During the nineteenth century an interpretive model of the relationship between religion and science known today as the conflict theory developed, according to which interaction between religion and science almost inevitably leads to open hostility, usually as a result of religion's aggressive challenges against new scientific ideas. A popular example was the misconception that people from the Middle Ages believed that the Earth was flat, and that only science, freed from religious dogma, had shown that it was spherical. This thesis was a popular historiographical approach during the late 19th and early 20th centuries, but most contemporary historians of science now reject it.[97][98][99]

This notion of a war between science and religion (especially Christianity) remained common in the historiography of science during the late 19th and early 20th centuries.[100] Most of today's historians of science consider that the conflict thesis has been superseded by subsequent historical research.[101]

However, the framing of the relationship between Christianity and science as being predominantly one of conflict is still prevalent in popular culture.[102] Similar views have also been supported by many scientists. The astronomer Carl Sagan, for example, mentions the dispute between the astronomical systems of Ptolemy (who thought that the sun and planets revolved around the earth) and Copernicus (who thought the earth and planets revolved around the sun). He states in his A personal Voyage that Ptolemy's belief was "supported by the church through the Dark Ages…[It] effectively prevented the advance of astronomy for 1,500 years."[103]

Moreover, many scientists throughout history held strong Christian beliefs and strove to reconcile science and religion. Isaac Newton, for example, believed that gravity caused the planets to revolve about the Sun, and credited God with the design, yet his religious views are generally considered heretical. In the concluding General Scholium to the Philosophiae Naturalis Principia Mathematica, he wrote: "This most beautiful System of the Sun, Planets and Comets, could only proceed from the counsel and dominion of an intelligent and powerful being." Other famous founders of science as we know it who adhered to Christian beliefs included Galileo, Johannes Kepler, and Blaise Pascal.[104][105]

Historians of science such as J.L. Heilbron,[107] Alistair Cameron Crombie, David Lindberg,[108] Edward Grant, Thomas Goldstein,[109] and Ted Davis also have been revising the common notion—the product of black legends say some—that medieval Christianity has had a negative influence in the development of civilization. These historians believe that not only did the monks save and cultivate the remnants of ancient civilization during the barbarian invasions, but the medieval church promoted learning and science through its sponsorship of many universities which, under its leadership, grew rapidly in Europe in the 11th and 12th centuries, St. Thomas Aquinas, the Church's "model theologian," not only argued that reason is in harmony with faith, he even recognized that reason can contribute to understanding revelation, and so encouraged intellectual development. He was not unlike other medieval theologians who sought out reason in the effort to defend his faith.[110] Also, some today's scholars, such as Stanley Jaki, have suggested that Christianity with its particular worldview was actually a crucial factor for the emergence of modern science.[111]

David C. Lindberg states that the widespread popular belief that the Middle Ages was a time of ignorance and superstition due to the Christian church is a "caricature". According to Lindberg, while there are some portions of the classical tradition which suggest this view, these were exceptional cases. It was common to tolerate and encourage critical thinking about the nature of the world. The relation between Christianity and science is complex, according to Lindberg.[112] Lindberg reports that "the late medieval scholar rarely experienced the coercive power of the church and would have regarded himself as free (particularly in the natural sciences) to follow reason and observation wherever they led. There was no warfare between science and the church."[113] Ted Peters in Encyclopedia of Religion writes that although there is some truth in the "Galileo's condemnation" story but through exaggerations, it has now become "a modern myth perpetuated by those wishing to see warfare between science and religion who were allegedly persecuted by an atavistic and dogma-bound ecclesiastical authority."[114]In 1992 the Catholic Church's seeming vindication of Galileo attracted much comment in the media (see Galileo affair).