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same year he was appointed by the assembly one of a committee for collecting the various acts of parliament against papists, with a view to their confirmation on the king's coming of age (Calderwood, iv. 627); and in 1588 he was appointed one of a committee to confer with six of the king's council regarding the best methods of suppressing papacy and extending the influence of the kirk (ib. p. 652); and also one of a commission to visit the northern parts, from Dee to the diocese of Caithness inclusive, with a view to the institution of proceedings against the papists, the planting of kirks with qualified ministers, and the deposition of all ministers who were unqualified, whether in life or doctrine (ib. pp. 671–2). On 15 Oct. 1589 he was appointed by the king one of a commission to try beneficed persons (ib. v. 64). He was one of those sent by the presbytery of Edinburgh to hold a conference with the king at the Tolbooth on 8 June 1591 regarding the king's objections to ‘particular reproofs in the pulpit;’ and replied to the king's claim of sovereign judgment in all things by affirming that there was a judgment above his—namely, ‘God's—put in the hand of the ministry’ (ib. pp. 130–131). On 8 Dec. he was deputed, along with other two ministers, to go to Holyrood Palace ‘to visit the king's house,’ when after various communications they urged the king ‘to have the Scriptures read at dinner and supper’ (ib. p. 139). At the meeting of the assembly at Edinburgh on 21 May 1592 he was appointed one of a committee for putting certain articles in reference to popery and the authority of the kirk ‘in good form’ (ib. p. 156). When the Act of Abolition granting pardon to the Earls of Huntly, Angus, Erroll, and other papists on certain conditions was on 26 Nov. 1593 intimated by the king to the ministers of Edinburgh, Pont proposed that it should be disannulled rather than revised (ib. 289). He again acted as moderator of the assembly which met in March 1596. On 16 May 1597 he was appointed one of a commission to converse with the king ‘in all matters concerning the weal of the kirk’ (ib. p. 645); and he was also a member of the renewed commission in the following year (ib. p. 692). At the general assembly which met in March 1597–8 he was one of the chief supporters of the proposal of the king that the ministry, as the third estate of the realm, should have a vote in parliament (ib. pp. 697–700). By the assembly which met at Burntisland on 12 May 1601 he was appointed to revise the translation of the Psalms in metre. On 15 Nov. of the following year he was ‘relieved of the burden of ordinary teaching.’ He died on 8 May 1606, in his eighty-second year, and was buried in the churchyard of St. Cuthbert's, Edinburgh. He had had a tombstone prepared for himself, but this was removed and another set up by his widow. Thereupon the session of St. Cuthbert's, on 14 May 1607, ordained that the stone she had set up ‘be presentlie taen down.’ Against this decision she appealed to the presbytery of Edinburgh, and from it to the privy council, which on 4 June ordained ‘the pursuers to permit the stone made by her to remain, instead of that made by her husband’ (Reg. P. C. Scotl. vii. 381).

Pont was three times married. By his first wife, Catherine, daughter of Masterton of Grange, he had two sons and two daughters: Timothy [q. v.]; Zachary, minister of Bower in Caithness, who married Elizabeth, daughter of John Knox; Catherine; and Helen, married to Adam Blackadder of Blairhall, grandfather of Rev. John Blackadder [q. v.] By his second wife, Sarah Denholme, he had a daughter Beatrix, married to Charles Lumsden, minister of Duddingston. By his third wife, Margaret Smith, he had three sons: James, Robert, and Jonathan.

Wodrow states that Pont ‘had a discovery of Queen Elizabeth's death that same day she died.’ He came to the king late at night, and after, with difficulty, obtaining access to him, saluted him ‘King of Great Britain, France, and Ireland.’ The king said ‘I still told you you would go distracted with your learning, and now I see you are so.’ ‘No, no,’ said Pont, ‘I am not distempered. The thing is certain; she is dead, I assure you’ (Analecta, ii. 341–2). The ‘discovery’ was attributed either to a revelation or to his knowledge of the science of the stars.

Besides several of the metrical Psalms, 1565, his translation of the Helvetic Confession, 1566, his contributions to the ‘Second Book of Discipline,’ his calendar and preface to Bassandyne's edition of the ‘English Bible,’ 1579, his recommendatory verses to ‘Archbishop Adamson's Catechism,’ 1581, and to the ‘Schediasmata’ of Sir Hadrian Damman, 1590, and his lines on Robert Rollock (Sibbaldi Elogia, p. 66, in the Advocates' Library, Edinburgh), Pont was the author of: 1. ‘Parvulus Catechismus quo examinari possunt juniores qui ad sacram cœnam admittuntur,’ St. Andrews, 1573. 2. ‘Three Sermons against Sacrilege,’ 1599 (against the spoiling of the patrimony of the kirk and undertaken at the request of the assembly in 1591). 3. ‘A Newe Treatise on the Right Reckoning of Yeares and Ages of the World, and Mens Liues, and of the