Witchcraft and the Dark Ages
Although some folk apply the term "Dark Ages" to the entire medieval period, others apply it only to the early middle ages and refer to the High Middle Ages as the Early Renaissance. This is done in service to belief, of course. It is not how the historians generally view things. (In fact, those have been abandoning such propaganda labels in favor of century labels.) But in any case, one of the most cherished foundation myths of the Modern Ages is that of the West's struggle to free itself from the violence of religious intolerance. This is almost as basic as the myth of Galileo springing pristine from the brow of Copernicus.
One aspect of that violence was the witch mania.
1. The Age of Faith
Now, belief in sorcery had been common enough among the Romans, who distinguished three classes of witches and prescribed death for the worst class. It was common, too, among the Germans, though the details differed. So it's no surprise if the folk of the Middle Ages, who were after all the descendants of those self-same Romans and Germans, also believed in such things.
The Church however either ignored magic or treated it leniently; this for the very good reason that she taught that magic was a mere superstition. St. Patrick's Synod in the 5th century anathematized anyone who believed that there really were witches with magical powers. Charlemagne issued a Capitulary for Saxony that declared it criminal for anyone acting on a heathen belief in magic to burn or devour the flesh of accused sorcerers. (This suggests that pagan Germans did not treat sorcerers very nicely.) The Canon episcopi about the same time declares that women who believe they fly through the air in Diana's train are simply deluded and orders expelled from the congregation anyone who insists on the reality of it.
When Archbishop Abogard of Lyons (9th cent) learned that rustics in his diocese believed that witches destroyed their crops with hailstones and colluded with men from Mangonia (who sailed ships through the sky to steal crops). He felt obliged to tell his flock that men could not control the weather, sail ships through the sky, or wield any magical powers. Also there was no such place as Mangonia. He had to personally intervene to save four "captured Mangonians". (From an SF point of view, ships sailing through the sky and stealing crops has a cool ring to it.)
Ecclesiastical discipline (ascr. to Regino von Prüm) advises clergy to warn their congregants against credulous belief in covens of witches flying through the night sky and worshiping Diana. Bishop Burchard of Worms (late 10th cent.) prescribed penance for those who believed in the powers of witches. Pope Gregory VII forbade the Danish courts to execute people accused of witchcraft.
Vincent of Beauvais, to disabuse a woman convinced she was a witch who could pass through keyholes, locked the door and chased her about the room with a stick, while exhorting her to escape through the keyhole. (Now THAT is the scientific spirit, right there!)
And so it went through the "Dark Ages."
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2. The Age of Science
Things began to change as the Middle Ages waned into the Renaissance. The cult of Hermes Trismegistus and the Corpus hermeticum - a late Roman compendium of Neoplatonic, Gnostic, alchemical, magical, astrological, and devotional texts - was resdiscovered. (The Middle Ages went in for Aristotle and Euclid; the Renaissance went in for Neoplatonic woo-woo.)
The Malleus maleficarum was written by two Dominicans about 1486. The principal author, Heinrich Kramer, was widely recognized as a "demented imbecile" by contemporaries. The bishop of Innsbruck thwarted his attempt to convict women there of witchcraft and forced him out of town. The Malleus competed with the Carmelite Jan van Beetz's Expositio decem catalogie praeceptum, "an icily skeptical treatment of tales of black magic. Of course, exposés never get the circulation of the lurid originals. Look at The Da Vinci Code.
Two things were happening at the beginning of the Modern Ages. The power of the State was increasing and Science was revolutionized into its Baconian form. Jean Bodin (De la démonomanie des sorciers) wrote that witches should be burned at the stake and nations that did not seek out witches and exterminate them would suffer famine, plague, and war, and that torture should be used on the mere suspicion of sorcery. No one so much as accused of witchcraft should be acquitted unless the accuser's bad faith could be convincingly demonstrated. But Bodin was also the first great proponent of the absolute power of the secular state.
England made sorcery a capital crime in 1542 - after the State had nationalized the Church of England. In the same year, in the Concordat of Liège, the Emperor (Charles V) placed sorcery prosecutions entirely in the hands of secular tribunals.
The Great Witch Hunts began.
Thomas Hobbes, in the next generation, thought all religion was mendacious and did not himself believe in witches -- but he thought witches should be punished anyhow "for the good of society."
Francis Bacon based his program to gear science not only to knowledge of the natural world but to conquer the material world on the hermetic books' emphasis on humanity's godlike prerogatives over "the lower orders of material creation" and on alchemy's focus on "wracking elemental nature to force it to yield up its secrets."
Early members of the Royal Society, like Robert Boyle, were firmly convinced of the reality of witches and the need for their elimination; and one, Joseph Glanvill, thought that sorcery was scientifically demonstrable.
So why did the Dark Ages of Faith preach that sorcery and witchcraft were unreal and delusional while the Early Modern Ages of Science taught they were real and in need of extermination?
The post-Christian notion of "human mastery of the world," so well developed by Francis Bacon and the Scientific Revolutionaries, gave birth to twins: sorcery and science. Both were based on "wracking nature" to pry out her secrets for human benefit. Magic was a form of materialism, after all. It was the belief that matter had "hidden" [occult] powers that were impersonal and morally neutral. If these were invisible, they were not supernatural. Gravity is invisible, too.
IOW, magic and science are only distinguishable retrospectively. In the long run, one worked and the other did not. Or rather the "hidden" [occult] powers gradually became "known" [manifest] powers, and magic was absorbed into science. At the time, however, science and magic simply fell along the same continuum of Man Dominates the Lower Orders.
And so in the mean time, the modern scientific age believed in witches and sorcery and naturally was afraid of them, and so naturally hunted them down in large numbers as a civic, secular duty. No one was immune, not even members of the rump Church, and certainly not members of the nationalized "established" churches, which had effectively been brought to heel. Yet, it is curious to note where the fewest witches were tried. There are on record only two cases in which witches were put on trial in Spain - and the Inquisition ordered them released. (The old notion that witches were deluded still hung on in those quasi-medieval parts of Europe.)
h/t David B. Hart