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Baillie the Scottish metropolis in recommendation of the Canon and Service Book then published. He did not see his way to do so, and his letter giving his reasons for refusal is still of interest. Events were thickening to disaster. In 1638 he was chosen by his own presbytery of Irvine a member of the historic general assembly at Glasgow, which heralded the civil war. He spoke out courageously and unmistakably against the obtrusion and Arminanism of Laud. In 1640 he was sent by the covenanting lords to London, to draw up an accusation against the archbishop. His 'Letters and Journals' of the period reflect the lights and shadows of events. In 1641 he published his 'Antidote against Arminianism;' 'The Unlawfulness and Danger of a Limited Prelacie and Episcopacie;' 'A Parallel or Briefe Comparison of the Liturgie with the Masse-Book, the Breviarie, the Ceremoniall, and other Romish Ritualls;' 'Laudensium Aὐτοκατάκρισις;' and 'The Canterburian's Self-Conviction; or an Evident Demonstration of the avowed Arminianisme, Poperie, and Tyrannie of that Faction, by their owne Confessions; with a Postscript to the Personat Jesuite Lysimachus Nicauor.' These extraordinary books had been preceded by daring action. For in 1639 he accepted the chaplaincy of Lord Eglinton's regiment, and was with the army of the covenanters at Dunse Law under Leslie (Letters and Journals, ed. Laing, i. 174). The treaty of Berwick led to a temporary cessation of the unhappy strife. But again in 1640 he appeared in arms with the covenanters. It was from the heat of these bold acts that he proceeded to London. In 1642 he was again in Scotland, and appointed professor of divinity along with David Dickson, in Glasgow University. His reputation was great, so much so that the other three Scottish universities contended for his services. He was frequently absent in London, having formed one of the renowned Westminster Assembly. He returned to settle finally in Scotland in 1646. Other theological and ecclesiastical books had in the interval, and in this year, appeared—e.g. 'Satan the Leader in Chief to all who resist the Reparation of Sins; as it was cleared in a Sermon to the Honourable House of Commons at their late Solemn Fast, Feb. 28, 1643:' 'Errours and Induration are the great Sins and the great Judgments of the Time; preached in a Sermon before the Right Honourable the House of Peers in the Abbey Church of Westminster, July 30, 1645;' 'An Historicall Vindication of the Government of the Church of Scotland, from the manifold base Calumnies which the most malignant of the Prelates did invent of old, and now lately have been published with great industry in two pamphlets at London: the one intituled "Issachars Burden," &c., written and published at Oxford by John Maxwell, a Scottish Prelate, &c.," 1646;' 'A Dissuasive from the Errours of the Time; wherein the Tenets of the Principall Sects, especially of the Independents, are drawn together in a Map, 1645-6; ' 'Anabaptism, the True Fountaine of Independency, Brownisme, Antinomy, Familisme, &c., or a Second Part of the Dissuasive from the Errours of the Time, 1647.' His larger books, published later, are: 'A Review of Dr. Bramhall, late Bishop of Londonderry, his Faire Warning against the Scotes Disciplin,' 1649; 'A Scotch Antidote against the English Infection of Arminianism,' 1652; 'The Dissuasive from the Errours of the Time, vindicated from the Exceptions of Mr. Cotton and Mr. Tombes,' 1655; 'Opus Historicum et Chronologicum,' published at Amsterdam, 1663.

When, after the beheading of Charles I, Charles II was proclaimed in Scotland, Baillie was one of the divines appointed by the general assembly to wait upon his majesty at the Hague. On 27 March 1649 he addressed Charles in a remarkable speech. He was emphatic against the execution of Charles I; but his acceptance of Charles II was limited by all the niceties of casuistry. At the Restoration he was full of ardent hope. By the influence of Lauderdale he was appointed principal of the university of Glasgow on his refusal of a bishopric. He was not destined to hold his ultimate dignity very long. In the spring of 1662 he was 'sick and weak.' In his last illness he was visited by the new-made archbishop of Glasgow, and whilst he could not address him as 'my lord,' they got on excellently. He died in July 1662, aged 63. His 'Letters and Journals,' dating from 1637 to 1662, remained for many years in manuscript in the hands of Baillie's heirs. Many transcripts were made from them in the early part of the eighteenth century, of which one is now in the British Museum, and another in the Advocates' Library, Edinburgh. They were printed for the first time at Edinburgh in two octavo volumes in 1775, at the suggestion (it has been doubtfully asserted) of Robertson and Hume. This work was very poorly edited by 'Mr. Robert Aiken, schoolmaster of Anderton,' and is disfigured by careless omissions and errors. The Bannatyne Club issued the best edition in 1841-2, in three volumes, edited by David Laing.

Baillie was twice married, firstly to Lilias Fleming, of the family of Cardarroch—by whom he had a large number of children, but only five survived him; she died in June