As bells tolled for the dead in Charleston on Sunday, Reverend Alfred Zadig, head of the predominantly white-membership St Michael’s Church, asked forgiveness “for failing to be a pastor who reaches out beyond my world”.

Speaking to about 60 worshippers in the large 17th-century white stone church towering over City Hall, he said he did not know a single victim of Wednesday’s massacre, when a shooter authorities have identified as a 21-year-old white man killed nine African-Americans at a mainly black church 1.6 kilometres away.

“You and I are so good at compartmentalising grief,” he told congregants. “Today I’m asking you to feel the unthinkable pain.”

Last week’s attack at the Emanuel African Methodist Episcopal Church highlighted a truth about American religion and race that dates back to the 19th century: churches are among the most segregated parts of American life.

The tradition of religious separation remained intact through the civil rights era, and has proven mostly immune to progress since, according to race and religion experts.

About eight in 10 congregants in America attend services where a single racial or ethnic group makes up at least 80 per cent of the congregation, according to Pew Research Center, using data from the 2012 National Congregations Study.

In 1998, 85 per cent of Americans reported worshipping in largely segregated congregations.

“Until blacks and whites pray together, US race relations are fundamentally unhealthy. There is no getting around this,” said Michael Emerson, provost at North Park University in Chicago, and author of Divided by Faith: Evangelical Religion and the Problem of Race in America.

“Segregated churches have been and will continue to be a direct reflection on America divided.”

The story of this division began in America’s earliest moments, when slaves and freed African-Americans alike were often expected to pray in the same churches as whites, but in areas cordoned off, often called ‘slave galleries’.

I don’t think the shooting was a way to divide us. It was meant to, but I don’t think it will work

In 1816, an association of free men in Philadelphia seeking to escape racial bias in the church founded the African Methodist Episcopal church, the oldest independent Christian denomination founded by blacks in the world.

“When you kneel to pray, you don’t want your humanity questioned,” said Tukufu Zuberi, professor of sociology at the University of Pennsylvania, explaining their motivation. “It was the same master, but this time using the Bible to justify the enslavement of Africans.”

Churchgoers in Charleston believe tragedy has potential to bring congregations together.Churchgoers in Charleston believe tragedy has potential to bring congregations together.

The issue remained after the emancipation proclamation that ended slavery, North Park’s Emerson said, leading to an exodus of African-Americans from white churches to black denominations, and ultimately to a broad divergence in religious culture and worship practices.

“One hundred and fifty years of this has led to the number-one reason people today say why they worship in racially separate congregations: they just feel more comfortable with the worship and practices, and they know people there,” Emerson said.

For decades, however, the Sunday divide has worried some religious leaders. In 1963, during the civil rights movement, Martin Luther King Jr told an audience at Western Michigan University that 11am on Sunday morning is “the most segregated hour in this nation” and called it a tragedy.

“Now, I’m sure that if the Church had taken a stronger stand all along, we wouldn’t have many of the problems that we have,” he said.

Josef Sorett, assistant professor of religion and African-American studies at Columbia University, said it is unsurprising that the tradition of segregated worship has lingered.

“You can look across a variety of indicators, housing, income, incarceration, and you can see that racial inequality is still very prevalent,” he said. “To put it in the language of the Church, it would be a miracle if we had resolved all the history within just a few decades.”

On Sunday morning in Charleston, 51-year-old UPS driver Everett Williams stood outside the Emanuel AME church to photograph a shrine of yellow sunflowers, white roses and pale lilies spilling off the church grounds, and notes left by mourners dedicated to the victims.

Williams, an African-American man, said that, even as the city pulls together to denounce the shooting, he was not confident Church life would change much. Even when black and white churches are just a stone’s throw from one another, “they don’t ever intermingle. It’s just the way it is,” Williams said.

Ed Kosak, minister at Unity Church, who, like 80 per cent of the members of his Church, is white, said the effects of race on the Church are deeply ingrained. “We look at white and black, rather than we’re all souls,” he said.

But for St Michael’s member Chris Meredith, a white woman, church membership in the city is more a matter of family tradition, rather than being about race. “There are churches that people have gone to for generations, I don’t think it’s a black or white thing,” she said.

St Michael’s and another predominantly white downtown Anglican Church, St Philip’s shurch, on Sunday organised a bus to bring parishioners to Emanuel AME at noon to gather in support of its members.

Handing out water to people gathered there, Lercy Bourque, 74, a white man and unit leader of the Charleston Baptist Association, said he believes the shooting will bring people closer together rather than cause greater divide – though he said churches will likely remain largely segregated.

“I don’t think the shooting was a way to divide us. It was meant to, but I don’t think it will work,” he said.

For St Michael’s rector Zadig, the contact between white and black congregations in Charleston should have deeper meaning.

“This can’t be a one-day event,” Zadig said. “It has to be a life changer.”

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