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Owen's church-book presents the names of some of the chiefs of Nonconformity as members of his flock, and "honourable women not a few." Among others, there have been found the names of more than one of the heroes of the army of the Commonwealth, - such as Lord Charles Fleetwood and Colonel Desborough; certain members of the Abney family, in whose hospitable mansion the saintly Isaac Watts in after times found shelter for more than thirty years; the Countess of Anglesea; and Mrs Bendish, the grand-daughter of Cromwell, in whom, it is said, may of the bodily and mental features of the Protector remarkably reappeared. Some of these might be able at times to throw their shield over the head of Owen in those changeful and stormy years. And there were other persons more powerful still, - such as the Earl of Orrery, the Earl of Anglesea, Lord Berkeley, Lord Willoughby, Lord Wharton, and Sir John Trevor, one of the principal secretaries of state; who, though not members of Owen's church, were religiously disposed, and Owen's friends, and inclined, as far as their influence went, to mitigate the severities against the Nonconformists generally.

Owen's intimacy with these noblemen probably accounts for that interview to which he was invited by the King and the Duke of York, and which has been faithfully chronicled by all his biographers. Happening to be at Tunbridge Wells when his majesty and the duke were also there, he was introduced to the royal tent. The king freely conversed with him on the subject of religious liberty, and expressed his wish to see the Dissenters relieved of their disabilities.

On his return to London, he invited Owen to repeated interviews, uttering the same sentiments as he had done during the first conversation, and at length intrusted him with a thousand guineas, to be employed by him in mitigating the sufferings of his poorer brethren. The general policy of Charles sufficiently accounts for these gleams of royal sunshine.

But the importance of those friendships is not seen by us until we have marked the use which Owen made of them in the cause of his suffering brethren. It is well known that when the Parliament again assembled, it expressed its strong displeasure at the king's indulgence, and never ceased its remonstrances until the licenses to places of worship had been withdrawn. A disposition, it is true, began to show itself to distinguish between the Protestant Nonconformists and the Romanists, and to point restriction more particularly against the latter; but the act, which was professedly intended to bear against them was so clumsily constructed as to be capable of reaching all who did not conform, and Churchmen were not slow in giving it this direction. The Nonconformists were exposed anew to the persecuting storm; informers were goaded by increased rewards; and among thousands of less illustrious sufferers, Richard Baxter suffered joyfully the spoiling of his goods, and was condemned to what his ardent spirit did indeed feel bitterly, - a year of almost unbroken silence.

Owen, however, appears to have been left comparatively unmolested, - probably owing to the influences we have specified; and it is interesting to learn from an adversary with what zeal and constancy he employed his advantages to warn and succour the oppressed. "Witness his fishing out the king's counsels, and inquiring whether things went well to his great Diana, liberty of conscience? - how his majesty stood affected to it? - whether he would connive at it and the execution of the laws against it? -- who were or could be made his friends at court? - what bills were like to be put up in Parliament? -- how that assembly was united or divided? And according to the disposition of affairs he did acquaint his under officers; and they, by their letters each post, were to inform their fraternity in each corner of the kingdom how things were likely to go with them, how they should order their business, and either for a time omit or continue their conventicles."

Surely this was being able to find nothing against him, except as concerning the law of his God. There was no sufferer in whose behalf Owen exerted his influence more earnestly than John Bunyan. It is well known that, as a preacher, Bunyan excited, wherever he went, an interest not surpassed even by the ministry of Baxter. When he preached in barns or on commons, he gathered eager thousands around him; and when he came to London, twelve hundred people would be found gathered together at seven on the dark morning of a winter working-day, to hear him expound the Word of God. Among these admiring multitudes Owen had often been discovered; - the most learned of the Puritans hung for hours, that seemed like moments, upon the lips of this untutored genius. The king is reported to have asked Owen, on one occasion, how a learned man like him could go "to hear a tinker prate;" to which the great theologian answered "May it please your majesty, could I possess the tinker's abilities for preaching, I would willingly relinquish all my learning."

