John Cotton (minister)
Painting by John Smibert
|Born||4 December 1585
|Died||23 December 1652
|Resting place||King's Chapel Burying Ground, Boston|
|Education||B.A. 1603 Trinity College
M.A. 1606 Emmanuel College
B.D. 1613 Emmanuel College
|Spouse(s)||(1) Elizabeth Horrocks
(2) Sarah (Hawkred) Story
|Children||(all with second wife) Seaborn, Sariah, Elizabeth, John, Maria, Rowland, William|
|Parent(s)||Mary Hurlbert and Rowland Cotton|
|Relatives||grandfather of Cotton Mather|
John Cotton (4 December 1585 – 23 December 1652) was a clergyman in England and the American colonies and, by most accounts, the preeminent minister and theologian of the Massachusetts Bay Colony. Following five years of study at Trinity College, Cambridge, and another nine years at Emmanuel College, Cambridge, he had already built a reputation as a scholar and outstanding preacher when he accepted the position of minister at Saint Botolph's Church in Boston, Lincolnshire, in 1612. As a Puritan, he wanted to do away with the ceremony and vestments associated with the established Anglican Church and preach in a simpler, more consensual manner. Though he felt the English church needed significant reforms, he nevertheless was adamant about not separating from it; his preference was to change it from within. While many ministers were removed from their pulpits for their puritan practices, Cotton thrived at St. Botolph's for nearly 20 years because of supportive aldermen, lenient bishops, and his very conciliatory and gentle demeanor. By 1632, however, the Anglican church had greatly increased its pressure on the non-conforming clergy, and Cotton was forced to go into hiding. The following year he and his wife boarded a ship for New England.
Cotton was highly sought as a minister in Massachusetts and was quickly installed as the second pastor of the Boston church, sharing the ministry with John Wilson. He generated more religious conversions in his first six months than had been made the previous year. While early in his Boston tenure, Cotton became only peripherally involved in the banishment of Roger Williams, Williams blamed much of his troubles on Cotton. Soon thereafter, Cotton became embroiled in the colony's Antinomian Controversy, when several adherents of his "free grace" theology, most notably Anne Hutchinson, began criticizing other ministers in the colony. While he tended to support his adherents through much of the controversy, it was not until near its conclusion that he came to realize that many of his followers held theological positions that were well outside the mainstream of Puritan orthodoxy, which he did not condone.
Following the controversy, Cotton was able to mend fences with his fellow ministers; and he continued to preach in the Boston church until his death. A great part of his effort during his late career was devoted to the governance of the New England churches, and he was the one who gave the name Congregationalism to this form of church polity. In the early 1640s, as the Puritans in England gained power on the eve of the English Civil War, a new form of polity for the Anglican Church was being decided, and Cotton wrote numerous letters and books in support of the "New England Way". Ultimately, Presbyterianism was chosen as the form of governance during the Westminster Assembly in 1643, though Cotton continued to engage in a polemic contest with several prominent Presbyterians on this issue. As Cotton became more conservative with age, he not only battled the separatist attitude of Roger Williams, but also agreed with the severe punishment, including death, of those whom he deemed were heretics such as Samuel Gorton. A scholar, avid letter writer, and author of many books, Cotton was considered the "prime mover" among New England's ministers. He died in December 1652 at the age of 67, following a month-long illness. His grandson, Cotton Mather, also became a prominent New England minister and historian.
- 1 Early life
- 2 New England
- 3 Late career
- 4 Later life, death and legacy
- 5 Family and descendants
- 6 Works
- 7 See also
- 8 References
- 9 Further reading
- 10 External links
Born in Derby in the county of Derbyshire, England on 4 December 1585, John Cotton was baptized 11 days later at Saint Alkmund's, an ancient church in the city. He was the second of four children of Rowland Cotton, a Derby lawyer, and Mary Hurlbert, who was "a gracious and pious mother" according to Cotton's grandson, Cotton Mather. John Cotton was educated at Derby School, in buildings which are now the Derby Heritage Centre, and was taught under the tutelage of Richard Johnson, an ordained priest of the Anglican Church. Following his Derby education, he matriculated at Trinity College, Cambridge in 1598 as a sizar, the lowest class of paying student, requiring some financial assistance. Here he followed a curriculum of rhetoric, logic and philosophy, and then gave four Latin disputations for an evaluation. He received his B.A. in 1603 and then attended Emmanuel College, Cambridge, "the most Puritan college in the kingdom", earning an M.A. in 1606 following a course of study that included Greek, astronomy, and perspective. After receiving his M.A., he continued with his studies for another five years, this time focusing on Hebrew, theology and disputation, and was also allowed to preach during this time. While an understanding of Latin was necessary for all scholars, his study of Greek and Hebrew gave him much greater insights into scripture.
During his time as a graduate student Cotton became recognized for both his scholarship and preaching. He also tutored and worked as a dean, supervising his juniors. His biographer, Larzer Ziff, called his learning "profound," and his knowledge of languages "phenomenal." Cotton became famous at Cambridge when he preached the funeral sermon of Robert Some, the late master of Peterhouse, and developed a large following from both his "manner and matter". After five years, he left the university, but didn't receive his Bachelor of Divinity degree until 1613, following the compulsory seven-year wait after his Masters. He was ordained as both deacon and priest on 13 July 1610. In 1612 he left Emmanuel College to become the minister at Saint Botolph's Church in Boston, Lincolnshire, described as "the most magnificent parochial edifice in the kingdom." Though only 27 years old, his scholarly, vigorous and persuasive preaching made him one of the leading Puritans in England.
While at Emmanuel, one of the greatest influences on Cotton's thinking was the teaching of William Perkins. From Perkins, Cotton learned to be flexible, sensible, and practical, and he learned to deal with the political realities of being a non-conformist Puritan within a disapproving Anglican Church. From him, Cotton also learned the art of disagreeing while maintaining the appearance of conformity. As Cotton steadily became more famous for his preaching, he struggled internally about his own spiritual estate. His state of uncertainty became one of desperation, as he spent three years searching for any sign that the "Lord had chosen him as one predestined to live in glory." His sincere prayers were answered in about 1611 when he received the intuition that "he had been called to salvation."
Cotton considered the doctrine and preaching of his spiritual counselor Richard Sibbes to have been the greatest influence on his conversion. Sibbes' "heart religion" was attractive to Cotton; he once wrote, "The ambassadors of so gentle a Savior should not be overly masterly." Once converted, Cotton's style of pulpit oratory became more simple in expression, though disappointing to those who liked his former polished manner of speaking. Even in his new subdued manner, however, Cotton had a profound impact on those hearing his message. It was Cotton's preaching that was responsible for the conversion of John Preston, the future master of Emmanuel College and the most influential Puritan minister of his day.
