In his History of the Conflict between Religion and Science (1874), Draper commences his historical review of the interactions between science and religion by declaring that “modern science” was born in the aftermath of the conquests of Alexander the Great, and indicates that Alexandria, particularly its Museum, was the first civilization to pursue a “practical interrogation of Nature.” This was the enlightenment of humanity before Christianity arose. He then follows with a more elaborate and gloomy account of the origin, spread, and ultimate degeneration of Christianity. He relates a common idealized image of primitive Christianity when he writes that
Jewish people at that time entertained a belief, founded on old traditions, that a deliver would arise among them, who would restore them to their ancient splendor. The disciples of Jesus regarded him as this long-expected Messiah. But the priesthood, believing that the doctrines he taught were prejudicial to their interests, denounced him to the Roman governor, who, to satisfy their clamors, reluctantly delivered him over to death. His doctrines of benevolence and human brotherhood outlasted that event. The disciples, instead of scattering, organized. They associated themselves on a principle of communism, each throwing into the common stock whatever property he possessed, and all his gains. The widows and orphans of the community were this supported, the poor and the sick sustained.
The primitive church, the early followers of Jesus, was thus a movement of purity, according to Draper. It was a matter of life and practical goodness, enjoining veneration toward God, purity in personal virtues, and benevolence in social life.
But the purity of the Christian movement did not last, according to Draper. It became popular, and was eventually adopted by many solely from interest and expediency. “Crowds of worldly persons,” he writes, “who cared nothing about its religious ideas, became its warmest supporters.” It thus relapsed into many of the forms and ceremonials of paganism, and subsequently incorporated pseudo-Christian dogmas. Indeed, according to Draper, Christianity had become “paganized” by the reign of Constantine, the first “Christian” emperor. These “modifications,” Draper argues, is what “eventually brought it in conflict with science.” He then offers an exposition of Tertullian’s famous second-century Apology as an example of Christianity’s purer days, exemplifying a life of innocence, justice, patience, temperance, chastity under persecution and struggle. All that changed, he says, when Christianity gained imperial power. “Great is the difference between Christianity under Severus and Christianity after Constantine,” he declares.
It should be clear that Draper’s account of the rise, spread, and corruption of the Church was imbued with Protestant polemics. To strengthen his case, Draper even quoted a long passage from English cleric Bishop Thomas Newton’s (1704-1782) Dissertation on the prophecies, which have been remarkably fulfilled, and are at this time fulfilling in the world (1754) to demonstrate the paganization of Christianity:
Is not the worship of saints and angels now in all respects the same that the worship of demons was in former times? The name only is different, the thing is identically the same,…the deified men of the Christians are substituted for the deified men of the heathens. The promoters of this worship were sensible that it was the same, and that the one succeeded to the other; and, as the worship is the same, so likewise it is performed with the same ceremonies. The burning of incense or perfumes on several altars at one and the same time; the sprinkling of holy water, or a mixture of salt and common water, at going into and coming out of places of public worship; the lighting up of a great number of lamps and wax-candles in broad daylight before altars and statues of these deities; the hanging up of votive offerings and rich presents as attestations of so many miraculous cures and deliverances from diseases and dangers; the canonization or deification of deceased worthies; the assigning of distinct provinces or prefectures to departed heroes and saints; the worshiping and adoring of the dead in their sepulchres, shrines, and relics; the consecrating and bowing down to images; the attributing of miraculous powers and virtues to idols; the setting up of little oratories, altars, and statues in the streets and highways, and on the tops of mountains; the carrying of images and relics in pompous procession, with numerous lights and with music and singing; flagellations at solemn seasons under the notion of penance ; a great variety of religious orders and fraternities of priests; the shaving of priests, or the tonsure as it is called, on the crown of their heads; the imposing of celibacy and vows of chastity on the religious of both sexes—all these and many more rites and ceremonies are equally parts of pagan and popish superstition. Nay, the very same temples, the very same images, which were once consecrated to Jupiter and the other demons, are now consecrated to the Virgin Mary and the other saints. The very same rites and inscriptions are ascribed to both, the very same prodigies and miracles are related of these as of those. In short, almost the whole of paganism is converted and applied to popery; the one is manifestly formed upon the same plan and principles as the other; so that there is not only a conformity, but even a uniformity, in the worship of ancient and modern, of heathen and Christian Rome.
 Ibid., 19-23, 33.
 Ibid., 36-37.
 Ibid., 38.
 Ibid., 39-45.