The chairman of the commission, Martin R. Castro, went to the hot spot of the debate with a separate statement in the report that uncloaks what often, but certainly not always, lurks behind protestations about freedom of religion.

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“The phrases ‘religious liberty’ and ‘religious freedom’ will stand for nothing except hypocrisy so long as they remain code words for discrimination, intolerance, racism, sexism, homophobia, Islamophobia, Christian supremacy or any form of intolerance,” Castro wrote.

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Castro headed his statement with a quote attributed to John Adams: “The government of the United States is not, in any sense, founded on the Christian religion.” That language comes from the Treaty of Tripoli, signed by Adams in 1797.

For Roger Severino, director of the DeVos Center for Religion and Civil Society at the conservative Heritage Foundation, a particularly troubling aspect of the report is what he called “the attempt to discredit sincere religious believers as being motivated by hate instead of faith and the implied recommendation that religious groups should change their beliefs on sexual morality to conform with liberal norms for the good of the country. I would expect to see such a slanted and anti-religious report come out of China or France perhaps, but am disappointed to see it come from the U.S. Commission on Civil Rights.”

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The report follows a meeting the commission held in March 2013 to explore “the uncertain boundaries of religious freedom.” Its findings and recommendations place the boundary at the point where religious freedom conflicts with civil rights.

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Finding No. 1 makes it clear which set of rights should be on top: “Civil rights protections ensuring nondiscrimination, as embodied in the Constitution, laws, and policies, are of preeminent importance in American jurisprudence.”

The commission also said:

“Religious exemptions from nondiscrimination laws and policies must be weighed carefully and defined narrowly on a fact-specific basis”

“Third parties, such as employees, should not be forced to live under the religious doctrines of their employers”

“A basic right as important as the freedom to marry should not be subject to religious beliefs.”

The report was adopted by a majority vote of the eight-member commission, an equal number appointed by the president and Congress. No more than four can be members of the same political party. Yet, a vote for the report doesn’t necessarily mean agreement with it.

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In a long statement in the report, Commissioner Peter Kirsanow, a Republican appointed by Congress, called the findings and recommendations “an alarm to liberty-loving Americans.” Nonetheless, he voted in favor “only because this report has already been delayed for over three years, and was concerned that a ‘no’ vote from me would be used as an excuse to further delay the report.”

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Saying “the conflict between religious liberty and nondiscrimination principles is profound,” Kirsanow said the tension “appears most acute when religious liberty and sexual liberty conflict.”

Are those rights of equal importance?

Kirsanow says no: “In our constitutional order, the first reason that religious liberty takes precedence over sexual liberty is that this is enshrined in our Constitution.” He argues that the commission elevates “nondiscrimination laws, which with the exception of the Fourteenth Amendment are mere statutes, not constitutional provisions, over the provisions of the Constitution.

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In practice, he added, this is “hostile to religion.”

Yet, in practice, religion has been used as hostile weapon against human and civil rights.