply the places of those of the clergy who refused the oaths, just after the time was terminated for them to take the same, 9 Feb. 1689 (Ath. Oxon. 335). Barlow died at Buckden in the eighty-fifth year of his age, 8 Oct. 1691, and was buried in the chancel of the parish church, by his own desire occupying the same grave as his predecessor, William Barlow (d. 1613) [q. v.], a monument being affixed to the north wall commemorating both in an epitaph of his own