Probably one of the most significant shifts in the way we think about higher education today has resulted from the widespread questioning of the secularization thesis which had long held sway over the way we conceive of the history of higher education. The thesis, in the academic context, typically maintained an inverse relationship between the advance of science and continued adherence to religious beliefs. In other words, as science progressed and continued to shape and improve our lives, the need for religion in people’s lives would decrease and eventually disappear. In keeping with this narrative, histories of higher education in the United States have tended to focus on various episodes which would demonstrate the slow working-out of the secularization principle as institutions such as Princeton University (formerly The College of New Jersey) morphed from religious colleges deeply shaped by colonial piety to “secular universities” which trumpet the values of critical thinking, societal improvement, and progress.
Not only is this narrative completely wrong, but it has also seriously affected the way that Christians have tended to approach the task of scientific research by framing the question in terms of “faith” and “science”. Whereas those who touted the secularization thesis tended to see the former as disappearing as the latter gains ascendency, Christians engaging in the latter tend to take an apologetic stance which insists that the two are somehow “compatible”. This, however, tends to obscure the very real philosophical and theological issues at play in the social practice of science. Even if the practice itself – after the innovation of making physics without metaphysics possible with Boyle’s invention of experimental science  – may be metaphysically minimalist (i.e. one merely needs to commit to some form of “methodological naturalism”), the who, what, where, when, why and how of practitioners engaging in the practice is often quite theologically fraught . In the words of Abraham Kuyper, “Does not everyone who practices science as a man and not as a measuring stick view things through a subjective lens and always fill in the unseen part of the circle according to subjective opinion?” 
This becomes increasingly clear once we actually go back to the history and take a look at how various important figures in the history of higher education conceived of their work. Take, for instance, the “Father of the American University”, Daniel Coit Gilman (1831-1908). Gilman played a crucial role in the founding of Yale’s Sheffield School of Science, was essentially the founding president of what is today known as UC Berkeley, the founding president of the Johns Hopkins University – the first genuine graduate school program in the US, meaning that a huge number of the first generation of Ph.D.s given in the U.S. stemmed from his school – as well as the founding president of the Carnegie Institute (which funded scientific research). Charles Eliot, the president of Harvard (yes, the Charles Eliot of the Harvard Classics fame), admitted that it was not really until Gilman’s Johns Hopkins came along that Harvard’s graduate program actually figured out what it was doing .
Gilman was a man possessed with great singular vision, a vision which would forever leave the landscape of higher education in the United States changed. Before Gilman, American higher education was dominated by various denominational colleges which saw their role as the formation of the next generation of societal elites by inculcating them with the knowledge of the classical tradition. The idea of the “liberal arts” – those studies taken by those who are “free” of the need to labor for their livings – was that of the mastery of a particular body of knowledge which would provide the leaders of society with the common sensibilities with which they would be able to govern and serve. As such, lectures would be supplemented with “recitations” in which students would be tested on how well they were retaining and understanding the material which they were being taught.
Gilman, on the other hand, possessed a quite dynamic vision for the great universities of the future. In the aftermath of the failure of the religious and intellectual elite to broker some kind of solution to the slavery problem, he proposed a move away from the formation of classes of college graduates towards a focus on excellent individuals – from whatever background  – who would give their lives to the advance of Science. Instead of merely passing on knowledge, universities now had the role of advancing it via research. Instead of the recitation, one would now build the university around the experimental methods of the laboratory. Thus, the Johns Hopkins University would begin, not as an undergraduate institution, but as a graduate school, with the undergraduate college only added later as a result of popular pressure from the citizens of Baltimore. From the beginning, the advance, conservation, refining, and dissemination of knowledge would be the aim of Gilman’s new university, which would stand at the center of an entire network of new scientific institutions made possible by the philanthropy of the nouveau riche – libraries, museums, academies, technical schools, and scientific societies. These would, in Gilman’s words, orbit around a strong university as “planets around the sun”. What, for Gilman, was the significance of these new universities?
It is a reaching out for a better state of society than now exists; it is a dim but an indelible impression of the value of knowledge; it is a craving for intellectual and moral growth; it is a longing to interpret the laws of creation; it means a wish for less misery among the poor, less ignorance in schools, less bigotry in religion, less suffering in the hospital, less fraud in business, less folly in politics; it means more study of nature, more love of art, more lessons from history, more security in property, more health in cities, more virtue in the country, more wisdom in legislation; it implies more intelligence, more happiness, more religion. 
