Human sacrifice and witch-burnings are just two examples of the harm that can result from people pursuing ends that involve figments of their imagination. Another may be seen in psychotics who kill in pursuit of a delusion, such as Charles Manson's plan to hasten an apocalyptic race war, and John Hinckley's scheme to impress Jodie Foster. But the greatest damage comes from religious beliefs that downgrade the lives of flesh-and-blood people, such as the faith that suffering in this world will be rewarded in the next, or that flying a plane into a skyscraper will earn the pilot seventy-two virgins in heaven. As we saw in chapter 1, the belief that one may escape from an eternity in hell only by accepting Jesus as a savior makes it a moral imperative to coerce people into accepting that belief and to silence anyone who might sow doubt about it.

A broader danger of unverifiable beliefs is the temptation to defend them by violent means. People become wedded to their beliefs, because the validity of those beliefs reflects on their competence, commends them as authorities, and rationalizes their mandate to lead. Challenge a person's beliefs, and you challenge his dignity, standing, and power. And when those beliefs are based on nothing but faith, they are chronically fragile. No one gets upset about the belief that rocks fall down as opposed to up, because all sane people can see it with their own eyes. Not so for the belief that babies are born with original sin or that God exists in three persons or that Ali was the second-most divinely inspired man after Muhammad. When people organize their lives around these beliefs, and then learn of other people who seem to be doing just fine without them -- or worse, who credibly rebut them -- they are in danger of looking like fools. Since one cannot defend a belief based on faith by persuading skeptics it is true, the faithful are apt to react to unbelief with rage, and may try to eliminate that affront to everything that makes their lives meaningful.

The human toll of the persecution of heretics and nonbelievers in medieval and early modern Christendom beggars the imagination and belies the conventional wisdom that the 20th century was an unusually violent era. Though no one knows exactly how many people were killed in these holy slaughters, we can get a sense from numerical estimates by atrocitologists such as the political scientist R. J. Rummel in his books Death by Government and Statistics of Democide and the historian Matthew White in his Great Big Book of Horrible Things and his "Deaths by Mass Unpleasantness" Web site. They have tried to put numbers on the death tolls of wars and massacres, including those for which conventional statistics are unavailable, by combing the available sources, assessing their credibility with sanity checks and allowances for bias, and selecting a middle value, often the geometric mean of the lowest and the highest credible figures. I'll present Rummel's estimates for this era, which are generally lower than White's.

In the 13th century the Cathars of southern France embraced the Albigensian heresy, according to which there are two gods, one of good and one of evil. An infuriated papacy, in collusion with the king of France, sent waves of armies to the region, which killed around 200,000 of them. To give you a sense of the armies' tactics, after capturing the city of Bram in 1210 they took a hundred of the defeated soldiers, cut off their noses and upper lips, gouged out the eyes of all but one, and had him lead the others to the city of Cabaret to terrorize its citizens into surrendering. The reason you have never met a Cathar is that the Albigensian Crusade exterminated them. Historians classify this episode as a clear instance of genocide.

Between 1095 and 1208 Crusader armies were mobilized to fight a "just war" to retake Jerusalem from Muslim Turks, earning them remission from their sins and a ticket to heaven. They massacred Jewish communities on the way, and after besieging and sacking Nicea, Antioch, Jerusalem, and Constantinople, they slaughtered their Muslim and Jewish populations. Rummel estimates the death toll at 1 million. The world had around 400 million people at the time, about a sixth of the number in the mid-20th century, so the death toll of the Crusader massacres as a proportion of the world population would today come out at around 6 million, equivalent to the Nazis' genocide of the Jews.

Shortly after the suppression of the Albigensian heresy, the Inquisition was set up to root out other heresies in Europe. Between the late 15th and early 18th centuries, the Spanish branch took aim at converts from Judaism and Islam who were suspected of backsliding into their old practices. One transcript from 16th-century Toledo describes the inquisition of a woman who was accused of wearing clean underwear on Saturday, a sign that she was a secret Jew. She was subjected to the rack and the water torture (I'll spare you the details -- it was worse than waterboarding), given several days to recover, and tortured again while she desperately tried to figure out what she should confess to. The Vatican today claims that the Inquisition killed only a few thousand people, but it leaves off the books the larger number of victims who were remanded to secular authorities for execution or imprisonment (often a slow death sentence), together with the victims of branch offices in the New World. Rummel estimates the death toll from the Spanish Inquisition at 350,000.