As Cotton's theology changed, he began placing less emphasis on preparation ("works") to obtain God's salvation, and more emphasis on the "transforming character of the moment of religious conversion in which mortal man [is] infused with a divine grace." Cotton's theology was molded by a number of individuals, besides influences such as Perkins and Sibbes; his basic tenets stemmed from reformer John Calvin. At one point he wrote, "I have read the fathers, and the schoolmen and Calvin too, but I find that he that has Calvin has them all." Other inspirations to his theology, as revealed in his writings, include the models of the Apostle Paul and Bishop Cyprian, and reformation leaders Zacharias Ursinus, Theodore Beza, Franciscus Junius, Jerome Zanchius, Peter Martyr, Johannes Piscator, and Martin Bucer. Additional English role models include Paul Baynes, Thomas Cartwright, Laurence Chaderton, Arthur Hildersham, William Ames, William Whitaker, John Jewel, and John Whitgift.
In the religious theory developed by Cotton, the believer is totally passive in his personal religious experience, while the Holy Spirit provides spiritual regeneration. This model was in contrast to the theology of most other Puritan ministers, particularly those who later became Cotton's colleagues in New England. These "preparationist" preachers such as Thomas Hooker, Peter Bulkley, and Thomas Shepard taught that good deeds and morality were necessary to generate the spiritual activity leading to God's salvation.
Cotton's sentiments, clearly evident in his writings, were strongly anti-catholic. This led him to oppose the established English church, which had separated from the Catholic church in name only, in his view and that of most other Puritans. The English church had an "officially sanctioned form of worship and an established ecclesiastical structure." He felt that the Anglican church polity and ceremonies, like those of the Catholics, were not authorized by scripture. Cotton and others wanted to purify such practices, and were pejoratively labelled as "puritans," a term that stuck. He was opposed to the essence of the established church, yet he was just as opposed to separating from it because he viewed the puritan movement as a way to change the church from within.
Puritanism is described by author Everett Emerson as "an effort to continue and complete the reformation of the Church of England" which had begun under Henry VIII. Following the reformation, Queen Elizabeth chose a middle path for the Anglican Church between the two extremes of Calvinism and Catholicism. The Puritans, however, wanted to reform the Anglican Church so that it would resemble "the best reformed churches" on the Continent. To do this, their intention was to eliminate the observation of Saint's days, do away with making the sign of the cross and kneeling while receiving communion, and eliminate the requirement for ministers to wear the surplice. They also wanted church governance to change as well, favoring Presbyterianism over Episcopacy.
The Puritans were greatly influenced by Continental reformer Theodore Beza and had four primary agendas: seeking moral transformation; urging the practice of piety; urging the return to the Christianity of the Bible, as opposed to prayer books, ceremonies, and vestments; and the strict recognition of the Sabbath. Cotton embraced all four of these practices. He received a small amount of Puritan influence while at Trinity; but at Emmanuel, Puritan practices were much more visible under Master Laurence Chaderton, including non-prayer-book services, ministers wearing no surplice, and communion being given around a table.
The Puritan movement hinged largely on the notion that "a holy commonwealth could be established on earth." This had an important effect on what Cotton taught and the way that he taught it. He believed that the Bible could not save souls only by being read. To him, the first step in conversion was the "pricking of the hardened heart" of the individual by hearing the word of God. In this regard, Puritanism "emphasized the importance of preaching" with the focus on the pulpit, while Catholicism emphasized sacraments where the focus was on the altar. In Puritanism, therefore, salvation required hearing sermons.
Tenure at St. Botolph's
In 1603 when James became England's monarch, religious oppression united Puritans into a strong party. All ministers were required to subscribe to "the Thirty-Nine Articles" which involved conforming to a myriad of details of Episcopal worship practice. Most Puritans found such practices unacceptable. While small numbers of them such as the Brownists sought complete separation from the Anglican church and left England for the Continent, most Puritans wanted to stay and reform the church from within.
Once established at St. Botolph's Church in Boston, Cotton was not quick in learning the political realities of pacifying the bishops or manipulating their aides in order to be able to be an effective Puritan. The first Bishop of Lincoln under whom he worked, William Barlow, was critical of the parish for selecting Cotton as their preacher. With this criticism Cotton was ready to return to the university; however, the bishop's constant business in London allowed Cotton to ultimately stay and preach in his somewhat non-conformist manner. One great help to Cotton was the assistance of the great Puritan, John Preston, whose religious conversion was attributed to Cotton. Preston had become a political force at Queen's College, and later the Master of Emmanuel, and held favor with the King. In his collegiate roles, Preston sent a steady stream of students to live with and learn from Cotton, giving Cotton the epithet of "Dr. Preston's seasoning vessel."
When Cotton arrived at St. Botolph's in 1612, non-conformity had already been practiced for nearly 30 years. Nevertheless, Cotton attempted to conform to the practices of the Anglican Church during his early tenure there, until his conscience no longer allowed him to do so. At this point he wrote a defense of his new position, which he circulated among his sympathizers.
In time Cotton's preaching became so celebrated and his lectures so well-attended, that in addition to the usual Sunday morning sermon and Thursday afternoon lecture, three more lectures were added to his week, including one Sunday afternoon as well as one each on Wednesday and Thursday mornings. Puritans throughout the kingdom sought to either correspond with him or interview him, including the zealous young Roger Williams, with whom he would later have a very strained relationship. By 1615 Cotton was earning £100 per year, a substantial sum for a parish priest. In that same year he established a church within his church by identifying "the elect" members of his congregation, and holding special services with them where puritanism in its true sense could be practiced, and the offensive practices of the established church could be totally avoided. As those not included became aware of the alternate services, they became offended, and registered their complaints with the bishop's court in Lincoln. Cotton was suspended, but his alderman, Thomas Leverett, was able to negotiate an appeal, after which Cotton was reinstated. This interference maintained by Leverett and other aldermen was successful in protecting Cotton from Anglican church officials. Because of such effective political practices, Cotton was able to maintain his course of puritanism under four different Anglican bishops of Lincoln: William Barlow, Richard Neile, George Montaigne, and John Williams. The last 12 years of Cotton's tenure at St. Botolph's was under the tenure of Williams, who was a very tolerant bishop with whom Cotton could be fairly frank about his non-conformist views. Cotton nurtured this relationship by agreeing with the bishop to the extent his conscience allowed, and then being very humble and cooperative when forced to disagree. The earliest letter of John Cotton that has been preserved was written to Williams.
