Tom Gjelten

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During his campaign, Donald Trump criticized President Obama for his reluctance to use the words "radical Islamic extremism."

One of Obama's key anti-terrorism programs was just called "Countering Violent Extremism," with no reference to Islam. The Trump administration may now want to refocus that program exclusively on Muslim extremists.

The Obama program made no reference to Islam largely because it didn't want to suggest that terrorism, even by Muslim extremists, had its roots in religion.

In his address to the National Prayer Breakfast on Thursday, President Trump vowed to "get rid of and totally destroy the Johnson Amendment and allow our representatives of faith to speak freely and without fear of retribution."

Some conservative Christian groups will welcome the promise, but many Americans may wonder what Trump was talking about. Here are five basic questions that we can answer.

1. What is the Johnson Amendment?

The Johnson Amendment regulates what tax-exempt organizations such as churches can do in the political arena.

The U.S. Constitution prohibits "an establishment of religion," but U.S. presidents have long paid tribute to the importance of faith in a divine power.

"Every free government is imbedded soundly in a deeply-felt religious faith, or it makes no sense," said Dwight D. Eisenhower, speaking at the first National Prayer Breakfast in 1953. Since then, all presidents have spoken at the annual event, often highlighting their own faith or the role of prayer in their personal lives.

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President Trump is promising to give priority to Christians fleeing persecution — yet some of the strongest criticism of his executive order is coming from Christian leaders themselves.

Some say the temporary ban on admitting refugees challenges the Christian ethic of welcoming the stranger. Others worry that favoring Christians over other immigrants could actually backfire.

President Trump's temporary ban on the admission of refugees is not going over well with the churches and religious organizations that handle most refugee resettlements in the United States.

"The faith groups are going to kick and scream and object to every aspect of this disgusting, vile executive order," says Mark Hetfield, president of HIAS, a Jewish refugee society. "[It] makes America out to be something that it is not. We are a country that welcomes refugees."

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President Trump faces the challenge of making good on many promises, including this from his inauguration speech.

(SOUNDBITE OF ARCHIVED RECORDING)

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A prominent evangelical leader who harshly criticized Donald Trump during the presidential campaign now faces a backlash from fellow evangelicals who backed Trump.

Russell Moore, who presides over the political arm of the Southern Baptist Convention, called Trump "an awful candidate" and criticized "the old-guard religious right political establishment" for supporting him, notwithstanding Trump's "serious moral problems" and a Southern Baptist tradition of opposing politicians whose personal behavior is considered un-Christian.

Opus Dei, the powerful but somewhat controversial Roman Catholic organization, faces a transition to new leadership following the death of its prelate, Bishop Javier Echevarría.

Echevarría, who died Monday at the age of 84, was the last link to the first generation of the group's leadership, having served as a personal secretary for more than 20 years to Opus Dei founder Josemaría Escrivá.

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For more than 30 years, conservative evangelical Christians have been tied to the Republican Party. While the pattern seems to be holding this year, with most conservative white Christians supporting Donald Trump, some evangelical leaders are now questioning the logic behind the political alliance.

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Freedom of religion is enshrined in the U.S. Constitution, but to Dan Meyer, a North Carolina businessman, that does not mean the Founding Fathers were not inspired by God.

"Many documents demonstrate that they really received divine guidance in putting together that constitution," he says. "It's not the Bible. It is a man-made document. But most of the writers of that document acknowledged that God gave them guidance and wisdom in putting that document together."

Fifteen years after the attacks of Sept. 11, Americans have grown aware not only of the danger of terrorism but also of the reality that their nation is far less white, Christian and European than it used to be.

"Culturally, we're a country of Bollywood and bhangra and tai chi and yoga and salsa and burritos and halal and kosher," says Diana Eck, professor of comparative religion at Harvard University and author of A New Religious America.

(Editor's note: Both major presidential candidates this year are Protestants. Both of their running mates were raised as Catholics. Beyond that, their faith profiles are very different. We dug into the faiths of the Republican candidates below and of the Democratic ticket here.)

(Editor's note: Both major presidential candidates this year are Protestants. Both of their running mates were raised as Catholics. Beyond that, their faith profiles are very different. We dug into the faiths of the Democratic candidates below and of the Republican ticket here.)

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A newspaper correspondent observing Abraham Lincoln's second inauguration in March 1865 — delivered to a crowd "as far as the eye could reach" — noted that the president laid his right hand on a Bible and, facing Supreme Court Chief Justice Salmon Chase, swore to preserve, protect and defend the U.S. Constitution.

"Then," the reporter noted, "solemnly repeating 'So help me God!' he bent forward and reverently kissed the Book."

The Jews who immigrated to America in the early 20th century brought with them their history as a persecuted people. Many were fleeing pogroms and anti-Semitic attacks in Europe, and those experiences bonded them to other groups that also faced discrimination.

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America's culture war, waged in recent years over gender roles, sexuality and the definition of marriage, is increasingly being fought inside evangelical Christian circles. On one side are the Christians determined to resist trends in secular society that appear to conflict with biblical teaching. On the other side are the evangelicals willing to live with those trends.

For Albert Mohler, president of the Southern Baptist Theological Seminary in Louisville, Ky., the key question is "whether or not there is a binding morality to which everyone is accountable."

The global refugee crisis, political strife and economic dislocation all contributed to a worldwide deterioration of religious freedom in 2015 and an increase in "societal intolerance," according to the U.S. Commission on International Religious Freedom.

"At best, in most of the countries we cover, religious freedom conditions have failed to improve," says Princeton professor Robert George, the USCIRF chairman. "At worst, they've spiraled downward."

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Editor's note: Radovan Karadzic was one of the dominant figures of the Bosnian war, serving as president of the "Serb Republic" in Bosnia from 1992 to 1995. The International Criminal Tribunal in The Hague on Thursday found him guilty of multiple crimes, including the slaughter of about 8,000 Muslim men and boys in the town of Srebrenica. NPR's Tom Gjelten covered the war in Bosnia, and Karadzic, for years.

Given all that has happened in the last 20 years, many people will not recall the war in Bosnia. Remind us what happened.

President Obama's speech to the Cuban people, delivered live from the Gran Teatro in Havana, presented both a risk and an opportunity.

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