"Islam has always been a part of America," President Obama said during his first visit to a U.S. mosque Wednesday.

Indeed, a number of the Founding Fathers explicitly mentioned Muslims — along with other believers outside the prevailing Protestant mainstream — as they outlined the parameters of religious freedom and equal protection.

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"When enshrining the freedom of religion in our Constitution and our Bill of Rights, our Founders meant what they said when they said it applied to all religions," Obama said Wednesday at the Islamic Society of Baltimore. "Back then, Muslims were often called Mahometans, and Thomas Jefferson explained that the Virginia Statue for Religious Freedom that he wrote was designed to protect all faiths — and I'm quoting Thomas Jefferson now — 'the Jew and the gentile, the Christian and the Mahometan.'"

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Muslims, who were also alluded to in those years as "Turks," did live in this country at the time, Obama said. An estimated 20 percent of enslaved Africans were Muslim, but much of the citizenry at the time didn't acknowledge that Muslims existed in America, according to several historians.

So unlike Jews and Catholics, Muslims were discussed in the hypothetical — and often with negative opinions, including those held by Jefferson — to show "how far tolerance and equal civil rights extends," said Denise Spellberg, author of "Thomas Jefferson's Qur'an: Islam and the Founders."

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"In the formation of the American ideal and principles of what we consider to be exceptional American values, Muslims were, at the beginning, the litmus test for whether the reach of American constitutional principles would include every believer, every kind, or not," Spellberg said in an interview.

Thomas Jefferson's defense of religious liberty

Jefferson authored the Virginia Statute for Religious Freedom and asked that it be one of just three accomplishments listed on his tombstone. The Virginia law became the foundation of the religious freedom protections later delineated in the Constitution.

Virginia went from having a strong state-established church, which Virginians had to pay taxes to support, to protecting freedom of conscience and separating church and state. Jefferson specifically mentioned Muslims when describing the broad scope of protections he intended by his legislation, which was passed in 1786.

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"What he wanted to do was get the state of Virginia out of the business of deciding which was the best religion, and who had to pay taxes to support it," said Spellberg, a professor of history and Islamic studies at the University of Texas at Austin.

During the bill's debate, some legislators wanted to insert the term "Jesus Christ," which was rejected. Writing in 1821, Jefferson reflected that "singular proposition proved that [the bill's] protection of opinion was meant to be universal."

Where the preamble declares, that coercion is a departure from the plan of the holy author of our religion, an amendment was proposed, by inserting the word "Jesus Christ," so that it should read, "a departure from the plan of Jesus Christ, the holy author of our religion;" the insertion was rejected by a great majority, in proof that they meant to comprehend, within the mantle of its protection, the Jew and the Gentile, the Christian and Mahometan [Muslim], the Hindoo [Hindu], and Infidel of every denomination."

Jefferson's opinions on religious liberty were heavily influenced by John Locke, as noted by James H. Hutson, writing in 2002 as chief of the Library of Congress's Manuscript Division:

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In his seminal Letter on Toleration (1689), John Locke insisted that Muslims and all others who believed in God be tolerated in England. Campaigning for religious freedom in Virginia, Jefferson followed Locke, his idol, in demanding recognition of the religious rights of the "Mahamdan," the Jew and the "pagan." Supporting Jefferson was his old ally, Richard Henry Lee, who had made a motion in Congress on June 7, 1776, that the American colonies declare independence. "True freedom," Lee asserted, "embraces the Mahomitan and the Gentoo (Hindu) as well as the Christian religion."

James Madison, whose views on religious liberty aligned with Jefferson's, helped usher the Virginia bill to final passage. In a document arguing against religious taxes that received thousands of signatures, Madison referenced foreign religious persecution — specifically the Inquisition.

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He also argued that separation of church and state would actually promote Christianity, writing that an open society would be welcoming to those "remaining under the dominion of false Religions." Establishing an official church, he wrote, "discourages those who are strangers to the light of revelation."

'Clearly going out of their way'

It's not as if Muslims were an overarching concern for early Americans, a Monticello scholar says.

"There just wasn't a large Muslim presence" in the United States — at least not an acknowledged one, said Andrew Jackson O'Shaughnessy, vice president of the Thomas Jefferson Foundation and Saunders Director of the Robert H. Smith International Center for Jefferson Studies at Monticello.

"The real significance" was that Muslims were mentioned at all, O’Shaughnessy said, pointing to specific mentions of Muslims in "several petitions" — some written by Baptists — in favor of Jefferson's religious freedom statute.

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"It is very significant because they were clearly going out of their way to show just how broad and complete was the idea of religious freedom," O’Shaughnessy said.

Indeed, it wasn't just Jefferson and Madison who were discussing the bounds of religious freedom in the crucial Virginia debate, said historian John Ragosta, author of numerous books on Jefferson and religious freedom.

