Sometime around the time of his marriage, John Winthrop became interested in a growing sect of the Protestant community called the Puritans, a church with a more individual focus than the Church of England. His training at Trinity no doubt reinforced his desire to cleanse his own life and devote himself to God, and he found exactly what he needed in the Puritan community.

The Puritan movement grew out of a growing dissatisfaction with the Church of England among some Presbyterians, Independents, and Baptists in the late sixteenth century. Some Anglicans were upset by the religious compromise of 1559 made by Queen Elizabeth I to avert civil war; they longed for a stricter sect of biblically based Calvinistic Protestantism–hence the root of their sect's name, "Puritan." They believed that the government should strictly enforce the civil laws and crack down on ostentatious dress, Sabbath breaking, and other crimes of moral virtue. The Puritans also insisted that the Church of England do away with all remnants of the Catholic Church–like the hierarchy of bishops and cardinals and the Anglican's elaborate liturgies–and refocus the church on the individual.

As stated earlier, the main focus of the new movement lay on the individual. The Puritans adopted the Calvinistic idea of predestination;mainly that human beings were innately sinful since they inherited the original sin of Adam and Eve. However, Calvin also taught that some people, the "elect," would be saved from eternal damnation at some point in their lives. The Puritans held themselves as the "elect" and thus were left with the complicated paradox that while they should devote their lives to God, they–as humans–were only capable of evil. That meant, however, that they shunned many traditional pastimes that they considered frivolous, like playing chess, and hunting for sport.

As he converted to Puritanism, Winthrop wrestled with the paradox left by his new faith. On the one hand, it taught him to place his hope and faith in Christ while on the other hand telling him that Christ would likely reject him outright–unless he had been preordained as elect." He even considered attending divinity school and entering the ministry so that he could more fully work for God, but he eventually decided he could not leave his life at Groton manor. Puritanism also taught that one should work for Christ "in this world" and not withdraw to a different life. As Winthrop's life progressed, it would be this teaching that became the most problematic for him.

With his upbringing as a country gentleman, he had been taught to enjoy many of the pastimes–hunting, fishing, good food and wine, that Puritanism now insisted he avoid. After a long debate with himself, he gave up hunting and "tinkering" and contented himself "with such things as were lefte by our forefathers." The satisfaction he got from both hobbies was not worth the time and effort he put into them, Winthrop decided.

Marriage caused him more worries. Although clearly God meant marriage to be an important factor in one's life, Winthrop struggled to keep himself from relying on it too much. Mary Forth, his first wife, never matched Winthrop's interest in Puritanism. However, she served Winthrop faithfully, bearing six children–though two died in infancy–in the ten years they were married. She died in 1615. His third wife, Margaret Tyndal, was much more pious, and the letters Winthrop exchanged with her from London showed his preaching side, as he expounded in sermon-like letters on the meaning of biblical passages. He taught that the love one feels in marriage must be supplanted by a greater love for God.

Throughout his early life, Winthrop vacillated between self-denial and self- indulgence, abstaining from Puritan vices and then giving in to his desires–for instance, eating a large dinner of good food and wine. He would compensate by punishing himself for his excesses. The constant roller- coaster brought him much pain; he wrote once that "[W]hen I had some tyme abstained from suche worldly delights as my heart desired, I grewe very melancholik and uncomfortable." However, he again became caught in the paradox that he could not entirely give up such pleasures because then he would not be living "in this world." On trips to London, where he was removed from the temptations of the Groton estate, he would run himself down "without any great sence of either guilt or peace." Over time, he strengthened his spirit, his faith, and his resolve so that he could handle the complex life of a Puritan.

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