For some years Bunyan's confinement in the prison of Bedford had, through the kindness of his good jailer, been attended with many mitigations; but towards the latter part of it, its severities had been greatly increased, and Owen used every effort to engage the interest of his old friend and tutor, Dr Barlow, for his release. Some of the details of this matter have been questioned by Southey, and its date is uncertain; but the leading facts seem above reasonable suspicion, and it is pleasing to know, that after some perplexing delay, Owen's interposition was successful in obtaining Bunyan's enlargement.

During these chequered and anxious years, Owen's untiring pen had been as active as ever. In 1669 he had published "A brief Vindication of the Doctrine of the Trinity; as also, of the Person and Satisfaction of Christ;" a little treatise, containing the condensed substance of his great controversial work against Biddle and the Continental Socinians, - the "Vindiciae Evangelicae." There was wisdom in thus supplying the church with a less controversial manual on those vital questions. ...

In 1672 he had published "A Discourse concerning Evangelical Love, Church Peace and Unity," etc.; a work combining enlarged and generous sentiment with wise discrimination, and in which Owen enters at great length into the question respecting the occasional attendance of Nonconformists on the parish churches, - a question which found him and Baxter once more ranged on opposite sides. And there were other works whose origin dated from this period, ... "Treatise on the Sabbath" ... "The Nature and Punishment of Apostasy Declared, in an Exposition of Hebrews vi. 4-6." It was emphatically a book for the times; when the multitudes who had merely played a part in religion in Cromwell's days had long since thrown off the mask, and taken amends for their restraints in the most shameless excesses; when to be sternly moral was almost to incur the suspicion of disloyalty; when to be called a Puritan was, with many, more discreditable than to be called a debauchee; and when the noon-day licentiousness of Charles' court, descending through the inferior ranks of life, carried every thing before it but what was rooted and grounded in a living piety.

But the greatest work of Owen at this period was one which we leave its elaborate title to describe, -- "A Discourse concerning the Holy Spirit; in which an account is given of his name, nature, personality, dispensation, operations, and effects. His whole work in the Old and New Creation is explained; the doctrine concerning it vindicated from opposition and reproaches. The nature and necessity also of Gospel holiness, the difference between grace and morality, or a spiritual life to God in evangelical obedience and a course of moral virtues, is stated and explained." ...

Few glimpses are given us of Owen's domestic history; but it appears that, in January 1676, he was bereaved of his first wife. One of his early biographers says that she "was an excellent and comely person, very affectionate towards him, and met with suitable returns." He remained a widower for about 18 months, when he married a lady of the name of Michel, the daughter of a family of rank in Dorsetshire, and the widow of Thomas D'Oyley, Esq. of Chiselhampton, near Stadham. This lady brought Dr Owen a considerable fortune; which, with his own property, and a legacy that was left him about the same time by his cousin, Martyn Owen, made his condition easy, and even affluent, so that he was able to keep a carriage during his remaining years. On all which Anthony Wood remarks, with monkish spite, that "Owen took all occasions to enjoy the comfortable importances of this life."

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A fit instrument for this work presented himself in Samuel Parker, a man of menial origin, who had for a time been connected with the Puritans, but who, deserting them when they became sufferers, was now aspiring after preferment in the Episcopal Church, and whom Burnet describes as "full of satirical vivacity, considerably learned, but of no judgment; and as to religion, rather impious." In his "Discourse of Ecclesiastical Polity," the "authority of the civil magistrate over the consciences of subjects in matters of external religion is asserted, the mischief and inconveniences of toleration are represented, and all pretences pleaded in favour of liberty of conscience are fully answered." Such is the atrocious title-page of his book, and to a modern reader, the undertaking to which it pledges him must seem rather bold; but the confident author is reported to have firmly believed in his own success. Holding out his book to the Earl of Anglesea, he said, "Let us see, my lord, whether any of your chaplains can answer it;" and the bigoted Sheldon, sympathizing with its spirit, naturally believed also in the exceeding force of its arguments.