Role as counselor and teacher
The surviving correspondence of John Cotton reveals the growth of his importance as a pastoral counselor to his church colleagues during the 1620s and into the 1630s. Among those seeking his counsel were young ministers beginning their careers or facing some crisis. Others desiring his aide were older colleagues, including those who had left England to preach on the Continent. Cotton had become the experienced veteran who assisted his fellow ministers, particularly in their struggles with conformity forced upon them by the established church. Besides assisting ministers from England and abroad, Cotton also trained many students from Cambridge.
Ministers came to Cotton with a wide range of questions and concerns. In the years before Cotton's immigration to the Massachusetts Bay Colony, he gave advice to his former Cambridge student, Reverend Ralph Levett, a Yorkshire native serving in 1625 as the private chaplain to Sir William and Lady Frances Wray at Ashby cum Fenby, Lincolnshire. As the family minister, Levett struggled to align his Puritan beliefs with this fun-loving household, which enjoyed dancing and exchanging valentines sentiments. Cotton's advice was that valentines were like a lottery, and "a takeinge of Gods name in vaine," though dancing was acceptable, if not done in a lewd way. Levett, who later became the brother-in-law of Reverend John Wheelwright, Cotton's colleague in New England, was satisfied with the guidance.
When Charles I became the English monarch in 1625, the situation grew worse for Puritans, and an increased number of them moved to the Netherlands. Charles, who tended to be inflexible, would not compromise with his rivals. This resulted in Parliament becoming dominated by Puritans followed by civil war in the 1640s. Under Charles, the Anglican church reverted to more ceremonial worship, approaching that of Catholicism, and there was increased hostility towards the Calvinism that Cotton followed. While his colleagues were being summoned to the High Court for their Puritan practices, Cotton continued to thrive because of his supportive aldermen, sympathetic superiors, and his conciliatory demeanor. The minister Samuel Ward of Ipswich remarked, "Of all men in the world I envy Mr. Cotton, of Boston, most; for he doth nothing in way of conformity, and yet hath his liberty, and I do everything that way, and cannot enjoy mine."
North American colonization
The traditional options were to either go underground or to form a separatist church on the Continent, for Puritan ministers who lacked Cotton's success at avoiding the Anglican authorities. In the late 1620s, however, another option emerged as North America began to open for colonization. With this new prospect, a staging area was established at Tattersall, near Boston, which was the seat of Theophilus Clinton the Earl of Lincoln. Cotton and the Earl's chaplain Samuel Skelton conferred extensively, before Skelton left England to be the minister for the company of John Endicott in 1629. Cotton firmly opposed separatism, whereby newly established churches in New England or continental Europe refused communion with the Church of England or with the established continental reformed churches. For this reason, Cotton was upset to learn that Skelton's church at Naumkeg (later Salem) had opted for such separatism and had refused to offer communion to newly arriving colonists. In particular, he was grieved to learn that William Coddington, his friend and parishioner from Boston (Lincolnshire), was not allowed to have his child baptized "because he was no member of any particular reformed church, though of the catholic [universal]."
In July 1629, Cotton took part in a planning conference for emigration at Sempringham Castle in Lincolnshire. Other future emigrants who participated in the planning were Thomas Hooker, Roger Williams, John Winthrop, and Emmanuel Downing. Cotton did not emigrate for several more years, though he did travel to Southampton to preach the farewell sermon to Winthrop's party. Of Cotton's thousands of sermons, this was the earliest one to be published. He also offered support to those who had already sailed and, in a 1630 letter, he arranged for a hogshead of meal to be sent to his friend William Coddington who was at Naumkeg.
Shortly after seeing the New England colonists on their way, both Cotton and his wife became seriously ill from malaria. The Cottons stayed at the manor house of the Earl of Lincoln for nearly a year; Cotton eventually recovered, but his wife died. As a widower, Cotton decided to travel to complete his recovery, and while doing so he became much more aware of the dangers that Puritans were facing throughout England. In a December 1631 letter to Cotton, Nathaniel Ward wrote of his summons to court, and that Thomas Hooker had already fled from Essex and gone to Holland. The letter is representative of the "emotional agony" faced by these ministers, and Ward wrote it as a sort of "good-bye", knowing that he would be removed from his ministry. Cotton and Ward later met again in New England.
Flight from England
Cotton remarried on 6 April 1632 to the widow Sarah (Hawkred) Story, who had a daughter, and almost immediately thereafter got word that he was due to be summoned to the High Court for his non-conforming practices. This was less than a year after receiving the letter from Ward. Cotton asked the Earl of Dorset to intercede on his behalf, but the earl wrote back that non-conformity and puritanism were unpardonable offenses, and told Cotton "you must fly for your safety."
Cotton was to appear before William Laud, the Bishop of London, who was on a campaign to suppress Puritan practices. Cotton now felt that his best option was to disappear into the Puritan underground, and then decide his course of action from there. In October 1632 he wrote his wife a letter from hiding, saying he was being well cared for, but that she would be followed if she attempted to join him. When Cotton was forced underground, two very prominent Puritans came to visit him in hiding, Thomas Goodwin and John Davenport. Both men came to convince him that it would be acceptable for him to conform to the established church rather than deal with possible imprisonment. Instead, Cotton compelled these two men into further non-conformity, and Goodwin went on to be the voice of the independents (Congregationalists) at the Westminster Assembly in 1643, while Davenport became the founder of the Puritan New Haven Colony in North America, using Cotton's theocratic model of government. It was Cotton's influence on men of such prominence as these that made him "the most important of the Congregational leaders," and later a prime target for attacks by the Presbyterians.
While in hiding, Cotton moved about in an underground puritan network, staying at times in Northamptonshire, Surrey, and different places around London. He contemplated going to Holland like many non-conformists before him. This option allowed for a quick return to England should the political situation become favorable, appeasing the sense that a "great reformation [was] to take place soon." He soon ruled out Holland, however, because of the negative feedback from fellow minister Thomas Hooker who had previously gone there.
When members of the Massachusetts Bay Colony heard about Cotton's flight, they sent him letters urging him to come to New England. None of the great puritan clergymen had gone there, and he felt it would put him at too great a distance to return should the situation in England warrant. Despite this, he made his decision to emigrate by the spring of 1633, and on 7 May wrote a letter to Bishop Williams, resigning from his pastorate at St. Botolph's, and thanking the bishop for his flexibility and mildness. By the summer he had re-united with his wife, and the couple made their way to the coast of Kent. In June or July 1633 the 48-year-old Cotton, with his wife and step-daughter, boarded the ship Griffin along with two other ministers, Thomas Hooker and Samuel Stone. Also on board was the oldest son of Anne Hutchinson, Edward who was traveling with his uncle, also named Edward Hutchinson. Cotton's wife was pregnant during the voyage and so close to term, that she bore her child during the voyage, and they named him Seaborn. Eighteen months after his departure from England, Cotton wrote that his decision to emigrate was not difficult to make; he found preaching in a new land to be far preferable to "sitting in a loathsome prison."
