As thousands prayed across the nation Thursday in celebration of the National Day of Prayer, the Rev. Franklin Graham held his own vigil in the Pentagon parking lot.

Oh well, it doesn’t matter where one prays, right? All prayers lead to heaven. Or do they?

Not if you’re Graham, who lost his place at the Pentagon altar after he mocked other religions, specifically Islam and Hinduism. A plea to President Obama to reinstate him apparently fell on pitiless ears.

Graham’s offense was expressing his belief that only Christians have God’s ear, that Islam is evil, and that Muslims and Hindus don’t pray to the same God he does.

“No elephant with 100 arms can do anything for me,” Graham said in a USA Today interview, referring to one of the five main Hindu deities. “None of their 9,000 gods is going to lead me to salvation. We are fooling ourselves if we think we can have some big kumbaya service and all hold hands and it’s all going to get better in this world. It’s not going to get better.”

It’s not? If the whole world prays for a common good, will no good come of it? If so, then what’s the point of a National Day of Prayer? Oh ye of little faith.

Perhaps Graham was feeling cross after his rejection. As honorary chairman of the National Day of Prayer Task Force, a private evangelical group, Graham was to have led a prayer for the U.S. military. His son is on a fourth tour in Afghanistan.

But Graham’s views didn’t sit well with secular Americans or even non-evangelical Christians, who protested that the government is endorsing a certain flavor of Christianity. A Wisconsin court apparently agreed and ruled the day unconstitutional, appeals pending.

Graham isn’t alone in his views. A survey of 1,000 Protestant pastors, conducted by an evangelical polling firm, found that 47 percent agree that Islam is “a very evil and a very wicked religion.” But such opinions may be confined mostly to an older generation. Evangelicals under 30 believe that there are many ways to God, not just through Jesus.

David Campbell, a professor at Notre Dame and co-author (with Harvard’s Robert Putnam) of “American Grace: How Religion Is Reshaping Our Civic and Political Lives,” conducted surveys showing that nearly two-thirds of evangelicals under 35 believe non-Christians can go to heaven, vs. 39 percent of those over 65.

When it comes to whose prayers carry more weight in the heavenly realm, well, who really knows? But new brain research supports the likelihood that one man’s prayer is as good as any other’s.

Barbara Bradley Hagerty, the award-winning National Public Radio religion reporter, participated in a peyote ceremony in Arizona, meditated while wearing a brain scanner at the University of Wisconsin and donned a “God helmet” in a neuroscientist’s lab in Canada in her quest to discover the secrets of prayer and, possibly, proof of God.

In her book, “Fingerprints of God,” Hagerty tries to answer a question that has plagued her for years: Is there more than this? She couldn’t accept mainstream science’s answer that we are “a collection of molecules with no greater purpose than to eke out a few decades.” Instead, she sought out spiritual virtuosos (people who practice prayer, religiously), as well as neurologists, geneticists, physicists and medical researchers who are using the newest tools of science to discern the circumstantial evidence of God.

Her research led to some startling conclusions that have caused no small amount of Sturm und Drang among those who believe theirs is the one true way. She found that whether one is a Sikh, a Catholic nun, a Buddhist monk or a Sufi Muslim, the brain reacts to focused prayer and meditation much in the same way. The same parts light up and the same parts go dark during deep meditation.

Apparently, we have a “God spot” and “God genes.” And though some are more generously endowed than others, spiritual experience is a human phenomenon, not a religious one. Different routes to the same destination.

Understandably, these are not glad tidings to some. Centuries of blood have been shed for the sake of religious certitude. But transcending the notion that only some prayers are the right ones might get us closer to the enlightenment we purportedly seek.

Hagerty is optimistic that science eventually will demonstrate that we are more than mere matter. In the meantime, it would seem eminently rational to presume in our public affairs that God does not play political favorites with His creation.