Dr Owen was chosen to reply to Parker; which he did, in one of the noblest controversial treatises that were ever penned by him, - "Truth and Innocence Vindicated, in a Survey of a Discourse on Ecclesiastical Polity," etc. The mind of Owen seems to have been whetted by his deep sense of wrong, and he writes with a remarkable clearness and force of argument; while he indulges at times in a style of irony which is justified not more by the folly than by the baseness and wickedness of Parker's sentiments. ... Owen's work greatly increased his celebrity among his brethren; - even some of Parker's friends could with difficulty conceal the impression that he had found more than a match in the strong-minded and sturdy Puritan; and Parker, worsted in argument, next sought to overwhelm his opponent with a scurrility that breathed the most undisguised vindictiveness. He was "the great bell-wether of disturbance and sedition," - "a person who would have vied with Mahomet himself both for boldness and imposture," - "a viper, so swollen with venom that it must either burst or spit its poison;" so that whoever wished to do well to his country, "could never do it better service than by beating down the interest and reputation of such sons of Belial." On this principle, at least, Parker himself might have ranked high as a patriot.

But the controversy was not over. Parker had not time to recover from the ponderous club of Owen, when he was assailed by the keen edged wit of Andrew Marvell. This accomplished man, the under-secretary and bosom friend of Milton, reviewed Parker's work in his "Rehearsal Transposed," - a work of which critics have spoken as rivalling in some places the causticity and neatness of Swift, and in others equalling the eloquent invective of Junius and the playful exuberance of Burke.

The conceited ecclesiastic was overwhelmed, and a number of masked combatants perceiving his plight, now rushed to his defence; in all whom, however, Marvell refused to distinguish any but Parker. In a second part of his "Rehearsal," he returned to the pen-combat, as Wood has called it; and transfixed his victim with new arrows from his exhaustless quiver. It is impossible to read many parts of it yet, without sharing with the laughers of the age in the influence of Marvell's genius. Ridiculing his self-importance, he says, "If he chance but to sneeze, he prays that the foundations of the earth be not shaken. Ever since he crept up to be but the weather-cock of a steeple, he trembles and cracks at every puff of wind that blows about him, as if the Church of England were falling." Marvell's wit was triumphant; and even Charles and his court joined in laughing at Parker's discomfiture.

"Though the delinquent did not lay violent hands on himself," says D'Israeli, "he did what, for an author, may be considered as desperate a course, - withdraw from the town, and cease writing for many years," secretly nursing a revenge which he did not dare to gratify until he knew that Marvell was in his grave

It was one thing, however, to conquer in the field of argument, and another thing to disarm the intolerance of those in power. The Parliament which met in 1671, goaded on by those sleepless ecclesiastics who were animated by the malign spirit of Parker, confirmed all the old acts against the Nonconformists, and even passed others of yet more intolerable rigour.

It is impossible to predict to what consequences the enforcement of these measures must soon have led, had not Charles, by his declaration of indulgence, of his own authority suspended the penal statutes against Nonconformists and Popish recusants, and given them permission to renew their meetings for public worship on their procuring a license, which would be granted for that purpose. This measure was, no doubt, unconstitutional in its form, and more than doubtful in the motives which prompted it; but many of the Nonconformists, seeing in it only the restoration of a right of which they ought never to have been deprived, - and some of them, like Owen, regarding it as "an expedient, according to the custom in former times, for the peace and security of the kingdom, until the whole matter might be settled in Parliament," joyfully took shelter under its provisions.

The Nonconformists were prompt in improving their precarious breathing-time. A weekly lecture was instituted at Pinner's Hall by the Presbyterians and Independents, in testimony of their union of sentiment on fundamental truths, and as an antidote to Popish, Socinian, and Infidel opinions. Owen began to preach more publicly in London to a regular congregation; and his venerable friend, Joseph Caryl, having died soon after the declaration of indulgence, the congregations of the two ministers consented to unite under the ministry of Owen, in the place of worship in Leadenhall Street.