Cotton, and to a lesser extent Hooker, were the first truly eminent ministers to come to New England, according to Cotton's biographer Larzer Ziff. On his arrival in September 1633 Cotton was openly welcomed as one of the two ministers of the church in Boston in the Massachusetts Bay Colony, having been personally invited to the colony by Governor Winthrop. Ziff wrote, "It was only fitting, the majority felt, that the most eminent preacher in the colony should be located in the principal city," and besides, many settlers from Boston, Lincolnshire had settled in Boston in New England.
Far different from his surroundings in the spacious and comfortable church of St. Botolph's, the Boston meetinghouse of the 1630s was small and windowless, with clay walls and a thatched roof. Once established in his new church, Cotton's evangelical fervor brought about a religious revival, and there were more conversions during his first six months in the pastorate than there had been the previous year. He was recognized as the leading intellectual in the colony, and is the first minister known to have preached a theme of millennialism in New England. He also became the spokesman for the new church polity known as Congregationalism.
Roger Williams affair
Early in his New England tenure, Roger Williams began to be noticed for his activity in the Salem Church. This church, established in 1629, had already become a separatist church when in 1630 it denied communion to John Winthrop and his wife upon their arrival in Massachusetts, and it also refused to baptize a child born at sea. Roger Williams arrived in Boston in May 1631, and was offered the position of teacher in the Boston church, but refused the offer because the church was not sufficiently separated from "the corrupt Church of England". He even refused to become a member of the Boston church, but by May 1631 he had been selected as the teacher at Salem upon the death of Francis Higginson. Williams had a reputation for both non-conformity and piety, but historian Everett Emerson called him a "gadfly whose admirable personal qualities were mixed with an uncomfortable iconoclasm". When Boston's minister, John Wilson returned to England to get his wife in 1632, Williams again refused an invitation to fill in during Wilson's absence. The zealous Williams had distinctive theological views, and Cotton differed with him not only on the issue of separatism, but also on the matter of religious toleration. Williams had gone to Plymouth for a short while, but returned to Salem, and upon the death of Salem's minister, Samuel Skelton, Williams was called to replace him.
During his tenure at Salem Williams considered those who maintained ties with the Anglican Church to be "the unregenerate", and pushed for separation from them. He was supported by local magistrate John Endicott, who went so far as to remove the cross from the English flag as being a symbol of idolatry. As a result, in May 1635 Endicott was barred from the magistracy for a year, and two months later Salem's petition for additional land was refused by the Massachusetts Court because Williams was the minister there. Williams was soon banished from the colony, and though Cotton was not consulted on the issue, he nevertheless wrote to Williams, stating that the cause of banishment was "the tendency of Williams' doctrines to disturb the peace of the church and state." Williams was going to be shipped back to England by the Massachusetts magistrates, but instead he slipped away into the wilderness, spending the winter near Seekonk, and then establishing Providence near the Narragansett Bay the following spring. Though Cotton was able to deal with Williams more tactfully than the magistrates, Williams nevertheless considered Cotton "the chief spokesman for the colony and, indeed, the source of his problems." After Williams left for Narraganset, Cotton went to Salem in 1636 where he delivered a sermon to the congregation. His goal was to not only make peace with the parishioners, but to also convey the dangers of the separatist doctrine espoused by Williams.
Through his years of study and practice, Cotton had developed a theological model under which a person is helpless to affect his own salvation, and instead is totally dependent on God's free grace. In contrast, most of the other New England ministers were "preparationists", espousing the view that morality and good works were needed to prepare one for God's salvation. Most members of Cotton's Boston church became very attracted to his theology, including Cotton's admirer Anne Hutchinson, a charismatic woman who hosted 60 or more people at her home each week to discuss Cotton's sermons, but also to criticize the colony's other ministers. Another highly important advocate of Cotton's theology was the colony's young governor, Henry Vane, who had built an addition onto Cotton's house, where he lived during his time in Boston. While publicly both Hutchinson and Vane followed the teachings of Cotton, both of them also held some views that were not only considered unorthodox, but even radical.
In May 1636 the minister John Wheelwright, a brother-in-law of Hutchinson, arrived in New England and was the only other divine in the colony who shared Cotton's free grace theology. As early as the spring of 1636, the minister of Newtown (which later became Cambridge), Thomas Shepard, began writing letters to Cotton. In these letters, he expressed concern about Cotton's preaching, and about some of the unorthodox opinions found among his Boston parishioners. Shepard went even further when he began criticizing this unorthodoxy to his Newtown congregation during his sermons.
Hutchinson and the other free grace advocates continuously questioned the orthodox ministers in the colony. As ministers and magistrates began sensing the religious unrest, John Winthrop gave the first public warning of the ensuing crisis with an entry in his journal on or shortly after 21 October 1636. Instead of pinning blame on one of the godly ministers such as Cotton, he instead blamed the developing situation on Hutchinson.
On 25 October 1636 seven ministers gathered at the home of Cotton to confront the developing discord, and held a "private conference" which included Hutchinson and other lay leaders from the Boston church. Hutchinson, when coaxed by some ministers, admitted that she had criticized them during her home gatherings, but did this only when prompted, and insisted that her admissions were private and confidential. Concerning the theological differences, some agreement was reached, and Cotton "gave satisfaction to [the other ministers], so as he agreed with them all in the point of sanctification, and so did Mr. Wheelwright; so as they all did hold, that sanctification did help to evidence justification." The agreement was short-lived, and by late 1636 Hutchinson and her supporters were being accused of a number of heresies, including antinomianism and familism. Antinomianism means "against or opposed to the law" and theologically means "the moral law is not binding upon Christians, who are under the law of grace." Familism, named for a 16th-century sect called the Family of Love, involved perfect union with God under the Holy Spirit, coupled with freedom from both sin and the responsibility for it. While Hutchinson, Wheelwright and Vane were antagonists of the orthodox party, theologically it was Cotton's differences of opinion with the colony's other ministers that was at the center of the controversy.
By winter the theological schism had become great enough that the General Court called for a day of fasting to help ease the colony's difficulties. During the appointed fast-day on Thursday, 19 January 1637, Cotton preached a conciliatory sermon at the Boston church in the morning, followed by Wheelwright in the afternoon. While in the eyes of a lay person Wheelwright's sermon may have appeared benign and non-threatening, to the Puritan clergy it was "censurable and incited mischief." Cotton considered this sermon to be "ill-advised in manner, although ... valid enough in content."