First,… set fire to their synagogues or schools and… bury and cover with dirt whatever will not burn, so that no man will ever again see a stone or cinder of them… Second, I advise that their houses also be razed and destroyed… Third, I advise that all their prayer books and Talmudic writings, in which such idolatry, lies, cursing, and blasphemy are taught, be taken from them… Fourth, I advise that their rabbis be forbidden to teach henceforth on pain of loss of life and limb… Fifth, I advise that safe-conduct on the highways be abolished completely for the Jews… Sixth, I advise that usury be prohibited to them, and that all cash and treasure of silver and gold be taken from them and put aside for safekeeping. Seventh, I recommend putting a flail, an ax, a hoe, a spade, a distaff, or a spindle into the hands of young, strong Jews and Jewesses and letting them earn their bread in the sweat of their brow, as was imposed on the children of Adam (Gen. 3[:19]). For it is not fitting that they should let us accursed Goyim toil in the sweat of our faces while they, the holy people, idle away their time behind the stove, feasting and farting, and on top of all, boasting blasphemously of their lordship over the Christians by means of our sweat. Let us emulate the common sense of other nations… [and] eject them forever from the country.

After the Reformation, the Catholic Church had to deal with the vast number of people in northern Europe who became Protestants, often involuntarily after their local prince or king had converted. The Protestants, for their part, had to deal with the breakaway sects that wanted nothing to do with either branch of Christianity, and of course with the Jews. One might think that Protestants, who had been persecuted so viciously for their heresies against Catholic doctrines, would take a dim view of the idea of persecuting heretics, but no. In his 65,000-word treatise On the Jews and Their Lies, Martin Luther offered the following advice on what Christians should do with this "rejected and condemned people":

At least he suffered most of them to live. The Anabaptists (forerunners of today's Amish and Mennonites) got no such mercy. They believed that people should not be baptized at birth but should affirm their faith for themselves, so Luther declared they should be put to death. The other major founder of Protestantism, John Calvin, had a similar view about blasphemy and heresy:

Some say that because the crime consists only of words there is no cause for such severe punishment. But we muzzle dogs; shall we leave men free to open their mouths and say what they please?… God makes it plain that the false prophet is to be stoned without mercy. We are to crush beneath our heels all natural affections when his honour is at stake. The father should not spare his child, nor the husband his wife, nor the friend that friend who is dearer to him than life.

Calvin put his argument into practice by ordering, among other things, that the writer Michael Servetus (who had questioned the trinity) be burned at the stake. The third major rebel against Catholicism was Henry VIII, whose administration burned, on average, 3.25 heretics per year.

With the people who brought us the Crusades and Inquisition on one side, and the people who wanted to kill rabbis, Anabaptists, and Unitarians on the other, it's not surprising that the European Wars of Religion between 1520 and 1648 were nasty, brutish, and long. The wars were fought, to be sure, not just over religion but also over territorial and dynastic power, but the religious differences kept tempers at a fever pitch. According to the classification of the military historian Quincy Wright, the Wars of Religion embrace the French Huguenot Wars (1562-94), the Dutch Wars of Independence, also known as the Eighty Years' War (1568-1648), the Thirty Years' War (1618-48), the English Civil War (1642-48), the wars of Elizabeth I in Ireland, Scotland, and Spain (1586-1603), the War of the Holy League (1508-16), and Charles V's wars in Mexico, Peru, France, and the Ottoman Empire (1521-52). The rates of death in these wars were staggering. During the Thirty Years' War soldiers laid waste to much of present-day Germany, reducing its population by around a third. Rummel puts the death toll at 5.75 million, which as a proportion of the world's population at the time was more than double the death rate of World War I and was in the range of World War II in Europe. The historian Simon Schama estimates that the English Civil War killed almost half a million people, a loss that is proportionally greater than that in World War I.