Interpreting the laws of creation. Less bigotry in religion. More religion. Historians of higher education in the clutches of the secularization thesis have tended to interpret these and other similar statements made by Gilman and his fellow university builders in the late 19th century as mere rhetoric made for the sake of winning the support of the yet-pious populate while secretly pushing the science that would put an end to such superstitious nonsense. Gilman and his companions did indeed seek to combat dogmatic religion, but they did so by articulating an alternate theological vision. Indeed, as historian D.G. Hart argues, Gilman preached an “intellectual gospel” that did for the natural sciences what the “social gospel” would do for the social sciences – articulate a theological justification for them that would stand roughly in continuity with the religious background of American evangelicalism while adapting to developments in science such as that of evolutionary theory .
From Gilman’s perspective, he and his colleagues were standing at the dawn of another new era in theological development. Theology, once dominated by dogma, was given a shake-up in the Renaissance with the re-introduction of the study of the classics into the university curriculum. Now, the sciences were clambering for a hearing. And just as the dogmatic theologians persecuted those influenced by the classical learning at first (i.e. the Reformation), now the defenders of the classical education would persecute the sciences. He and his friends believed that they were in the midst of witnessing “the most striking evolution of morals and religion in the history of our race” in which the legends and myths of Dogmatic Theology were being swept away in favor of a purified form of Religion centered around scientific criticism and the “comparative method.” In the words of his Yale classmate Andrew Dickson White,
The races dominant in religion and morals have been lifted from the idea of a ‘chosen people’ stimulated and abetted by their tribal god in every sort of cruelty and injustice, to the conception of a vast community in which the fatherhood of God overarches all, and the brotherhood of man permeates all. 
The language of the “fatherhood of God” and the “brotherhood of man” should be familiar to anyone who has passing familiarity with what would eventually be known as “theological liberalism” at the dawn of the 20th century. While it would be unfair to label Gilman a “liberal”, he certainly shared the sympathies of the proto-liberal movement known as the “New Theology” at the end of the 19th century which drew inspiration from the revised Romanticism of Horace Bushnell, the evolutionary theory of Joseph LeConte, and the preaching of the popular pastor Lyman Abbott. At the core of Gilman’s convictions was not that science was compatible with theology, but rather, that the work of scientific research was theology.
The wisdom of God was not to be discovered by reflection on Jesus Christ – in other words, in Christology – but by the study of nature. Indeed, whereas Paul of Tarsus would sing a paean of praise to Christ, the wisdom and knowledge of God in whom, for whom, and to whom are all things, Gilman would sing his hymns to Science, mediator between God and man. Where Paul would declare that it was the cross of Christ which has broken down the “dividing walls of hostility” between men, Gilman would declare that the study of comparative linguistics
has broken down the middle wall of partition between kindred races and kindred studies; …it has taught us that the study of language is one study. As man is the same in all ages, the history of man is one in all ages. 
In a speech on the new word that had arisen to describe the new task of study, “research”, Gilman would offer his gloss on the Nicene Creed:
The study of nature has usurped the throne of human authority… so that many men of many minds find in an ancient Credo the best expression of their knowledge and their faith: ‘I believe in God the Father Almighty, maker of Heaven and Earth, and of all things visible and invisible.’
He does not go on to confess faith in Jesus in the next line. Nor the Holy Spirit. Though if one asked, there is no doubt that Gilman would readily affirm faith. The election of Christ and the fellowship of the church, however, did not play a huge role in Gilman’s theology. Indeed, having replaced Christology with the study of the world – nature and history – there is no need to wade into divisive sectarian controversies over theological details such as Christology when one can merely appeal to what everyone can see in common – the world around us. In making this move, Gilman was by no means innovating. Indeed, he was merely re-articulating the Enlightenment synthesis that had already dominated American colleges as early as the American Revolution in a new form. Instead of teaching theology, on which various Christians disagreed, America’s early evangelicals (this is a comprehensive term that includes both theological conservatives and liberals who inherit the tradition) emphasized moral philosophy and natural theology/apologetics instead.
Unhinged from Christology, Pneumatology (the study of the Holy Spirit) took a different turn as well. Instead of being centered about the church, all mankind (gender-specific language intended) was brought into a “brotherhood” for the advancement of “civilization”. Yet, in a way, this was merely a further development of the Halfway Covenant of the Puritan state-church synthesis which was, in its turn, a legacy of Constantinian Christianity. Instead of a distinction between the church and the world grounded in an already-but-not-yet eschatology, Gilman and his colleagues would operate from a post-millenial conception of the progressive organic “evolution” of the kingdom of God through the course of human history and culture. There is good reason that today’s academy is dominated by conversations about the legacy of colonialism vacillating between affirming the goods brought about by modern “civilization” and condemning the arrogance of Western imperialism. The very foundations of the American university are grounded in a vision for a universal church of mankind’s progress and civilization.