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In the midst of these growing rigours, which were rapidly filling the prisons with victims, and crowding the emigrant ships with exiles, the plague appeared, sweeping London as with a whirlwind of death. Then it was seen who had been the true spiritual shepherds of the people, and who had been the strangers and the hirelings. The clerical oppressors of the Puritans fled from the presence of the plague, while the proscribed preachers emerged from their hiding-places, shared the dangers of that dreadful hour, addressed instruction and consolation to the perishing and bereaved, and stood between the living and the dead, until the plague was stayed.

One thing, however, had been disclosed by these occurrences; and this was the undiminished influence of the Nonconformist pastors over their people, and the increased love of their people to them; nor could the pastors ever be cut off from the means of temporal support, so long as intercourse between them and their people was maintained. This led to the passing of another act, whose ingenious cruelty historians have vied with each other adequately to describe. In the Parliament at Oxford, which had fled thither in order to escape the ravages of the plague, a law was enacted which virtually banished all Nonconformist ministers five miles from any city, town, or borough, that sent members to Parliament, and five miles from any place whatsoever where they had at any time in a number of years past preached; unless they would take an oath which it was well-known no Nonconformist could take, and which the Earl of Southampton even declared, in his place in Parliament, no honest man could subscribe. This was equivalent to driving them into exile in their own land; and, in addition to the universal severance of the pastors from their people, by banishing them into remote rural districts, it exposed them not only to the caprice of those who were the instruments of government, and to all the vile acts of spies and informers, but often to the insults and the violence of ignorant and licentious mobs.

Dr Owen suffered in the midst of all these troubles; and one anecdote, which most probably belongs to this period, presents us with another picture of the times. He had gone down to visit his old friends in the neighbourhood of Oxford, and adopting the usual precautions of the period, had approached his lodging after nightfall. But notwithstanding all his privacy, he was observed, and information given of the place where he lay. Early in the morning, a company of troopers came and knocked at the door. The mistress coming down, boldly opened the door, and asked them what they would have. -- "Have you any lodgers in your house?" they inquired. Instead of directly answering their question, she asked "whether they were seeking for Dr Owen?" "Yes," said they; on which she assured them he had departed that morning at an earlier hour. The soldiers believing her word, immediately rode away. In the meantime the Doctor, whom the woman really supposed to have been gone, as he intended the night before, arose, and going into a neighbouring field, whither he ordered his horse to be brought to him, hastened away by an unfrequented path towards London.

A second terrible visitation of Heaven was needed, in order to obtain for the persecuted Puritans a temporary breathing-time: and this second visitation came. The fire followed quickly in the footsteps of the plague, and the hand of intolerance was for the moment paralysed, if, indeed, its heart did not for a time relent. The greater number of the churches were consumed in the dreadful conflagration. Large wooden houses called tabernacles were quickly reared, amid the scorched and blackened ruins; and in these, the Nonconformist ministers preached to anxious and solemnized multitudes. The long silent voices of Owen, and Manton, and Caryl, and others, awoke the remembrance of other times; and earnest Baxter "Preached as though he never should preach again; And like a dying man to dying men." There was no possibility of silencing these preachers at such a moment. And the fall of Clarendon and the disgrace of Sheldon soon afterwards helped to prolong and enlarge their precarious liberty. Many tracts, for the most part published anonymously, and without even the printer's name, had issued from Owen's pen during these distracting years, having for their object to represent the impolicy and injustice of persecution for conscience' sake.

He had also published "A Brief Instruction in the Worship of God and Discipline of the Churches of the New Testament, by way of question and answer" ... and ... "Discourse concerning Liturgies and their Imposition" ...

... his publications during the following year show with what untiring assiduity, in the midst of all those outward storms, he had been plying the work of authorship, and laying up rich stores for posterity. Three of Owen's best works bear the date of 1668 ... "On the Nature, Power, Deceit, and Prevalence of Indwelling Sin in Believers" ... "Exposition of the 130th Psalm"  ... Then appeared the first volume of Owen's greatest work, his "Exposition of the Epistle to the Hebrews" ...