It wasn't until the second half of the 17th century that Europeans finally began to lose their zeal for killing people with the wrong supernatural beliefs. The Peace of Westphalia, which ended the Thirty Years' War in 1648, confirmed the principle that each local prince could decide whether his state would be Protestant or Catholic and that the minority denomination in each one could more or less live in peace. (Pope Innocent X was not a good sport about this: he declared the Peace "null, void, invalid, unjust, damnable, reprobate, inane, empty of meaning and effect for all time.") The Spanish and Portuguese Inquisitions began to run out of steam in the 17th century, declined further in the 18th, and were shut down in 1834 and 1821, respectively. England put religious killing behind it after the Glorious Revolution of 1688. Though the divisions of Christianity have sporadically continued to skirmish right up to the present (Protestants and Catholics in Northern Ireland, and Catholics and Orthodox Christians in the Balkans), today the disputes are more ethnic and political than theological. Beginning in the 1790s, Jews were granted legal equality in the West, first in the United States, France, and the Netherlands, and then, over the following century, in most of the rest of Europe.

What made Europeans finally decide that it was all right to let their dissenting compatriots risk eternal damnation and, by their bad example, lure others to that fate? Perhaps they were exhausted by the Wars of Religion, but it's not clear why it took thirty years to exhaust them rather than ten or twenty. One gets a sense that people started to place a higher value on human life. Part of this newfound appreciation was an emotional change: a habit of identifying with the pains and pleasures of others. And another part was an intellectual and moral change: a shift from valuing souls to valuing lives. The doctrine of the sacredness of the soul sounds vaguely uplifting, but in fact is highly malignant. It discounts life on earth as just a temporary phase that people pass through, indeed, an infinitesimal fraction of their existence. Death becomes a mere rite of passage, like puberty or a midlife crisis.

The gradual replacement of lives for souls as the locus of moral value was helped along by the ascendancy of skepticism and reason. No one can deny the difference between life and death or the existence of suffering, but it takes indoctrination to hold beliefs about what becomes of an immortal soul after it has parted company from the body. The 17th century is called the Age of Reason, an age when writers began to insist that beliefs be justified by experience and logic. That undermines dogmas about souls and salvation, and it undermines the policy of forcing people to believe unbelievable things at the point of a sword (or a Judas's Cradle).

Calvin says that he is certain, and [other sects] say that they are; Calvin says that they are wrong and wishes to judge them, and so do they. Who shall be judge? Who made Calvin the arbiter of all the sects, that he alone should kill? He has the Word of God and so have they. If the matter is certain, to whom is it so? To Calvin? But then why does he write so many books about manifest truth?… In view of the uncertainty we must define the heretic simply as one with whom we disagree. And if then we are going to kill heretics, the logical outcome will be a war of extermination, since each is sure of himself. Calvin would have to invade France and all other nations, wipe out cities, put all the inhabitants to the sword, sparing neither sex nor age, not even babies and the beasts.

Erasmus and other skeptical philosophers noted that human knowledge was inherently fragile. If our eyes can be fooled by a visual illusion (such as an oar that appears to be broken at the water's surface, or a cylindrical tower in the distance that appears to be square), why should we trust our beliefs about more vaporous objects? Calvin's burning of Michael Servetus in 1553 prompted a widespread scrutiny of the very idea of religious persecution. The French scholar Sebastian Castellio led the charge by calling attention to the absurdity of different people being unshakably certain of the truth of their mutually incompatible beliefs. He also noted the horrific moral consequences of acting on these beliefs.

The arguments were picked up in the 17th century by, among others, Baruch Spinoza, John Milton (who wrote, "Let truth and falsehood grapple… truth is strong"), Isaac Newton, and John Locke. The emergence of modern science proved that deeply held beliefs could be entirely false, and that the world worked by physical laws rather than by divine whims. The Catholic Church did itself no favor by threatening Galileo with torture and committing him to a life sentence of house arrest for espousing what turned out to be correct beliefs about the physical world. And the skeptical mindset, sometimes spiced with humor and common sense, was increasingly allowed to challenge superstition. In Henry IV, Part 1, Glendower boasts, "I can call spirits from the vasty deep." Hotspur replies, "Why, so can I, or so can any man; / But will they come when you do call for them?" Francis Bacon, often credited with the principle that beliefs must be grounded in observation, wrote of a man who was taken to a house of worship and shown a painting of sailors who had escaped shipwreck by paying their holy vows. The man was asked whether this didn't prove the power of the gods. "Aye," he answered, "but where are they painted that were drowned after their vows?"