In the three decades preceding the Civil War a variety of pseudo-scientific theories and practices entered the nascent but still embryonic scientific community. One of the more sensational (and for a while popular) new theories was that of phrenology. Pulitzer-winning historian Walter MacDougall explained that phrenology was “the study of skull sizes and shapes in search of clues to racial characteristics.” George Calvert and Samuel Morton brought the theory to the forefront of respectable, or near-respectable scientific inquiry in the 1830s. Morton’s Crania Americana, and subsequent works like Josiah C. Nott and George R. Glidden’s Types of Mankind formed the core texts of this staringly racist school of thought before 1860. “Morton,” noted MacDougall, eventually “concluded that the intellectual faculties of American Indians were of ‘a decidedly inferior cast when compared with types of the Caucasian and Mongolian races’” Nott became one of the first major devotees of Darwinian theory in the United States and particularly the American South. He also affirmed polygenesis in a time when even vigorous defenders of slavery affirmed the essential unity of mankind. Presbyterian cleric and South Carolina College president James Henley Thornwell, a firm proponent of southern slaveholding, nonetheless denounced those who would “defend slavery upon the plea that the African is not of the same stock with Ourselves.” Defenses of slavery that rested on polygenesis and racialized science conflicted “with the dearest doctrines of the Gospel.”
Racialized science in the form of phrenology attracted the attention of Unitarians in New England. The first major phrenology society in the Boston area devoted itself to the memory of Johann Spurzheim, phrenology’s ostensible founder. “The prominence of clergymen in the Boston Phrenological Society gave it a profile of social and religious respectability. Its first president was Reverend John Pierpont, who had written the emotional ode for Spurzheim’s funeral.” Clergy devotees of phrenology—Reverend Henry Ware, Jr., and Reverend Henry T. Tuckerman—overwhelmingly came from Unitarian ranks. 
Walter Cosner in his God and the Natural World: Religion and Science in Antebellum America noted that “most Christians (as well as most American scientists) rejected polygenesis,” an apparently inevitable intellectual consequence of phrenology. Protestant intellectuals, particularly those involved in colleges, universities, and seminaries, denounced phrenology and racialized science as incompatible with Christianity. Josiah Nott’s rejection of the biblical Genesis account of human origins and embrace of racialized science in the 1850s occurred against the backdrop of an intellectual and religious conflict between secularized and religious scientists.
In 1840, John Augustine Smith, a physician, son of an Episcopal minister, and president of William & Mary took up his pen to rebut phrenology. Smith was hardly a biblicist or fundamentalist. He rejected a strictly literal reading of the Hebrew scriptures but did not embrace German higher criticism that called in to question the inerrancy of the Christian Bible. His Select Discourses on the Functions of the Nervous System: In Opposition to Phrenology, Materialism, and Atheism constitutes two hundred pages painstakingly rebuking phrenology on Christian and scientific grounds. Smith disliked using scripture to litigate scientific questions. He dismissed “crude inferences from the Bible, being obtruded upon us as revealed knowledge, whatsoever may be the nature of our investigations.” He did not imply the Bible was fantasy. “To associate that book, in any manner, with fanciful notions,” he warned, was “exceedingly objectionable,” but the “heterogeneous mixture of devout opinions, and philosophical ignorance, and blunders, operates most injuriously.” In minds that were “pious, though weak, or uncultivated,” conceit was mistaken for learning, and a spirit of persecution usurps the place of charity.”
Raw biblicism, Smith cautioned, had made the work of scientists difficult in ages past because it turned scientists into infidels for merely admitting that the scientific process has led them to certain empirical conclusions. This meant that scientists who arrived at conclusions at odds with a literal interpretation of Scripture could not “be communed with, as an erring philosopher” but were instead too easily “denounced as a daring infidel.” Biblicism, “the darling offspring of an enthusiastic parent, ardent, and sincere, though more deeply versed in the Pentateuch of Moses, than in the Principia of Newton,” had made it difficult for religious scientists in days gone by. But Smith happily announced “the dawn of brighter prospects. Liberty of philosophizing has been proclaimed from Cambridge, from Oxford, and from Rome.” Given the liberalizing intellectual trends that allowed for religion and science and reason to coexist in the universities of the Old World—Oxford, Cambridge, and Rome—it was reasonable to expect American scientists to have freedom to pursue science without the fear of religious censure. “Surely, then, we, on this side of the Atlantic, with not more of faith, and far less of learning, will receive with joy, and, it is to be hoped, use with discretion, the freedom thus proffered from the high places of Christianity; and, what is of incomparably greater importance, RATIFIED by the SOUND DICTATES of RIGHT REASON.” 
Smith’s arguments against phrenology were hardly those of a biblicist or a religious fundamentalist. Andrew Boardman, a defender of phrenology, nonetheless found them objectionable. Smith’s association of phrenology with materialism and atheism particularly angered phrenologists. Boardman accused Smith of using “one of the most ungenerous means that can be resorted to, in order to bring a subject into odium, is to associate it with that which is odious.”
Although the major debates over Darwinian racialization of science would not take place until the late 1850s, Protestant polemicists rejected phrenology and other pseudo-scientific theory throughout the Early Republic. Smith, Thornwell, and others showed that far from being biblicist and wedded to anti-scientific expressions of religion, Protestant academics habitually worked within scientific and religious frameworks without resorting to a biblicist invasion of science, or a scientific invasion of the biblical narratives.
 Walter A. McDougall, Throes of Democracy The American Civil War Era 1829–1877 (New York: HarperCollins, 2008); James Henley Thornwell, “National Sins: A Fast-Day Sermon,” Southern Presbyterian Review 13 (Jan. 1861): 682–83.
 Lisle Woodruff Dalton, “Between the Enlightenment and Public Protestantism: Religion and the American Phrenological Movement.” University of California, Santa Barbara, 1998.
 Walter Cosner, God and the Natural World: Religion and Science in Antebellum America (Columbia: University of South Carolina Press, 1993), 23-24.
 John Augustine Smith, Select Discourses on the Functions of the Nervous System: In Opposition to Phrenology, Materialism, and Atheism (New York: D. Appleton and Co., 1840), 90-91.
 Andrew Boardman, A Defence of Phrenology (New York: Edward Kearney, 1847), 84-85.
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