Events of 1637
By March, the political tide began to turn against the free grace advocates. Wheelwright was tried for contempt and sedition for his fast-day sermon, and in a close vote he was convicted, but not yet sentenced. During the election of May 1637, not only was Henry Vane replaced as governor by John Winthrop, but all of the other Boston magistrates who supported Hutchinson and Wheelwright were voted out of office. In the summer of 1637 Vane sailed back to England, never to return, and with this strong ally of the free grace advocates out of the way, the time was ripe for the orthodox party to deal with the remainder of its rivals. At the autumn court in 1637, which convened on 2 November, Wheelwright was sentenced to banishment, and ordered to leave the colony within 14 days. Then, several of the other supporters of Hutchinson and Wheelwright were given varied sentences. Following these preliminaries, Anne Hutchinson was tried.
Hutchinson was brought before the court on 7 November 1637, presided over by Governor John Winthrop, on the charge of "traducing [slandering] the ministers". Other charges against her were laid out by Winthrop including being one who "troubled the peace of the commonwealth and churches", promoting and divulging opinions that had caused recent troubles, and continuing to hold meetings at her home despite a recent synod that had condemned them. Most of the trial was spent on the charge that Hutchinson had made disparaging remarks about the colony's ministers, and to use the October meeting as their evidence.
During the first day of the proceedings Hutchinson had done well by out-fencing her prosecutors in a battle of wits, and Cotton listened but took no active role. During the second day, however, Cotton was the third of three defense witnesses called to testify. After the other two witnesses, deacon John Coggeshall and lay leader Thomas Leverett, made brief statements, Cotton was interrogated extensively. When he testified, he tended to not remember many events of the October meeting, and attempted to soften the meaning of statements that Hutchinson was being accused of. He further stressed that the ministers were not as upset about any Hutchinson remarks at the end of the October meeting as they appeared to be later. When magistrate Thomas Dudley reiterated that Hutchinson had told the ministers that they were not able ministers of the New Testament, Cotton replied that he did not remember her saying that.
There was more parrying between Cotton and the court, but the exchanges were not picked up in the transcript of the proceedings. Hutchinson then asked the court's permission to "give you the ground of what I know to be true." She then addressed the court with a statement describing how she knew the colony's ministers to be unable, and ending by prophesying the destruction of the colony. While her intention, according to historian Michael Winship, was to be instructive and teach the court, what she had actually done was to simplify the task of her prosecutors. Her revelation was not only seditious, but also in contempt of court. Cotton, pressed by Dudley on whether or not he supported Hutchinson's revelation, said he could find theological justification for it. Cotton may have still been angry over the zeal with which some opponents had come after the dissidents within his congregation. The court then sentenced Hutchinson to banishment, but she was put under house arrest at the home of Joseph Weld until her release in the spring. As ministers visited with her over the winter, they were not only trying to correct her theological errors, but also were collecting evidence against her. Thomas Shepard, who was there to "collect errors", concluded that she was a dangerous woman. Shepard and the other ministers who visited her drew up a list of her theological errors and presented them to the Boston church, which then decided that she should stand trial for these views.
Hutchinson's church trial
Hutchinson was brought before the clergy and congregation at the Boston meeting house on Thursday, 15 March 1638. A list of numerous theological errors was presented, and after a nine-hour session, only four of these errors were addressed. Then Cotton was put in the uncomfortable position of delivering the admonition to his admirer. He spoke, "I would speake it to Gods Glory [that] you have bine an Instrument of doing some good amongst us ... he hath given you a sharp apprehension, a ready utterance and abilitie to exprese yourselfe in the Cause of God." With this said, it was the overwhelming conclusion of the ministers that Hutchinson's unsound beliefs outweighed all the good she had done, and that she endangered the spiritual welfare of the community. Cotton continued, "You cannot Evade the Argument ... that filthie Sinne of the Communitie of Woemen; and all promiscuous and filthie cominge togeather of men and Woemen without Distinction or Relation of Mariage, will necessarily follow ... Though I have not herd, nayther do I thinke you have bine unfaythfull to your Husband in his Marriage Covenant, yet that will follow upon it." Here Cotton was making a link between Hutchinson's theological ideas and the more extreme behavior credited to the antinomians and familists. He then concluded, "Therefor, I doe Admonish you, and alsoe charge you in the name of Ch[rist] Je[sus], in whose place I stand ... that you would sadly consider the just hand of God agaynst you, the great hurt you have done to the Churches, the great Dishonour you have brought to Je[sus] Ch[rist], and the Evell that you have done to many a poore soule." With this, Hutchinson was instructed to return on the next lecture day, in one week.
Cotton had not yet given up on his parishioner, and with the permission of the court Hutchinson was allowed to spend the week at his home, where the recently arrived Reverend John Davenport was also staying. All week the two ministers worked with her, and under their supervision she had written out a formal recantation of her unorthodox opinions. At the next meeting, on Thursday, 22 March, Hutchinson stood and read her recantation to the congregation. Here she admitted that she had been wrong about many of her beliefs. This was not acceptable to several of the ministers, however, and they had to continue with her examination. When at one point she felt compelled to lie about her theological positions, any defense she had unraveled, and at this point Cotton signaled that he had given up on her. Cotton's fellow minister in the Boston church, John Wilson, then read the order of excommunication.
Cotton had been deeply complicit in the controversy because his theological views differed from those of the other ministers in New England, and he suffered in attempting to remain supportive of Hutchinson, while being conciliatory towards his fellow ministers. Nevertheless, some of his followers were taking his singular doctrine, and carrying it well beyond Puritan orthodoxy. As with the magistrates, Cotton attempted to downplay the appearance of colonial discord in communicating with his brethren in England. When a group of colonists departed for a return trip to England in February 1637, Cotton asked them to report that the controversy was about magnifying the grace of God: one party focused on grace within man, the other on grace toward man; and that New England was still a good place for new colonists.
Following the controversy Cotton was able to summarize some of the events in his correspondence. In one letter he asserted that "the radical voices consciously sheltered themselves" behind his reputation. In a March 1638 letter to Samuel Stone at Hartford he referred to Hutchinson and others as being those who "would have corrupted and destroyed Faith and Religion had not they bene timely discovered." His most complete statement on the subject appeared in a long letter to Wheelwright in April 1640, in which he reviewed the failings of both men as the controversy developed. He discussed his own failure in not understanding the extent to which members of his congregation knowingly went beyond his religious views, specifically mentioning the heterodox opinions of William Aspinwall and John Coggeshall. He also suggested that Wheelwright should have picked up on the gist of what Hutchinson and Coggeshall were saying.
