How did Christians lose formerly Christian institutions like Harvard, Yale, and Princeton to the humanists? The humanists never fired a shot. The take over came by way of a generous spirit of acceptance of less orthodox views in the name of tolerance. At his founding, Harvard required students to base their studies on the foundation of a comprehensive biblical worldview with Jesus Christ as the foundation. The directive was codified in 1636 in the following statement:
Let every student be plainly instructed, and earnestly pressed to consider well, the main end of his life and studies is, to know God and Jesus Christ which is eternal life, John 17:3, and therefore to lay Christ in the bottom as the only foundation of all sound knowledge and learning. And seeing the Lord only giveth wisdom, let every one seriously set himself by prayer in secret to seek it of him. Prov. 2, 3
Harvard remained steadfast in following the guidelines of this simple but profound directive until the presidency of Increase Mather, who served from 1685 to 1701. “His young colleagues regarded him as too conservative, or unmovable, out of touch with their generation.” Mather was frequently absent from the school. He often traveled to England in an attempt to secure the school’s charter and that of the Bay Colony itself. It was during his trips abroad that some began to promote “a new spirit of innovation on the campus. The main instigators of this ‘broad and catholic spirit.’. . .”
The changes were not direct attacks on theology or morality. But there was as call for an attitude of tolerance for differing opinions in areas where compromise did not seem to affect core issues. In time, there was not only a breakdown in doctrinal beliefs but in morality as well. Samuel Morison describes life at Harvard in the first quarter of the eighteenth century in rather modern terms:
It was an era of internal turbulence: for [President Benjamin] Wadsworth was no disciplinarian, and the young men resented a puritan restraint that was fast becoming obsolete. The faculty records, which begin with Wadsworth’s administration, are full of “drinking frolicks,” poultry-stealing, profane cursing and swearing, card-playing, live snakes in tutors’ chambers, bringing “Rhum” into college rooms, and “shamefull and scandalous Routs and Noises for sundry nights in the College Yard.”
By 1805, Harvard had appointed Henry Ware, a Unitarian, to the Hollis Chair of Divinity. Harvard was now lost. The tolerance door had been opened in the spirit of fair play and an irenic spirit. But once the intruders had made their way through the door, the original Puritan orthodoxy would be shut out forever.
 David Beale, “The Rise and Fall of Harvard (1636–1805),” Detroit Baptist Seminary Journal (Fall 1998), 94.  Samuel Morison, Three Centuries of Harvard: 1636–1936 (Cambridge: The Belknap Press of Harvard University Press, 1964), 78.