Theological honesty further demands that we acknowledge the vast difference between a theological system centered in Jesus Christ, who told Peter to put away his sword, and one that takes as its central example Mohammed, whose status as a mighty warrior is an issue of enduring Muslim pride. The strategic fact of our current times is that the terrorism feared by the West is deeply rooted in a theological worldview, and that worldview is Islam.

Presidents of the United States are usually awful as theologians. In far too many cases, the closer they get to anything theological, the bigger the mess they make. President Obama seems rather adept at making such messes, but he is hardly the first. The only President of the United States to be baptized while in office was Dwight D. Eisenhower. In remarks made at the Freedoms Forum at the Waldorf-Astoria hotel in 1952, the recently-elected Eisenhower said: “In other words, our form of government has no sense unless it is founded in a deeply felt religious faith, and I don’t care what it is.”

Of recent presidents, Jimmy Carter and Bill Clinton were probably the most theologically literate, and both claimed deep roots as Southern Baptists. In his infamous Playboy interview of 1976, Carter cited Reinhold Niebuhr and Paul Tillich as influences and Clinton seemed cut from the same theological cloth. Both men have, in their own way, distanced themselves rather clearly from the theological and moral convictions held by Southern Baptists. Ronald Reagan’s evangelical faith seemed to be vague and he rarely attended church services during his eight years in office. George H. W. Bush seemed to be a very conventional mainline Protestant of the old establishment but his son, George W. Bush, may well have been the most clearly evangelical president of the modern age.

President Obama identifies openly with a very liberal version of Christian thinking and reasoning. He cites religious concerns from time to time, but he seems to operate more as a secular cosmopolitan. When he does address religious thoughts openly, as at the National Prayer Breakfast last week, he made a considerable mess.

That he holds to a universalistic understanding of religion is not in doubt. President Obama spoke of faith, of his own “faith journey,” and “professions of faith.” The common denominator in his thinking seems to be faith as an act without any concern for the content or object of that faith. Thus, “part of what I want to touch on today is the degree to which we’ve seen professions of faith used both as an instrument of great good, but also twisted and misused in the name of evil.”

When people do evil in the name of faith, the President asserted, it is because the faith has been perverted or distorted. Any faith can be perverted in this way, Mr. Obama said, and no religion is inherently violent. In his words: “Our job is not to ask that God respond to our notion of truth — our job is to be true to Him, His word, and His commandments.  And we should assume humbly that we’re confused and don’t always know what we’re doing and we’re staggering and stumbling towards Him, and have some humility in that process.  And that means we have to speak up against those who would misuse His name to justify oppression, or violence, or hatred with that fierce certainty.  No God condones terror.  No grievance justifies the taking of innocent lives, or the oppression of those who are weaker or fewer in number.”

The fact remains that Western civilization — and much of the world beyond — is directly threatened by a militant form of Islam that has the allegiance of millions of Muslims. While the vast majority of Muslims in the world are not fighters in a jihad against the West, and for that we must be thankful, the fact remains that the President’s own national security authorities directly disagree with the President when he recently said that “99.9 percent” of Muslims do not back Islamic terrorism.

On Islam, President Obama is not the first to sow confusion on the issue. In the aftermath of the terror attacks of September 11, 2001, President George W. Bush argued over and over again that America is not at war with Islam. We can understand why a president would say this, and we also need to admit that there is an important element of truth in the statement.

The West is not at war with Islam if that means a war against all Muslims and against all forms of Islam. But, true as that statement may be, we must also be clear that we are facing a great and grave civilizational challenge from millions of Muslims who believe, quite plausibly, that their version of Islam is more faithful to the essence of Islam and the Quran. This understanding of Islam is growing, not receding. It is now drawing thousands of young Muslims from both Europe and North America to join the jihad. We have seen the hopes of a moderating Arab Spring dashed and we have seen the rise of even more brutal and deadly forms of jihad in groups such as the Islamic State. Clearly, there are millions of Muslims who do believe that God condones terror. They celebrate the fact that Muhammad was a warrior, and they understand that it is their responsibility as faithful Muslims to bring the entire world under the rule of Sharia law. Their actions are driven by a theological logic that has roots in the Quran, in the founding of Islam, and in the history of Islamic conquest.

And yet, at virtually every turn, President Obama and his administration remain determined not to mention Islam in any negative light, and even to redefine some acts of terror committed in the name of Islam as “workplace violence.” His refusal to acknowledge the worldview of those who declare themselves to be our enemies is neither intellectually honest nor safe. It is a theological disaster, but it is a foreign policy disaster as well.

In the most controversial portion of his address, President Obama said:

“And lest we get on our high horse and think this is unique to some other place, remember that during the Crusades and the Inquisition, people committed terrible deeds in the name of Christ.  In our home country, slavery and Jim Crow all too often was justified in the name of Christ.”

President Obama would not mention Islam by name, but he did bring judgment on the Christian past, with specific reference to the Crusades. At that point a good measure of Christian humility and honesty are called for. The centuries of the Crusades were a brutal epoch in which horrible things were done, often in the name of Christ. The union of medieval Catholicism and the power of kings was disastrous, and there are lasting stains on the Christian conscience from this era. The same is true of the era of slavery and Jim Crow laws in the United States.

But honesty is hard to come by when it comes to distant history, and that is why we should be rigorously critical when it comes to the very real and horrifying reality that terrible acts have been perpetrated in the name of Christianity. At the same time, historical honesty and humility demands that we acknowledge that in the age of armed conflict between Christian kingdoms (as they claimed to be) and Muslim armies, even the stoutest secular critics of Christianity must recognize that our current age would be very different if Muslim armies had won, for example, when the forces of the Ottoman Empire were stopped at the gates of Vienna in 1683. All those professors of gender studies and post-colonial literature in European universities might well be professors of the Quran, instead.

Even as the West is not at war with Islam, in the sense of being at war with all Muslims, the existential threat to western freedoms and liberties is real, as is the fact that millions of Muslims (and their current governments) offer aid and support to groups clearly involved in jihad. There is reason to believe that groups like the Islamic State are also now understood as a existential threat to any number of Arab regimes and Islamic communities. After all, most of the victims of Islamic terror groups have been fellow Muslims.

Intellectual honesty also demands that we recognize that going back centuries to the era of the Crusades is not really helpful when looking at the fact that the current threat is a resurgent Islam, which understands full well that the modern secular West lacks a worldview that can lead to an adequate response. Secularism and Islam are not evenly matched.

Theological honesty further demands that we acknowledge the vast difference between a theological system centered in Jesus Christ, who told Peter to put away his sword, and one that takes as its central example Mohammed, whose status as a mighty warrior is an issue of enduring Muslim pride. The strategic fact of our current times is that the terrorism feared by the West is deeply rooted in a theological worldview, and that worldview is Islam.

The real problem with President Obama’s remarks at the National Prayer Breakfast was not his reference to Christian history, but his refusal to acknowledge the reality of our current challenge — a refusal growing more dangerous by the day.

Dr. R. Albert Mohler Jr. serves as president of The Southern Baptist Theological Seminary. This article is taken from his blog and is used with permission.