During the heat of the controversy, Cotton considered moving to New Haven, but at the August 1637 synod he first recognized that some of his parishioners were harboring unorthodox opinions, and that the other ministers may have been correct in their views about his followers. Some of the magistrates and church elders let him know in private that his departure from Boston would be most unwelcome, and once he saw a way to reconcile with his fellow ministers he decided to stay in Boston.
In the aftermath of the controversy Cotton continued a dialogue with some of those who had gone to Aquidneck Island. One of these correspondents was his friend from Lincolnshire, William Coddington. Coddington wrote that he and his wife had heard that Cotton's preaching had changed dramatically since the controversy ended, stating, "if we had not knowne what he had holden forth before we knew not how to understand him." Coddington then deflected suggestions by Cotton that he reform some of his own ideas and "errors in judgment". In 1640 the Boston church sent some messengers to Aquidneck, but they were poorly received. Young Francis Hutchinson, a son of Anne, attempted to withdraw his membership from the Boston church, but his request was denied by Cotton.
Cotton continued to be interested in helping Wheelwright get his order of banishment lifted. In the spring of 1640 he wrote to Wheelwright with details about how Wheelwright should frame a letter to the General Court. Wheelwright was not yet ready to concede the level of fault that was suggested by Cotton, though, and another four years transpired before Wheelwright could admit enough wrongdoing for the court to lift his banishment.
Some of Cotton's harshest critics during the controversy were able to reconcile with him following the event. A year after Hutchinson's excommunication, Thomas Dudley requested Cotton's assistance with counseling William Denison, a lay person in the Roxbury church. In 1646 when Thomas Shepard was working on his book about the Sabbath, Theses Sabbaticae, he asked for Cotton's opinion.
In New England, as in England, Cotton served both his parishioners and his fellow ministers as their teacher, as well as their authority on scripture. For example, he maintained a lengthy correspondence with the minister at Concord, Peter Bulkley, from 1635 to 1650. In his letters to Cotton, Bulkley requested help for doctrinal difficulties as well as for challenging situations emanating from his congregation. The Plymouth minister, John Reynes and his ruling elder, William Brewster, also sought Cotton's professional advice. In addition, Cotton continued an extensive correspondence with ministers and lay people across the Atlantic, viewing this work as supporting Christian unity, similar to what the Apostle Paul had done in biblical times.
Though Cotton's eminence in New England mirrored that which he enjoyed in Lincolnshire, there were some notable differences between the two worlds. In Lincolnshire Cotton preached to capacity audiences in a large stone church, while in New England he preached to small groups in a small wood-framed church. Also in England Cotton was able to travel extensively, and even visited his native town of Derby at least once a year. By contrast, he did very little traveling in New England. He occasionally visited the congregations at Concord or Lynn, but more often he was visited by other ministers and lay people, who came to his Thursday lectures. Cotton continued to board and mentor young scholars, as he did in England, but there were far fewer in early New England.
One of the major issues that consumed Cotton both before and after the Antinomian Controversy was the government, or polity, of the New England churches. By 1636 he had settled on the form of ecclesiastical organization that became "the way of the New England churches"; six years later he gave it a name, calling it Congregationalism. Cotton's plan involved independent churches governed from within, as opposed to Presbyterianism, with a more hierarchical polity, which had many supporters in England. Both systems were an effort to reform the Episcopal polity of the established Church of England.
Congregationalism, known as the "New England Way", was based on a limited membership of saved believers, and a separation from all other churches in matters of government. Even though congregationalists wanted each church to have its own governance, they generally opposed separation from the established Church of England. The Puritans continued to view the Anglican Church as being the true church, but one needing reform from within. Cotton, with his qualities of piety, learning and mildness of temper, became the "chief helmsman" for the Massachusetts Puritans in establishing congregationalism in New England. While several of his books and much of his correspondence dealt with church polity, one of his key sermons on the subject was his Sermon Deliver'd at Salem in 1636, given in the church that was forced to expel Roger Williams. While Cotton disagreed with Williams, he had hoped to convince Williams of his errors before his banishment. Cotton's sermon in Salem was designed to keep the church there from moving further towards separation from the English church. Cotton felt that the church and the state should be separate to a degree, but unlike Williams, he felt they should be intimately related. He viewed the best organization for the state to be a Biblical model from the Old Testament. He did not see democracy as being an option for the Massachusetts government, but instead felt that a theocracy would be the best model.
With Puritans in control of the English Parliament in the early 1640s, the issue of polity for the Anglican church was of major importance to congregations throughout England and its colonies. To address this issue, the Westminster Assembly was convened in 1643. A year earlier Lord Say and Seal, who had scrapped his plans to immigrate to New England, along with other members of Parliament, wrote to Cotton, Hooker and Davenport in New England, "urging them to return to England where they were needed as members of the Westminster Assembly". None of the three attended the meeting, where an overwhelming majority of members was Presbyterian, with only a handful representing independent (congregational) interests. Despite the lopsided numbers, Cotton was interested in attending, though John Winthrop quoted Hooker as saying he couldn't see the point of "travelling 3,000 miles to agree with three men."  Cotton changed his mind about attending as events leading to the First English Civil War began to unfold, and he decided that he could have a greater effect on the Assembly through his writings.
The New England response to the assembly was the book written by Cotton entitled The Keyes of the Kingdom of Heaven, published in 1644. This book was Cotton's attempt to persuade the assembly to adopt the Congregational way of church polity in England, and was endorsed by the English ministers Thomas Goodwin and Philip Nye. In this work Cotton revealed some of his thoughts on state governance, writing, "Democracy I do not conceive that ever God did ordain as a fit government either for church or commonwealth." Despite these views against democracy, congregationalism later became important to the democratization of the English colonies in North America. While this work on church polity had no effect on the view of most Presbyterians, it did change the stance of the Presbyterian John Owen who later became a leader of the independent party at the Restoration of the English monarchy in 1660. Owen had earlier been selected by Oliver Cromwell to be the vice-chancellor of Oxford.
While Congregationalism was New England's established church polity, it did have its detractors among the Puritan radicals, including Baptists, Seekers, Familists, and other sectaries. Their criticism, coupled with John Winthrop's Short Story about the Antinomian Controversy, published in 1644, prompted the Presbyterian spokesman, Robert Baillie, to publish A Dissuasive against the Errours of the Time in 1645. As a Presbyterian minister, Baillie was critical of Congregationalism, and targeted Cotton in his writings. Baillie considered congregationalism to be "unscriptural and unworkable," and thought Cotton's opinions and conduct to be "shaky."
