Daniel Seeger was twenty-one when he wrote to his local draft board to say, “I have concluded that war, from the practical standpoint, is futile and self-defeating, and from the more important moral standpoint, it is unethical.” Some time later, he received the United States Selective Service System’s Form 150, asking him to detail his objections to military service. It took him a few days to reply, because he had no answer for the form’s first question: “Do you believe in a Supreme Being?”

Unsatisfied with the two available options—“Yes” and “No”—Seeger finally decided to draw and check a third box: “See attached pages.” There were eight of those pages, and in them he described reading Plato, Aristotle, and Spinoza, all of whom “evolved comprehensive ethical systems of intellectual and moral integrity without belief in God,” and concluded that “the existence of God cannot be proven or disproven, and the essence of His nature cannot be determined.” For good measure, Seeger also used scare quotes and strike-throughs to doctor the printed statement he was required to sign, so that it read, “I am, by reason of my ‘religious’ training and belief, conscientiously opposed to participation in war in any form.”

By the time Seeger submitted his form, in the late nineteen-fifties, thousands of conscientious objectors in the U.S. had refused to fight in the two World Wars. Those who belonged to pacifist religious traditions, such as Mennonites and Quakers, were sent to war as noncombatants or to work as farmers or firefighters on the home front through the Civilian Public Service; eventually, so were those who could prove their own independent, religiously motivated pacifism. Those who could not were sent to prison or to labor camps. But while Selective Service laws had been revised again and again to clarify the criteria for conscientious objection, they still did not account for young men who, like Seeger, refused to say that their opposition to war came from belief in a Supreme Being.

Over time, draft boards came to resemble freshman philosophy seminars in their attempts to decide who did and did not qualify for C.O. status. A Jewish socialist who ran an engraving business did not, but a pulp artist and atheist who appealed to the idea of secular humanism did; some members of the Ethical Culture Society qualified, but not others; Jehovah’s Witnesses initially did not, on the theory that someone willing to fight the Devil during Armageddon ought to be willing to fight America’s enemies during a war; a writer turned financial consultant who belonged to no church but had read “philosophers, historians, and poets from Plato to Shaw” was granted C.O. status after two contradictory close readings of his antiwar play. Different boards reached very different conclusions, various appeal boards upheld and reversed those decisions without much consistency, and, inevitably, some of those appeals ended up before federal courts. When Seeger’s local board was unmoved by his argument, he took it all the way to the Supreme Court, where, in 1965, the Justices found unanimously that a draftee did not need to believe in God in order to have a conscience that could object.

Seeger’s victory helped mark a turning point for a minority that had once been denied so much as the right to testify in court, even in their own defense. Atheists, long discriminated against by civil authorities and derided by their fellow-citizens, were suddenly eligible for some of the exemptions and protections that had previously been restricted to believers. But, in the decades since U.S. v. Seeger, despite an increase in the number of people who identify as nonbelievers, their standing before the courts and in the public sphere has been slow to improve. Americans, in large numbers, still do not want atheists teaching their children, or marrying them. They would, according to surveys, prefer a female, gay, Mormon, or Muslim President to having an atheist in the White House, and some of them do not object to attempts to keep nonbelievers from holding other offices, even when the office is that of notary public. Atheists are not welcome in the Masonic Lodge, and while the Boy Scouts of America has opened its organization to gays and to girls, it continues to bar any participant who will not pledge “to do my duty to God.”

Such discrimination is both a cause and an effect of the crude way in which we parse belief, which has barely changed since Daniel Seeger completed his C.O. application: check “Yes” and endless questions follow; check “No” and the questioning ends. Lack of belief in God is still too often taken to mean the absence of any other meaningful moral beliefs, and that has made atheists an easy minority to revile. This is especially true in America, where an insistence on the idea that we are a Christian nation has tied patriotism to religiosity, leading to such strange paroxysms as the one produced by President Trump at last year’s Values Voter Summit: “In America, we don’t worship government—we worship God.”

As that remark suggests, the one wall the current Administration does not want to build is the one between church and state. The most evident manifestation of this resurgence of Christian nationalism has been animosity toward Muslims and Jews, but the group most literally excluded from any godly vision of America is, of course, atheists. Yet the national prejudice against them long predates Daniel Seeger and his draft board. It has its roots both in the intellectual history of the country and in a persistent anti-intellectual impulse: the widespread failure to consider what it is that unbelievers actually believe.

American antipathy for atheism is as old as America. Although many colonists came to this country seeking to practice their own faith freely, they brought with them a notion of religious liberty that extended only to other religions—often only to other denominations of Christianity. From John Locke they inherited the idea that atheists cannot be good citizens and should not be brought into the social contract; in “A Letter Concerning Toleration,” Locke had written, “Those are not at all to be tolerated who deny the being of a God.”

True religious liberty was rare in the colonies: dissenters were fined, flogged, jailed, and sometimes hanged. Yet, surprisingly, no atheist was ever executed. According to the Cornell professors R. Laurence Moore and Isaac Kramnick, the authors of the new book “Godless Citizens in a Godly Republic: Atheists in American Public Life” (Norton), that is only because no atheists presented themselves for execution. Nonbelievers were either few and far between in Colonial America or understandably cautious about making themselves known; clergy and magistrates rarely bothered to mention them, even derisively.

One of the few who did was Roger Williams, who, after he was banished from the Massachusetts Bay Colony for spreading “diverse, new, and dangerous opinions,” offered a view of the separation of church and state so extreme that it seemed to accommodate atheists. In his book “The Bloudy Tenent of Persecution, for Cause of Conscience,” published in London in 1644, Williams wrote that “a pagan or Antichristian pilot may be as skillful to carry the ship to its desired port, as any Christian mariner.” He was referring to the ship of state, but his tolerance was never fully tested: no atheist ever tried to hold office in Rhode Island, the colony that he founded. Still, his argument was audacious for an era when most colonies had established churches and collected ecclesiastical taxes to support them.