I reject every single word of what you wrote as specious and casuistic.
Where in “Christian Theology” does it say that objective, independent, scientific inquiry into natural processes is a good thing? The New Testament is opposed to natural reasoning as being inferior to spiritual discernment and as leading to satanic pride. Jesus and Paul said the world was about to end, so there should have been no need to study the workings of nature. All that was needed was to focus on purifying your soul so that you could pass muster in God’s imminent final judgment.
When that core of Christian theology proved to be false, the Catholic Church combined forces with the Roman Empire to create a social order we can call “Christendom.” From then on, so-called Christian theology was a Machiavellian ruse to sustain the Church’s earthly power. Anything which opposed the Church’s dominance was deemed heretical and was vigorously opposed. Christian theology became subject to Church politics.
You said earlier that Augustine set the agenda by maintaining that theology should yield to natural philosophy. On the contrary, as the Stanford Encyclopedia article on Augustine points out, ‘Augustine sharply criticizes the “philosophy of this world” censured in the New Testament that distracts from Christ…In his early work he usually limits this verdict to the Hellenistic materialist systems (Contra Academicos 3.42; De ordine 1.32); later he extends it even to Platonism because the latter denies the possibility of a history of salvation (De civitate dei 12.14). The main error he faults the philosophers with is arrogance or pride (superbia), a reproach that does not weigh lightly given that arrogance is, in Augustine’s view, the root of all sins. Out of arrogance the philosophers presume to be able to reach happiness through their own virtue.’ So Augustine embraced philosophy only in so far as “the true philosopher is a lover of God because true wisdom is, in the last resort, identical with God.”
The agenda Augustine set for the Church, rather, is that of the Church’s totalitarianism, as Paul Johnson says in _A History of Christianity_: “The idea of a total Christian society necessarily included the idea of a compulsory society. People could not choose to belong or not to belong. That included the Donatists. Augustine did not shrink from the logic of his position…Here, first articulated, is the appeal of the persecuting Church to all the authoritarian elements in society, indeed in human nature. Nor did Augustine operate solely at the intellectual level. He was a leading bishop, working actively with the State in the enforcement of imperial uniformity.”
As Sheldon Wolin puts it in _Politics and Vision_, Augustine’s task was to make excuses for the “embarrassments of a politicized religion.”
Science arose despite Christendom, because all that was needed for modern science was a return to ancient Greek philosophy and protoscience. Christianity stood in the way as a twisted bastardization of that pre-Christian tradition, much of which the Church destroyed in the first place when it acquired political power over paganism. At any rate, the Church filtered Greek philosophy through the faith-based prejudices and speculations of casuistic theologians like Augustine and Aquinas.
Your comparison of Christendom to the Muslim world is preposterous. There was a golden age of science in the Muslim world, thanks largely to Muhammad’s having conquered territory where Greek thought was dominant, and to later Caliphs’ having translated those Greek works. (See the two links below.) That’s the very same reason science thrived in Europe, because of the infusion of ancient Greek thought which the Church translated and with which it struggled until the heretical upshot of Greek naturalism burst the Church’s seams and led to the Renaissance and to the abolition of Christendom (i.e. the abolition of the Church’s political power, Christian Theology as an authentic going concern having been undermined centuries earlier by the machinations of the early Catholic Church).
Science in the Muslim world declined because of the rise of Muslim fundamentalism, of a Protestant-like idolizing of the Quran. A-Ghazali drove Muslims to the point of conservative anti-intellectualism where they remain to this day. He feared that independent reason can lead Muslims to lose their faith—and he was surely right since that’s what happened to Western Christianity.
Newton was indeed a theist or perhaps a deist, albeit a heretical one, but that doesn’t mean his scientific work depended on Christian theology. On the contrary, where his religion impacted his science, the former led him astray. He appealed to a God-of-the-gaps argument to explain the orbits of planets. If he lacked faith in such a deus ex machina, he might have puzzled out how planets could avoid falling into each other, without appealing to miracles, as Einstein later did. (Indeed, Einstein’s pantheistic quasi-Judaism led him astray too, when he rejected quantum mechanics because he presumed God doesn’t “play dice.”)
The Enlightenment was indeed “religious” in a broad sense, but that religion wasn’t the established one of Christianity. The religious or idealistic sensibility that propelled Western science was a modern reformulation of ancient Greek naturalism. That modern faith had elements of humanism, pantheism, and Gnosticism, and its upshot was precisely what the Church longed condemned on political grounds: “satanic,” promethean pride in our human potential to solve problems by thinking for ourselves and by becoming godlike masters of the world. The goal was evidently the secular progressive one of taming the hideous wilderness—that is to say, God’s implicitly inferior creation—and of using technology to build “Heaven” on earth, that is a liberated, secular civilization and empire of reason and liberty.
That’s where Protestantism fits in. Luther was instrumental in freeing Western Europe from the Catholic Church’s totalitarian hammerlock. The Bible was translated into vulgar languages, and Protestants took individual Christians to be their own priests and to be free to “work out their salvation in fear and trembling,” without having to go through the Church hierarchy. Protestant individualism promoted capitalism and democracy, which provided the tangible alternative to Christian theocracy.
Christian institutions financed philosophy and science in the early-modern period in Europe because there were no alternative financers. Christendom was a totalitarian political order, and its interest in theology and spirituality was superficial. What mattered to the Christian upper class was sustaining the Church’s political power, so naturally the Church controlled the universities and art patrons. The fact that philosophers and artists had to seek support from the Church in that context doesn’t mean that modern philosophy and art grew out of the content of Christian theology. That’s the genetic fallacy. On the contrary, those products emerged from that origin the way water molecules emerge from their components and take on autonomous (irreducible), higher-level properties.