The Conflict Thesis is a historical thesis that contends religion and science have historically been in a state of perpetual war against one another. Science, it argues, has been continuously impeded and opposed by religion and only makes progress when it is able to cast it aside. While this thesis has been at least partially held by some noteworthy scientists and popularizers, it is opposed by the vast majority of historians of science on the grounds that it is far too simplistic and is largely justified by false claims.
Thesis and Popularity
“”The antagonism we thus witness between Religion and Science is the continuation of a struggle that commenced when Christianity began to attain political power... The history of Science is not a mere record of isolated discoveries, it is a narrative of the conflict of two contending powers, the expansive force of the human intellect on one side, and the compression arising from traditionary faith and human interests on the other
|—John William Draper|
While the Conflict Thesis has roots in the anti-Catholic sentiment of the Reformation and the Enlightenment, it was popularized by 19th century historians and public intellectuals, John William Draper and Andrew Dickson White. They both argued that religion and science are in a perpetual state of conflict with one another and science, the good side, only progresses when it is able to overcome religion. To back up their claims, they cited historical claims like the "Dark Ages" were a period of no intellectual growth and Christopher Columbus' voyages proved Christians wrong in regards to thinking the Earth was flat. Several members of the skeptical and atheist communities have at least in part regurgitated Draper and White's line of reasoning. Carl Sagan, in particular, stated in Cosmos and Demon-Haunted World that the Dark Ages were a source of no intellectual growth. Brian Dunning, restated this sentiment in his documentary Here Be Dragons.
“”When we invest out faith in a pseudoscience without questioning its validity, we're recreating the Medieval Dark Ages. For 500 years, there was essentially no progress in any scientific field or in human rights. Scientific experimentation and, thus learning, was often illegal
Criticism of main claims
Many of the claims made by Draper, White, and other proponents of the Conflict Thesis have been debunked by mainstream historical scholarship. For example, the term "Dark Ages" is not used by historians to demarcate the period between the fall of the Roman Empire and the Italian Renaissance. Instead, the moniker "Middle Ages" is used. Unlike Brian Dunning, medieval historians view this as a period of intellectual and artistic progress that laid the foundations for the Renaissance. Even in the darkest days of early Middle Ages (right after Odoacer deposed of the Emperor Romulus Augustulus in 476 AD) there was still technological progress. Three field crop rotation, the plow, and the stirrup were all invented in the centuries following the fall of Rome. Grain mills, which the Romans had but never took advantage of, also spread across Western Europe like wildfire at this time. These innovations led to a rampant increase in population.
Charlemagne's sweeping reforms in the late 8th century had a debatable impact on European society as a whole, but undoubtedly reformed the clergy across his empire. They reinforced literacy among the clergy, pushed an effort to copy and preserve texts, made monasteries open up schools, and led to the development of the Carolingian script. By the late 11th century, Western Europe was on the verge of an intellectual transformation. The universities at Oxford, Cambridge, Bologna, Padua, and Paris were founded during this time and, just as important, Christian armies recaptured the city of Toledo from the Andalusian Caliphate in 1085. In the recaptured city, the Christian invaders found intact libraries with countless classical texts on mathematics and philosophy from the Islamic and Ancient Greek worlds  Given these facts, one would be hard-pressed to disagree with the idea that progress occurred during the middle ages.
A related myth is that Christopher Columbus' voyages proved Christian thinkers incorrect and demonstrated the roundness of the Earth. It has been known, however, since ancient Greece and Rome that the Earth is round. Claudius Ptolemy, Aristotle, and Eratosthenes, for example, all believed the Earth was a sphere. The Church Fathers St. Augustine and St. Jerome all held this view and this knowledge was never lost. Instead of proving the roundness of the Earth, Columbus was trying to show that it was in fact much smaller than the Greeks thought. If this was the case, he thought, Europeans could get to Asia much faster by sailing West than by sailing around Africa.
Criticism of overall logic
It is true that there are historical instances of organized religion and religious practitioners being hostile to science on theological grounds. For example, since the birth of their movement, Young Earth Creationists have rejected almost the entirety of the physical and life sciences because they conflict with a literal reading of the Bible. The Intelligent Design movement has similarly dismissed Darwinism, which is the bedrock of the modern life sciences because it entails naturalism. Since the founding of their movement in the late 19th century, Christian Scientists have rejected science-based medicine in favor of faith healing.
The Conflict Thesis, however, is far too simplistic to do justice to the complicated historical relationship between religion and the sciences. The Universities, as mentioned above, were founded by the Church of Rome. Many of the key figures of the Scientific Revolution pursued their research for theological reasons. Kepler, for example, wanted to know why God created exactly six planets and the Sun. There were also other times when nature knowledge was viewed as the "handmaiden of theology" and, despite being worthy of study, was viewed as irrelevant for salvation. This "handmaiden" view, however, was enough to justify the study of the natural world 
While the historical Conflict Thesis does not hold water, this does not mean that religion and science are not conflicting in other ways. It has been argued by scientists and philosophers of science alike that they are epistemologically incompatible. Modern science comes to truth by experimentation and the examination of publicly available evidence. It holds predictive power, organizing preexisting data into a coherent framework, and simplicity as explanatory virtues for theories. Scientists are supposed to strive to be open-minded and curious. Contrary to these standards, religious-based explanations, such as those offered by the intelligent design movement, do not make meaningful predictions, lack evidence, are unparsimonious, and aren't part of an explanatory framework. This lack of scientific virtue has has led philosophers of science like Gregory Dawes to reject ID on the grounds that its arguments are lousy explanations. Another philosopher of science, Maarten Boudry, has argued that supernatural explanations have failed so often that, even though they were once accepted, they are no longer worth taking seriously.
- James Hannam, Genesis of Science (Washington D.C.: Regnery Publishing, 2014), 4-8.
- Ibid., 13-15
- Robert Bartlett, The Making of Europe: Conquest, Colonization, and Cultural Change, 950-1350 (Princeton, New Jersey: Princeton University Press, 1993), 112.
- Cormack, Lesley. "Medieval Christianity and the Flat Earth" in Galileo Goes to Jail: And Other Myths about Science and Religion." Edited by Ronald L. Numbers. Cambridge, MA: Harvard University Press, 2010., 30-31
- Ibid, 34.
- H. Floris Cohen, The Rise of Modern Science Explained (Cambridge: Cambridge University Press, 2015), 106.
- Lindberg, David. "Christianity and the Demise of Ancient Science" in Galileo Goes to Jail: And Other Myths about Science and Religion." Edited by Ronald L. Numbers. Cambridge, MA: Harvard University Press, 2010., 17
- Dawes, Gregory W. Theism and Explanation. London: Routledge, 2015.
- Boudry, Maarten. 2011. “Here Be Dragons: Exploring the Hinterland of Science”. Ghent, Belgium: Ghent University. Faculty of Arts and Philosophy.