While unyielding in his religious orthodoxy at Edinburgh, i.e., never doubting the basic ideas and doctrines of Great Awakening evangelism, Rush was aroused to a compelling skepticism of his other accepted opinions. This was certainly true in the classroom, where Dr. Cullen made Rush aware of the importance of skeptically examined principles in medicine; it was even more true outside the classroom, where a fellow student, John Bostock, plied him with anti-monarchical arguments from Algernon Sidney's Discourses Concerning Government (1698), thus creating serious doubts in Rush's mind about the legitimacy of kingly power. In this way, Bostock introduced the colonial patriot to the literature of seventeenth-century English republicanism; and Rush now found, as many other Americans were finding too, a political hero in Sidney, who had been martyred for his Whig opposition to arbitrary government. As he read Sidney's famous refutation of Robert Filmer's argument in Patriarcha or the Natural Power of Kings (1680) that one should not 'meddle with mysteries of state,' Rush noted the Whig martyr's call to his countrymen 'to examine the original principles of government in general, and of our own in particular. We cannot distinguish,' Rush further noted in Sidney's Discourses, 'truth from falsehood, right from wrong, or know what obedience we owe to the magistrate, or what we may justly expect from him, unless we know what he is, why he is, and by whom he is made to be what he is.' Then the republican Sidney argued, and Rush approvingly read, that the original principles of government which honest men sought were natural, rational, and Scriptural, the principles of universal liberty and equality, and that 'the constitution of every government is referred to those who are concerned in it, and no other has any thing to do with it.' The object of the English government, wrote Sidney—as of all legitimate governments derived from the free consent of the people—was the good of the people. This was, of course, the kind of argument being heard increasingly in the colonies, and it made sense to the young American who had recently defied the Stamp Act. That Act had been arbitrary. Rush believed, and Sidney asserted that arbitrary power must be limited even if it took a revolution to do so. The evangelist was also pleased to read in the Discourses that the contrary absolutist doctrines of men like Filmer, Thomas Hobbes, and Archbishop Laud could 'have no title to Christianity.'
John Bostock, to whom Rush had carried a letter from Liverpool, proudly claimed to be descended from an officer in Cromwell's army, whereupon Rush informed his new friend that his ancestor. Captain John Rush, had served in Cromwell's cavalry. As a 'free born son of America,' Benjamin cherished the stories of Captain Rush's heroism in the great English war against tyranny, stories which formed a major part of Rush family tradition. Bostock confessed his attachment to the compact theory of government as advanced by Sidney and John Locke and invoked the memory of his and Rush's heroic ancestors to win the colonial patriot to the 'good old cause.' The effect of this personal appeal, combined with Rush's new liberal studies and colonial political experience, was dramatic:
Never before had I heard the authority of Kings called in question. I had been taught to consider them nearly as essential to political order as the Sun is to the order of our Solar System. For the first moment in my life I now exercised my reason upon the subject of government.This new skepticism about government prepared Rush for what can only be described as his conversion to republicanism, for he reasoned now that the doctrine of hereditary kingly power was patently false and absurd, as Sidney and Bostock argued, and that there could be only one true, rational, and constitutional species of government; namely, 'that which is derived from the Suffrages of the people who are the subjects of it.' This truth of reason was illustrated by the experience of England and of all nations, as Sidney had shown in the Discourses. That it was still held as a truth in Rush's own day, the American believed, was demonstrated by resistance to the Stamp Act and other unconstitutional measures. Republicanism was true for Rush not because of the lessons of experience, nor because of the bookish authority of Sidney, nor by virtue of the persuasive arguments of Bostock, but because of its rationality—a rationality that withstood every test of doubt.
Once admitted into Rush's thought, doubt cut deeply and generally. 'I now suspected error in every thing I had been taught, or believed,' Rush confided to his memoirs some thirty years later, 'and as far as I was able began to try the foundations of my opinions upon many other subjects.' This intellectual discovery, reminiscent of Descartes and basic to the philosophy of the Enlightenment, of employing doubt in the service of truth, marked the beginning of Rush the revolutionary. His beliefs in many areas, now exposed to new and searching criticism, proved untenable. Kings, Cullenism (as well as rival systems of pathology), oath-taking, severe and capital punishments, the priority of classical languages, traditional penal and medical institutions—all of these and more were sincerely questioned by Rush at various times in his life and found wanting in rationality.