Before John joined the military, he was uncertain. From his upbringing, he developed beliefs and attitudes that he found conflicted with those of his mentor, Gershom Bulkely. When he was with the doctor in public, he kept silent about his differing beliefs. After John’s time in the military, where he spent time as a captive of the enemy, he found his inner strength. When he returned to his studies with Reverend Gershom, he was no longer meek. With all due respect Bulkely as a scholar and a gentleman, he created an agreement with the man wherein John would learn theology and medicine, but he would also retain his ability to think for himself.
He returns to studying with him, and respects the good doctor's learning as far as religion and medicine. Since they differ on politics, he finds a way to approach Dr. Bulkeley's position as one where "he is obeying his own conscience." This he can respect, and they essentially agree to disagree.