We set the stage for this post on Duhem in "The Cat Lover's Almanac" by sketching a certain perspective. The quotation below is from a Quora article by Tim O'Neill. As is my procedure, I may rearrange the prose for a narrative flow based on other needs than the original author's.
The fact is that the idea of the [medieval] Church suppressing science and rational analysis of the physical world is a myth. Not one Medieval scholar was ever burned, imprisoned or oppressed by the Medieval Church for making a claim about the physical world. This why the modern proponents of the myth always have to fall back on an exceptional and post-Medieval example to prop up this idea: the Galileo case.....
....The idea that the cosmos was rational and could be analysed via reason was certainly resisted by some conservatives, but a new guard of scholars came increasingly to the fore, including William of Conches, Honorius of Autun, Bernard Silvester, Adelard of Bath, Thierry of Chartres and Clarenbold of Arras. William of Conches wrote with scorn of those who were suspicious of this worship of reason and rational analysis:
Ignorant themselves of the forces of nature and wanting to have company in their ignorance, they do not want people to look into anything; they want us to believe like peasants and not ask the reason behind things .... But we say the reason behind everything should be sought out!
(William of Conches (c. 1090-1154 AD), Philosophia mundi)
The closest the Church came to suppressing science in any way was when, in reaction to some of the ideas being debated in the University of Paris at the height of the rediscovery of Aristotelian learning in the Thirteenth Century, the Faculty of Theology attempted at putting some limits on what could be discussed by the Faculty of Arts. In 1210, 1270 and again in 1277 the Pope, at the request of the Parisian Theology Faculty, published lists of ideas proposed by Aristotle or implied by his philosophy that were contrary to Christian doctrine and so were forbidden. What is remarkable about this is, firstly, how little in Aristotle etc was actually proscribed by these Condemnations. Secondly, it's remarkable how ineffective the Condemnations were. They only applied to Paris, whereas discussion of all these topics continued at Oxford and other universities unaffected. And, as the fact that they had to be repeated twice indicates, they were widely ignored anyway. They also had another effect - by arguing that Aristotle was actually wrong on several key points, they stimulated a more critical examination of the Greek philosopher's work which led to several of his idea being critically analysed and found to be incorrect (eg the idea that a heavy object falls faster than a lighter one). In a strange way, the Condemnations failed to suppress science and actually helped to stimulate it.
[So] the claim that "science made little clear progress in Europe in the Middle Ages" is based on a profound ignorance of the period... Once Medieval Europe recovered from the chaos that followed the fall of Rome, it quickly revived the ancient tradition of natural philosophy that had been languishing since Roman times. Medieval scholars engaged in a remarkable process of examining the physical universe using reason and logic and, in doing so, developed principles that were to become the foundations of modern science proper. And they applied these principles in ways that corrected errors the Greeks had made and did the ground work for the later discoveries in physics and astronomy that made up the beginning of the Scientific Revolution. While people with no detailed knowledge of modern studies in the history of science still cling to Nineteenth Century myths about the Church suppressing science, it is now clear that without the flowering of speculation and analysis in the period from the Twelfth to the Fifteenth Century, western science would never have arisen at all.
O'Neill cites some books for further reading:
David C. Lindberg, The Beginnings of Western Science, 600 B.C. to A.D. 1450 (1992)
Ronald Numbers, Galileo Goes to Jail, and Other Myths about Science and Religion (ed.) (2009)
Edward Grant, The Foundations of Modern Science in the Middle Ages (1996)
James Hannam, God's Philosophers: How the Medieval World Laid the Foundations of Modern Science (2009)
The origin and persistence of this myth is explained by O'Neill:
The standard view of the Middle Ages as a scientific wasteland has persisted for so long and is so entrenched in the popular mind largely because it has deep cultural and sectarian roots, but not because it has any real basis in fact. It is partly based on anti-Catholic prejudices in the Protestant tradition, that saw the Middle Ages purely as a benighted period of Church oppression. It was also promulgated by Enlightenment scholars like Voltaire and Condorcet who had an axe to grind with Christianity in their own time and projected this onto the past in their polemical anti-clerical writings. By the later Nineteenth Century the "fact" that the Church suppressed science in the Middle Ages was generally unquestioned even though it had never been properly and objectively examined.
It was the early historian of science, the French physicist and mathematician Pierre Duhem, who first began to debunk this polemically-driven view of history. While researching the history of statics and classical mechanics in physics, Duhem looked at the work of the scientists of the Scientific Revolution, such as Newton, Bernoulli and Galileo. But in reading their work he was surprised to find some references to earlier scholars, ones working in the supposedly science-free zone of the Middle Ages. When he did what no historian before him had done before and actually read the work of Medieval physicists like Roger Bacon (1214-1294), Jean Buridan (c. 1300- c. 1358), and Nicholas Oresme (c. 1320-1382) he was amazed at their sophistication and he began a systematic study of the until then ignored Medieval scientific flowering of the Twelfth to Fifteenth Centuries.
What he and later modern historians of early science found is that the Enlightenment myths of the Middle Ages as a scientific dark age suppressed by the dead hand of an oppressive Church were nonsense. Duhem was a meticulous historical researcher and fluent in Latin, meaning he could read Medieval scientific works that had been ignored for centuries. And as one of the most renowned physicists of his day, he was also in a unique position to assess the sophistication of the works he was rediscovering and of recognising that these Medieval scholars had actually discovered elements in physics and mechanics that had long been attributed to much later scientists like Galileo and Newton.
[Later] Duhem was no longer alone in seeing the idea of the Middle Ages as a period of no science as a baseless myth. The American historian of science Lynn Thorndike had followed the same trail as Duhem and came to the same conclusions that Medieval scientists had been wrongfully ignored and neglected since the Enlightenment, largely for political and ideological reasons. In his eight volume History of Magic and Experimental Science (1923-1958) he too found that science in the Middle Ages was remarkably wide-ranging, speculative and highly sophisticated. These pioneers in the field of early science history have now been followed by a long list of historians of the subject that have made this neglected period in scientific history even more clear. Current leading scholars in the field such as David Lindberg, Ronald Numbers and Edward Grant have revolutionised our understanding of how the scientists of the Middle Ages built on the work they inherited from the Greeks and Arabs, advanced knowledge further and laid the foundations of modern science as we know it.
Stanley L. Jaki, who wrote Uneasy Genius: The Life And Work Of Pierre Duhem (1984)
also helps us situate Duhem within his time. His description of the siege of Paris (September 1870 to January, 1871) includes this note: the rich during the siege of Paris ate "Castor and Pollux" the two elephants at the zoo, while the poor had to eat dogs and cats that butchers prepared, if they could even afford that...
And regarding his intellectual milieu, O'Neill notes that anti-clerical prejudice of the 19th century resulted in Duhem not being able to even publish the entirety of his scholarship:
.... his publishers were pressured not to publish the later volumes of his Systeme de Monde: Histoire des Doctrines cosmologiques de Platon à Copernic - the establishment of the time was not comfortable with the idea of the Middle Ages as a scientific dark age being overturned. Duhem died with his painstaking work largely unpublished in 1916 and it was only the efforts of his daughter Helene's 30 year struggle for her father's opus to see the light of day that saw the whole 10 volume work finally released in 1959.