Cotton's response to Baillie was The Way of Congregational Churches Cleared published in 1648. This work brings out more personal views of Cotton, particularly in regards to the Antinomian Controversy. Cotton conceded that neither Congregationalism nor Presbyterianism would become dominant in the domain of the other, but he looked at both forms of church polity as being important in countering the heretics. The brief second part of this work was an answer to criticism by two other Presbyterian ministers, Samuel Rutherford and Daniel Cowdrey. Baillie made a further response to this work in conjunction with Rutherford, and to this Cotton made his final refutation in 1650 in his work Of the Holinesse of Church-members.
Synod and Cambridge Assembly
Following the Westminster Assembly in England, the New England ministers held a meeting of their own at Harvard College in Cambridge, addressing the issue of Presbyterianism in the New England colonies. Cotton and Hooker acted as moderators. Three years later, in September 1646, a synod was held, again in Cambridge, and was convened to prepare "a model of church government". The three ministers appointed to conduct the business were Cotton, Richard Mather, and Ralph Partridge. In 1648 a statement resulting from the synod, drawing heavily from the writings of Cotton and Mather, was adopted by the New England churches and called the Cambridge Platform. This platform, adopted by most of the churches in New England and endorsed by the Massachusetts General Court, provided an official statement of the Congregationalist method of church polity known as the "New England Way". 
Debate with Roger Williams
A letter that Cotton had written to Roger Williams immediately following his banishment in 1635 appeared in print in London in 1643. Though Williams denied any connection with its publication, he happened to be in England at the time getting a patent for the Rhode Island colony. The letter was published in 1644 as Mr. Cottons Letters Lately Printed, Examined and Answered. The same year Williams also published The Bloudy Tenent of Persecution. In these works, he discussed the purity of New England churches, the justice of his banishment, and "the propriety of the Massachusetts policy of religious intolerance." Williams felt that the root cause of conflict was the colony's relationship of church and state.
With this, Cotton became embattled with two different extremes. At one end were the Presbyterians who wanted more openness to church membership, while Williams thought the church should completely separate from any church hierarchy and only allow membership to those who completely separated from the corrupt Anglican church. Cotton chose a middle ground between the two extremes. Cotton felt that church members should "hate what separates them from Christ, [and] not denounce those Christians who have not yet rejected all impure practices." Cotton further felt that the policies of Williams were "too demanding upon the Christian". To this end historian Everett Emerson noted that "Cotton's God is far more generous and forgiving than Williams's".
Though Cotton and Williams both accepted the Bible as the basis for their theological understandings, Williams saw a marked distinction between the Old Testament and New Testament, in contrast to Cotton's perception that the two books formed a continuum. Cotton viewed the Old Testament as providing a model for Christian governance, and envisioned a society where church and state worked together cooperatively. Williams, in contrast, believed that with the arrival of Christ, God had dissolved the union between the Old and New Testaments; in fact this dissolution was "one of His purposes in sending Christ into the world." The debate between the two men continued in 1647 when Cotton replied to Williams's book with The Bloudy Tenant, Washed and Made White in the Bloud of the Lambe, after which Williams responded with yet another pamphlet.
Dealing with sectaries
During the first few decades of American colonization, a variety of religious sects had emerged, and were considered radicals by many orthodox Puritans. Some of these groups included the Separatists (such as the Pilgrims and Roger Williams), Radical Spiritists (Antinomians and Familists), Anabaptists (General and Particular Baptists), Millenarians, and Quakers. Many of these radicals had been expelled from Massachusetts and were able to find a haven in Rhode Island.
One of the most notorious of these sectaries was the zealous Samuel Gorton who had been expelled from both Plymouth and Aquidneck Island, then was refused freemanship in Providence. In 1642 he settled in what became Warwick, but the following year was arrested with some followers and brought to Boston for dubious legal reasons. Here he was forced to attend a Cotton sermon in October 1643, which he confuted. Further attempts at correcting his religious opinions were in vain. Cotton was willing to see Gorton to death in order to "preserve New England's good name in England" where he viewed such heresies as being greatly detrimental to Congregationalism. In the Massachusetts General Court, the magistrates sought the death penalty, but the deputies, more sympathetic to free expression, refused to agree, and the men were eventually released.
As Cotton became more conservative with age, he tended to side more with the "legalists" when it came to religious opinion. He was dismayed when the success of Parliament in England opened the floodgates of religious opinion. To Cotton, new arrivals from England as well as visitors from Rhode Island were bringing with them "horrifyingly erroneous opinions".
In July 1651 the Bay Colony was visited by three Rhode Islanders who had become Baptists: John Clarke, Obadiah Holmes and John Crandall. Massachusetts reacted harshly against the visit, imprisoning the three men, while Cotton preached "against the heinousness" of the Anabaptist opinions of these men. Despite public opinion against punishment, the three men were given exorbitant fines. Friends paid the fines for Clarke and Crandall, but when Holmes learned of this he refused to allow anyone to pay his fine. As a result, he was publicly whipped in such a cruel manner that he could only sleep on his elbows and knees for weeks afterwards. As news of the persecutions reached England, it met with a negative reaction. Sir Richard Saltonstall, a friend of Cotton's from Lincolnshire, wrote to Cotton and Wilson in 1652 rebuking them for the practices of the colony. He wrote, "It doth not a little grieve my spirit to heare what sadd things are reported dayly of your tyranny and persecutions in New-England as that you fyne, whip and imprison men for their consciences." He continued, "these rigid wayes have layed you very lowe in the hearts of the saynts." Roger Williams also wrote a treatise on these persecutions, which was published after Cotton's death.
Later life, death and legacy
During the final decade of his life, Cotton continued his extensive correspondence with people ranging from obscure figures to those who were highly prominent, such as Oliver Cromwell. His counsel was constantly requested, and in 1648 Winthrop asked for Cotton's help in rewriting the preface to the laws of New England. When William Pynchon published a book that was considered unsound by the Massachusetts General Court, copies were collected and burned on the Boston Common. A letter from Cotton and four other elders attempted to moderate the harsh reaction of the court.
Religious fervor in the Bay Colony had been waning since the time of the first settlements, and church membership was dropping off. To counter this, the minister Richard Mather suggested a means of allowing membership in the church without requiring a religious testimonial be made. Traditionally parishioners had to make a confession of faith in order to have their children baptized and in order to participate in the sacrament of Holy Communion (Last Supper). In the face of declining church membership Mather proposed the Half-way covenant, which was adopted. This policy allowed people to have their children baptized, even though they themselves did not offer a confession.
