At the start of his installation Mass this week, Pope Francis prayed at the tomb of Peter, near the place in the Vatican where the first bishop of Rome was martyred. The small group Francis asked to join him in the crypt under the main altar of St. Peter’s Basilica included Iraq’s Patriarch Louis Sako and other heads of the Eastern Catholic Churches. The Gospel at the Mass was chanted in Greek rather than the traditional Latin, and the pope’s homily took the theme of his”and our”duty “ to protect the whole of creation, to protect each person.”

Every public gesture and word of the Holy Father tends to have meaning. So what was the pope saying with this symbolism as he began his new ministry? I believe the persecuted Church figured prominently in his prayers.

The Chaldean and Syriac Catholic Churches of Iraq and Syria, while differing in rite and tradition from the Latin West, are integral members of the universal Catholic Church, in full communion with the bishop of Rome. The persecution they and other Middle Eastern Christians now suffer”so severe it threatens their continued existence in their ancient homelands”is a bitter wound for the Church and an unavoidable concern for the Holy Father.

Of the million or so Christians living in Iraq a decade ago, fewer than half likely remain. During this period, seventy Iraqi Christian churches were attacked. Christian laity and clergy have faced relentless violence. Between 2003 and May 2012, some nine hundred Christians were killed. Another two hundred were kidnapped, tortured, and released for ransom, according to the Iraq-based Hammurabi Organization for Human Rights.

Patriarch Sako, elected earlier this year to lead the Chaldean Catholic Church, recently noted that in the past, “There were three hundred churches in Iraq, and now there are only fifty-seven left. Even those that remain are targets.” The savage massacre inside Baghdad’s Our Lady of Salvation Church in October 2010, in which scores of worshippers were killed and the rest of the congregation injured, was seen as a turning point”the moment when many remaining Christians decided they had no future in their own nation.

Iraq’s Christians, whose roots in their country predate Islam by centuries and go back nearly two thousand years, now face complete eradication as a religious minority. Syria’s Christians, numbering as many as two million, also find themselves unwelcome as Islamists dominate the rebellion and take control. Many thousands have already fled to Lebanon, Turkey and points further west.

Meanwhile, Egypt’s eight to ten million Coptic Orthodox , by far the largest surviving Church in the Middle East and heir to an extraordinary cultural and religious history, face a growing wave of violence against their churches and villages, and the frequent kidnapping, rape, and forced conversion of Coptic women and young girls.

This pattern of hatred is not new. Anti-Christian violence in Egypt, often ignored by news media in the West, has been happening for decades. Now it’s worse. As a result, Copts too have begun to exit, spurred by the election of a Muslim Brotherhood president and the adoption of an Islamist constitution.

Iraq, Syria, and Egypt: These three countries, along with Lebanon, are home to the only sizeable Christian minorities left in the Middle East. Over the past century, the Middle East’s Christian population has dropped from as high as 30 percent to barely 3 percent, with religious persecution and intimidation largely to blame. If these remaining communities are destroyed, an indigenous Christian presence will disappear from the region where Jesus Christ first established his Church two thousand years ago. The annihilation of this Christian culture, the cradle of much of the West’s moral heritage, will have profound implications, not only for Catholics and other Christians, but for a world in urgent need of the ability to peacefully coexist.

In his past ministries of service, Pope Francis has consistently reached out to the poor with tenderness and personal humility. So did his namesake, the great Francis of Assisi. But we’d be wise to remember that the real man of Assisi, the flesh and blood person who became a saint, lived in a violent age much like our own. And he was far more unsettling in the demands he placed on himself and his brothers than the rosy legends that have grown up around him suggest.

The real St. Francis was a “radical” in the original sense of the word: committed down to his roots in his love for Jesus Christ and God’s people; radical in his self-denial; and radical in his solidarity with the suffering”whoever and wherever they might be. The lesson is simply this: The world might ignore the bitter suffering of Christians in the Middle East, but the real Francis of Assisi would not. And the pope who took his name is unlikely to do otherwise.

Charles J. Chaput, a Capuchin Franciscan, is the archbishop of Philadelphia, a former Commissioner (2003-06) with the United States Commission on International Religious Freedom, and a contributor to the newly released book Persecuted: The Global Assault on Christians .

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