Boston ? When I was a kid I just assumed the separation of church and hospital. It’s not that I didn’t believe in the power of prayer, but when my appendix burst I wanted a guy in a white coat, not a white collar.

The first time I realized how different things were in the Bush era was when W. David Hager was appointed to an advisory board of the Food and Drug Administration. Hager was an ob-gyn who prescribed Corinthians and Romans for PMS.

After that we saw the government take contraceptive information off one Web site and put phony links between abortion and breast cancer on another. That was just the beginning.

Welcome to the era of faith-based medicine. The administration has just announced that, for the first time ever, federal employees will be offered a Catholic health plan. Starting in November, workers in 31 Illinois counties can enroll in a plan created explicitly according to Catholic tenets and marketed as “faith-based.”

This plan is noted most for the things that it doesn’t provide: Abortion, of course, even in the case of rape. Contraception, including emergency contraception. Sterilization. Artificial insemination and most other fertility treatments.

We don’t know yet what the faith-based health plan will do about paying for other treatments that might challenge Catholic teachings. Will end-of-life care be determined by the patient or the latest directive from Rome?

This plan is defended as a “choice.” If you don’t want it, don’t choose it. But if this is an opening wedge, choice may not be so simple, especially in the 100 counties across the country where Catholic hospitals are the sole providers.

It’s no surprise that the first faith-based plan is Catholic since 11 percent of all hospitals are run by Catholics. Many provide the exact same services as their secular counterparts, but the church has long led the fight against abortion and also against state laws that mandate contraceptive coverage. At last count, only 28 percent of their 600 emergency rooms offered emergency contraception to rape victims.

But this health care “first” is only a piece of the growing story of faith-based medicine. Another piece is in the “conscience clauses” being pushed to let health care workers and whole institutions opt out of providing health care, especially reproductive care, on religious grounds.

Just this month, the House of Representatives passed a provision that protects employees and hospitals from laws requiring them to provide abortions or even abortion referrals. Last July, Mississippi joined Arkansas and South Dakota in giving health care workers and institutions the right to refuse performing any medical service on moral or religious grounds. Meanwhile we have pharmacists lobbying to refuse handing over emergency contraceptives as if the drugstore were their personal chapel.

Well, I have no problem with a “conscience clause” for an individual. No health care worker should perform a medical procedure against his beliefs. How would you like a doctor who opposes sterilization performing your vasectomy?

But how do you define an institution’s conscience? Is it the collective belief of the doctors, the employees, the patients? Or is it an edict of the bishops?

And while we are talking about faith-based medicine, since when is a hospital or a health care plan a religion? This year the California Supreme Court ruled that Catholic Charities of Sacramento had to provide its employees with birth control coverage because the charity didn’t just serve or employ Catholics. Well, neither does a hospital.

We used to talk about doctors playing God. Now religion is playing doctor. What happens when the church defines medicine and the government gives it a religious seal of approval?

Will there be a sign on the emergency room door warning that this hospital does not remove feeding tubes? Will a young woman even be told that she can have her eggs harvested before chemo for later use? Will an AIDS patient be advised about condoms?

“Can you imagine if Jehovah’s Witnesses opened a hospital, got funding, and then said oh, by the way, we don’t do transfusions?” asks Susan Berke Fogel, who co-chairs the American Bar Assn.’s ethics committee. What if a Jewish hospital insisted on circumcising all boys, she adds provocatively. Would that too be approved as faith-based medicine?

At some point doesn’t religious practice become medical malpractice? We can only pray.