Concerned with church polity until the end of his life, Cotton continued to write about the subject in his books and correspondence. His final published work concerning Congregationalism was Certain Queries Tending to Accommodation, and Communion of Presbyterian & Congregational Churches, completed in 1652. Evident in this work is that Cotton had become more liberal towards Presbyterian church polity. Despite this flexibility, he was nevertheless unhappy with the direction taken in his mother land. Author Everett Emerson wrote, "the course of English history was a disappointment to him, for not only did the English reject his Congregational practices developed in America, but the advocates of Congregationalism in England adopted a policy of toleration, which Cotton abhorred."
Sometime in the autumn of 1652 Cotton crossed the Charles River to preach to students at Harvard. He became ill from the exposure, and in November he and others realized that he was dying. He was at the time running a sermon series on the Book of Timothy for his Boston congregation, which he was able to finish, despite becoming bed-ridden in December. On 2 December 1652 Amos Richardson wrote to John Winthrop, Jr.: "Mr. Cotton is very ill and it is much feared will not escape this sickness to live. He hath great swellings in his legs and body". Though the Boston Vital Record gives his death date as 15 December, a multitude of other sources, likely correct, give the date as 23 December 1652. He was buried in the King's Chapel Burying Ground in Boston and is named on a stone which also names early First Church ministers John Davenport (d. 1670), John Oxenbridge (d. 1674) and Thomas Bridge (d. 1713). Exact burial sites and markers for many first-generation settlers in that ground were lost with the—probably deliberate—placement of Boston's first Anglican church, King's Chapel I (1686) over them; the present stone marker, placed by the church, is likely a cenotaph.
Most scholars, early and contemporary, consider Cotton to be the "preeminent minister and theologian of the Massachusetts Bay Colony." His fellow minister in the Boston Church, John Wilson, wrote "Mr. Cotton preaches with such authority, demonstration, and life that, methinks, when he preaches out of any prophet or apostle I hear not him; I hear that very prophet and apostle. Yea, I hear the Lord Jesus Christ speaking in my heart." Wilson also called Cotton deliberate, careful, and in touch with the wisdom of God. Another of Cotton's contemporaries, John Davenport, who founded the New Haven Colony, considered Cotton's opinion to be law. Cotton was highly regarded in England as well. His biographer, Larzer Ziff wrote, "John Cotton, the majority of the English Puritans knew, was the American with the widest reputation for scholarship and pulpit ability; of all the American ministers, he had been consulted most frequently by the prominent Englishmen interested in Massachusetts; of all of the American ministers, he had been the one to supply England not only with descriptions of his practice, but with the theoretical base for it. John Cotton, the majority of the English Puritans concluded, was the prime mover in New England's ecclesiastical polity." Even one of Cotton's opponents in England, Thomas Edwards, called Cotton "the greatest divine" and the "prime man of them all in New England".
Modern scholars agree that Cotton was the most eminent of New England's early ministers. Robert Charles Anderson, writing in the Great Migration series, commented "John Cotton's reputation and influence were unequaled among New England ministers, with the possible exception of Thomas Hooker."  Cotton's biographer, Larzer Ziff, wrote that Cotton "was undeniably the greatest preacher in the first decades of New England history, and he was, for his contemporaries, a greater theologian than he was a polemicist." Ziff also considers him the greatest Biblical scholar and ecclesiastical theorist in New England. Historian Sargeant Bush noted that Cotton provided leadership both in England and America through his preaching, books, and his life as a nonconformist preacher, and that he became a leader in congregational autonomy, responsible for giving congregationalism its name. Literary scholar Everett Emerson called Cotton a man of "mildness and profound piety" whose eminence was derived partly from his great learning.
Despite his position as a great New England minister, Cotton's place in American history has been greatly eclipsed by his theological adversary, Roger Williams. Emerson opined that "Cotton is probably best known in American intellectual history for his debate with Roger Williams over religious toleration" where Cotton is portrayed as "medieval" and Williams as "enlightened". Putting Cotton into the context of colonial America and its impact on modern society, Ziff writes, "An America in search of a past has gone to Roger Williams as a true parent and has remembered John Cotton chiefly as a monolithic foe of enlightenment."
Family and descendants
Cotton was married in Balsham, Cambridgeshire on 3 July 1613 to Elizabeth Horrocks, but this marriage produced no children. Following Elizabeth's death about 1630, Cotton married in Boston, Lincolnshire on 25 April 1632 Sarah, the daughter of Anthony Hawkred and widow of Roland Story. With his second wife Cotton had six children. His oldest child, Seaborn, was born during the crossing of the Atlantic on 12 August 1633 and married Dorothy, the daughter of Simon and Anne Bradstreet. Sariah was born in Boston on 12 September 1635 and died there in January 1650. Elizabeth, born 9 December 1637 married Jeremiah Eggington, and John, born 15 March 1640, attended Harvard and married Joanna Rossiter. Maria, born 16 February 1642 married Increase Mather, the son of Richard Mather. The youngest child, Rowland, was baptized in Boston on 24 December 1643, and like his older sister Sariah, died in January 1650 during a smallpox epidemic.
Following Cotton's death, his widow married the Reverend Richard Mather. Cotton had a grandson who was named for him, Cotton Mather, who also became a noted minister as well as a historian. Among Cotton's many descendants are the U.S. Supreme Court Justice Oliver Wendell Holmes Jr., Attorney General Elliot Richardson, actor John Lithgow and clergyman Phillips Brooks.
Cotton's written legacy includes a large body of correspondence, numerous sermons, a catechism, and a shorter catechism for children titled Spiritual Milk for Boston Babes. The latter is considered the first children's book by an American and was incorporated into The New England Primer around 1701 and remained a component of that work for over 150 years. This catechism, published in 1646, went through nine printings in the 17th century, and is composed of a list of questions with answers. Cotton's grandson, Cotton Mather, wrote, "the children of New England are to this day most usually fed with [t]his excellent catechism". Among Cotton's most famous sermons is God's Promise to His Plantation (1630), preached to the colonists preparing to depart from England with John Winthrop's fleet.
In May 1636 Cotton was appointed to a committee to make a draft of laws that agreed with the Word of God and would serve as a constitution. The resulting legal code was titled An Abstract of the laws of New England as they are now established. While this was only modestly used in Massachusetts, the code became the basis for John Davenport's legal system in the New Haven Colony, and also provided a model for the new settlement at Southampton, Long Island.
Cotton's most influential writings on church government were The Keyes of the Kingdom of Heaven and The Way of Congregational Churches Cleared, where he argued for Congregational polity in favor of Presbyterian governance. He also carried on a pamphlet war with Roger Williams concerning separatism and liberty of conscience. Williams's The Bloudy Tenent of Persecution (1644) brought forth Cotton's reply, The Bloudy Tenent washed and made white in the bloud of the Lamb.
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