It has been remarked, that there is no lesson so difficult to learn as that of true religious toleration, for almost every sect in turn, when tempted by the power, has resorted to the practice of persecution; and this remark has seldom obtained more striking confirmation than in what was occurring at this time in another part of the world. While in England the Independents, and Nonconformists generally, were passing from one degree of persecution to another, at the hands of the restored adherents of Prelacy; the Independents of New England were perpetrating even greater severities against the Baptists and Quakers in that infant colony. Whipping, fines, imprisonment, selling into slavery, were punishments inflicted by them on thousands who, after all, did not differ from their persecutors on any point that was fundamental in religion. ...

Owen and his friends heard of these events with indignation and shame, and even feared that they might be turned to their disadvantage in England; and, in a letter subscribed along with him by all his brethren in London, faithfully remonstrated with the New England persecutors. "We only make it our hearty request," said they, "that you will trust God with his truth and ways, so far as to suspend all rigorous proceedings in corporeal restraints or punishments on persons that dissent from you, and practice the principles of their dissent without danger or disturbance to the civil peace of the place." Sound advice is here given, but we should have relished a little more of the severity of stern rebuke.

We have seen that the great fire of London led to a temporary connivance at the public preaching of the Nonconformist ministers; "it being at the first," as Baxter remarked, "too gross to forbid an undone people all public worship with too great rigour." A scheme was soon after devised for giving to this liberty a legal sanction, and which might even perhaps incorporate many of the Nonconformists with the Established Church, - such men as Wilkins, bishop of Chester, Tillotson, and Stillingfleet, warmly espousing the proposal. But no sooner did the scheme become generally known, as well as the influential names by which it was approved, than the implacable adversaries of the Nonconformists anew bestirred themselves, and succeeded in extinguishing its generous provisions. It became necessary, however, in the temper of the nation, to do something in vindication of these severities; and no readier expedient suggested itself than to decry toleration as unfriendly to social order, and still more to blacken the character of the Nonconformist sufferers.  ...

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At the beginning of the Banner edition of Owen's works there is a 19th century biography by Andrew Thomson. It includes the years after 1662 and includes these words

A few months before the restoration of Charles, Owen had been displaced from the deanery of Christ Church, and thus his last official connection with Oxford severed. He now retired to his native village of Stadham in the neighbourhood, where he had become the proprietor of a small estate. During his vice-chancellorship, it had been his custom to preach in this place on the afternoons of those Sabbaths in which he was not employed at St Mary's (where he alternated with Thomas Goodwin); and a little congregation which he had gathered by this means now joyfully welcomed him among them as their pastor. It was probably while at Stadham that he finished the preparation of one of his most elaborate theological works ... "Theologoumena, etc.; or, six books on the nature, rise, progress, and study of true theology. ... in the Latin ... 

In all likelihood Owen hoped that he would be permitted to remain unmolested in his quiet village, and that his very obscurity would prove his protection; but he had miscalculated the leniency of the new rulers. An act passed against the Quakers, declared it illegal for more than five persons to assemble in any unauthorized place for religious worship; and this act admitting of application to all separatists, soon led to the expulsion of Owen from his charge, and to the dispersion of his little flock. In a little while he saw himself surrounded by many companions in tribulation. The Presbyterians, who had shown such eagerness for the restoration of Charles to his throne, naturally expected that such measures would be taken as would comprehend them within the establishment, without doing violence to their conscientious difficulties; and Charles and his ministers flattered the hope so long as they thought it unsafe to despise it; but it was not long ere the Act of Uniformity drove nearly 2000 of them from their churches into persecution and poverty, and brought once more into closer fellowship with Owen those excellent men whom he had continued to love and esteem in the midst of all their mutual differences.