Science, politics, economics, and religion all fused together into Gilman’s vision of a better humanity. The truth of America’s first great “secular” universities is not that they were without theology, but that they were dominated by a particular one, one that blinded itself to its own background and presuppositions. Little wonder, then, that the university would experience “secularization” once the first generation of scholars, aware of their religious motivations, died off. There is, as such, no non-theological answer to the question of “faith and science”. Any Christian who wants to adequately get at the roots of the problem will need to deal with the reasons why the various positions eventually adopted were ultimately adopted. For the American church, this means, at the very least, grappling with the legacy of the Enlightenment, the question of the relationship between church and state, and slavery. In doing so, one finds oneself confronting theological issues that have gone unresolved as far back as the Reformation and, indeed, perhaps even as early as the formulation of the Nicene Creed.
There are no easy answers to these questions, but they must be asked. The solution to bad theology is not no theology, but good theology. If, at the heart of America’s research universities is a particular theological vision of Christian participation in science, only an alternative vision will suffice. Only thus will we move beyond the “faith and science” dispute and the benign attempts of various Christian apologists to resolve the issue without really hitting to the deep theological presuppositions at the heart of the question.
 Historians of science Steven Shapin and Simon Schaffer discuss the political/epistemological implications of the debate between Robert Boyle and Thomas Hobbes in the 17th century. The fact that we see the former as a scientist and the latter as a political theorist despite the fact that both were engaged in political and epistemological reflections goes to show how much our contemporary debate is shaped by the results of the kind of sphere differentiation that is made possible by the victory of Boyle’s paradigm, in which his “metaphysically neutral” experimental method triumphed over Hobbes’ “metaphysically laden” natural philosophical approach. See Leviathan and the Air-Pump: Hobbes, Boyle, and the Experimental Life (1985).
 One of the more fascinating attempts to understand modernity can be found in Bruno Latour’s We Have Never Been Modern (1991), in which he suggests that modernity attempted to build society based on a nature-culture distinction that would differentiate between various spheres in society in which various principles would hold sway, but that this differentiation remained blind to the way in which various “hybrids” continued to cross-contaminate spheres such that they never completely operated according to their supposedly purifying principle. In other words, while we often think of politics, science, economics, religion, etc. as demarcating different sectors of society in which differing principles reign (i.e. economic principles in the market, scientific principles in science, political principles in politics, etc.), this has never been the case. Science has always been economic, political, and religious. And the other spheres as well, despite the fact that we try our hardest to police the boundaries between them. (Note: This blog roughly divides into categories which have stemmed from such a modern synthesis).
The problem with most attempts to reconcile faith and science (indeed, the very metaphor of “reconciliation” itself ought to be suspect) is that they have essentially bought into this “modern” division of labor and see their task as trying to demarcate exactly where the boundaries between two different realms lies. These strategies fail insofar as they continue to share the same assumptions as the view(s) they wish to contest. Any genuine attempt to do justice to the issue will need to bring many of the categories with which we use to interpret our history into question and try to more faithfully trace out the various neglected dimensions of our contemporary existence.
 cf. Kuyper’s essay “Common Grace in Science”.
 His words in a speech given in honor of Gilman’s accomplishments. “[T]he graduate school of Harvard University, [which] started feebly in 1870 and 1871, did not thrive until the example of Johns Hopkins forced our faculty to put their strength into the development of our instruction for graduates. And what was true of Harvard was true of every other university in the land which aspired to create an advanced school of arts and sciences.”
 The democratizing impulse present in Gilman would become even more pronounced in his friend, Andrew Dickson White, who would become the founding president of Cornell and a key player in orchestrating the passage of the Morrill Land Grant Act that would establish most of the land grant universities that make up today’s State universities.
 See Gilman’s inaugural address as president of Johns Hopkins.
 See Hart, D.G. “Faith and Learning in the Age of the University: The Academic Ministry of Daniel Coit Gilman” in The Secularization of the Academy ed. George Marsden and Bradley J. Longfield (New York: Oxford University Press, 1992), 107-145.
 White, Andrew Dickson. A History of the Warfare of Science with Theology in Christendom, reprint edition (Gloucester, MA: Peter Smith, 1978), 394-395. I have benefited from Mark Noll’s short essay on the figure: Noll, Mark. “Science, Religion, and A.D. White: Seeking Peace in the ‘Warfare Between Science and Theology’” The Biologos Foundation, accessed Dec. 16th, 2014, http://biologos.org/uploads/projects/noll_scholarly_essay2.pdf.
 cf. Gilman’s inaugural address as president of the University of California.