"Baptists and Presbyterians were really demanding religious freedom in the 18th century because they were dissenters from the established church," Ragosta said. "And they were talking about Muslims and ‘infidels’ and Jews."

Evangelicals had been subjected to religious persecution not long before. Prior to the American Revolution, more than half of Virginia's Baptist ministers were jailed for preaching, Ragosta said. "These people knew what they were talking about."

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Opponents of Jefferson's proposal wrote letters to the Virginia Gazette, arguing that it would allow atheists, Muslims and Jews to hold office — to which evangelicals responded, “that’s right,” Ragosta said.

The Hanover Presbytery sent a series of statements to the Virginia General Assembly during the debate on Jefferson's statute. In one, supporting freedom of religion and opposing a state-established religion, they mentioned Muslims:

In this enlightened age, and in a land where all of every denomination are united in the most strenuous efforts to be free, we hope and expect that our representatives will cheerfully concur in removing every species of religious as well as civil bondage. Certain it is that every argument for civil liberty gains additional strength when applied to liberty in the concerns of religion, and there is no argument in favor of establishing the Christian religion but what may be pleaded with equal propriety for establishing the tenets of Mohammed by those who believe the Al Koran.

Ragosta said that while people have more recently argued that "separation of church and state and religious freedom that applies to everybody is a 20th-century invention — no, it was something that was being talked about and thought about” during the founding of the United States.

A Muslim president?

At the time, Muslims were often grouped together with others who were viewed negatively or were outside of the religious mainstream, such as Catholics and Jews, said Spellberg, the "Islam and the Founders" author. While a Muslim citizen was theoretical, a Catholic one was not. And worries that a Catholic president would hold an allegiance to a foreign pope persisted well into the 20th century, during the campaign of John F. Kennedy.

Many early Americans supported religious tests to guard against such a prospect. And once again, Muslims were mentioned in debates over whether to ratify a constitution that explicitly forbade such tests.

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During North Carolina's 1788 constitution ratification debate, Muslims were mentioned five times, Jews seven times and Catholics 10 times, according to Spellberg. The connection between the presidency and Islam was raised three times.

During the North Carolina debate, anti-Federalist Henry Abbot argued that eliminating a religious test meant it would be possible "that pagans and deists, and Mahometans might obtain offices among us, and that the senators and representatives might all be pagans," as noted in Spellberg's book.

Federalist James Iredell, dubbed "the ablest defender of the Constitution," then mounted his counter-argument — while also trying to convince skeptical delegates that it was highly unlikely citizens would elect officials with beliefs so out of the mainstream.

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"It is to be objected that the people of America may, perhaps, choose representatives who have no religion at all, and that pagans and Mahometans may be admitted into offices," Iredell said. "But how is it possible to exclude any set of men, without taking away that principle of religious freedom which we ourselves so warmly contend for?”

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Eliminating religious tests was a major source of contention in New England. Madison wrote to Jefferson in 1788 that "one of the objections in New England was that the Constitution by prohibiting religious tests opened a door for Jews, Turks and infidels."

Jefferson on religion

Such defense of religious liberty didn't leave Jefferson immune to criticism. He was eventually accused of being an atheist and "infidel."

“Thomas Jefferson’s opponents tried to stir things up by suggesting that he was a Muslim; so, I was not the first," Obama said as the audience at the Islamic Society of Baltimore laughed. "No, it’s true. Look it up. I’m in good company.”

Raised in the Anglican church, Jefferson came to be associated with tenets of Unitarianism while remaining reluctant to publicly speak about his personal beliefs.

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He clearly favored Christianity as one of the greatest blueprints for a moral code. At one point, he asked a scientist friend to complete a comparative study of the world's major religions "to extract the essence they had in common," said O’Shaughnessy, the Monticello scholar.

"He saw Jesus as a great social philosopher in setting out the greatest system of morals, but no doubt he thought, if you integrated other faiths as well, you could even improve the system," O’Shaughnessy said.

Jefferson rejected miracles, and reason reigned supreme for him. In one letter, he urged his nephew to "question with boldness even the existence of god."

In 1765, while he was studying law, Jefferson purchased an English translation of the Koran. He later went on to criticize the religion as anti-science and anti-reason.

Despite his personal opinions, however, Jefferson staunchly defended the right of Americans to hold any religious belief, no matter how absurd or wrong they seemed to him.

"The legitimate powers of government extend to such acts only as are injurious to others," Jefferson wrote in "Notes on the State of Virginia," his only book. "But it does me no injury for my neighbor to say there are twenty gods, or no god. It neither picks my pocket nor breaks my leg."

This post was originally published on Dec. 11, 2015.