Sir Edward Hyde, the future Lord Clarendon, was now lord chancellor, and the most influential member of the government, and means were used to obtain an interview between Owen and him, with the view, it is probable, of inducing him to relax the growing severity of his measures against the Nonconformists. But the proud minister was inexorable. He insisted that Owen should abstain from preaching; but at the one time, not ignorant of the great talents of the Puritan, strongly urged him to employ his pen at the present juncture in writing against Popery. Owen did not comply with the first part of the injunction, but continued to preach in London and elsewhere, to little secret assemblies, and even at times more publicly, when the vigilance of informers was relaxed, or the winds of persecution blew for a little moment less fiercely. But circumstances soon put it in his power to comply with the latter part of it; and those circumstances are interesting ... John Vincent Cane, a Franciscan friar, had published a book entitled, "Fiat Lux; or, a Guide in Differences of Religion betwixt Papist and Protestant, Presbyterian and Independent;" in which, under the guise of recommending moderation and charity, he invites men over to the Church of Rome ...

it ... is believed to have been sent to him at length by Clarendon. Struck with the subtle and pernicious character of the work, ... Owen set himself to answer it, and soon produced his "Animadversions on Fiat Lux, by a Protestant".... 

Dr Owen's reputation was greatly extended by these writings; and this led to a new interview with Clarendon. His lordship acknowledged that he had done more for the cause of Protestantism than any other man in England; and, expressing his astonishment that so learned a man should have been led away by "the novelty of Independency," held out to him the hope of high preferment in the church if he would conform. Owen undertook to prove, in answer to any bishop that he might appoint, that the Independent form of church order, instead of being a novelty, was the only mode of government in the church for the first two centuries; and as for his wish to bestow upon him ecclesiastical honours, what he had to ask for himself and his brethren was, not preferment within the church, but simple toleration without it. The dazzling bait of a mitre appears to have been set before all the leading Nonconformists; but not one of them yielded to its lure.

This led the chancellor to inquire what was the measure of toleration he had to ask; - to which Owen is reported to have answered, "Liberty for all who assented to the doctrine of the Church of England." This answer has been remarked on by some at the expense of his consistency and courage; and the explanation has been suggested, that he now asked not all that he wished, but all that there was the most distant hope of receiving. It should be remembered, however, in addition, that many of the most liberal and enlightened men among the Nonconformists of those days objected to the full toleration of Papists; not, indeed, on religious, but on political grounds; - both because they were the subjects of a foreign power, and because of the bearings of the question on the succession of the Duke of York to the throne; and also, that Owen's plan would actually have comprehended in it almost the whole of the Protestant Nonconformists of that age.

A more honourable way of deliverance from his troubles than conformity was, about the same time, presented to Dr Owen, in an earnest invitation from the first Congregational church of Boston, in New England, to become their pastor. They had "seen his labours, and heard of the grace and wisdom communicated to him from the Father of lights;" and when so many candles were not permitted to shine in England, they were eager to secure such a burning light for their infant colony. It does not very clearly appear what sort of answer Owen returned. One biographer represents him as willing to go, and as even having some of his property embarked in a vessel bound for New England, when he was stopped by orders of the court; others represent him as unwilling to leave behind him the struggling cause, and disposed to wait in England for happier days.

But neither the representations of Owen nor of others who were friendly to the Nonconformists, had any influence in changing the policy of those who were now in power. The golden age to which Clarendon and his associates sought to bring back the government and the country, was that of Laud, with all the tortures of the Star Chamber, the dark machinery of the High Commission, and the dread alternative of abject conformity, or proscription and ruin. And the licentious Charles, while affecting at times a greater liberality, joined with his ministers in their worst measures; either from a secret sympathy with them, or, as is more probable, from a hope that the ranks of Nonconformity would at length be so greatly swelled as to render a measure of toleration necessary that would include in it the Romanist along with the Puritan. Pretexts were sought after and eagerly seized upon, in order to increase the rigours of persecution; and new acts passed, such as the Conventicle Act, which declared it penal to hold meetings for worship, even in barns and highways, and offered high rewards to informers, - and whose deliberate intention was, either to compel the sufferers to conformity, or to goad them on to violence and crime.