The Pap smear, in which a clinician gently scrapes and brushes cells from a woman’s cervix (the lower portion of her uterus or womb), swishes them in a bottle of fixative solution, and then sends them to the lab to determine if the cells show pre-cancerous or cancerous changes caused by the sexually transmitted human papilloma virus (HPV), is a pretty simple procedure that takes less than a minute to perform. Still, there’s a lot the person performing the Pap (named after Greek pathologist Georgios Papanikolaou, by the way) needs to consider.

No, I’m not thinking of the recently changed recommendations about how often women should be screened, or about the related and also recently much discussed issue of vaccinating adolescents for HPV.

I’m thinking of really important decisions, like whether to label the sample bottle before or after the test.

My primary care practice includes 18 physicians, all of whom have different preferences about the small details involved in actually performing and processing a Pap smear. Some prefer the medical assistant to label the bottle, lay out the instruments, and fill out the pathology form before the doctor enters the room, and some would rather meet with the patient, decide whether she needs the test, and then have the assistant finish setting things up–and then there are those who prefer that the medical assistant set things up partially, and to finish the prep themselves.

For many years, our practice allowed each doctor to do as he or she pleased, and relied on the medical assistants to remember everyone’s preferences.

This may seem trivial, but Pap smears were only one of many examples of this “have it your way” approach. Every little step of the patient’s visit–whether the gown would be open in the front or the back (we listen to both heart and lungs, so it’s a toss up), whether the patient would be undressed before seeing the doctor, whether the privacy curtain around the exam table would be drawn closed or left open (all behind a shut door so, again, a toss up), whether the chart should be placed on the rack in front of the doctor’s office or the exam room–was left to each doctor.

Then, a few years ago, the new manager of our practice had an idea: what if we replaced this chaos with a set of standard protocols? She reasoned that if everyone did things the same way, the medical assistants could work much more efficiently, patients’ visits would go more smoothly, and the general level of stress in the practice would lessen.

Not much to argue with, right?

Wrong. Many of us doctors did argue–and I was one of the loudest. You see, as hard as this may be to understand, many of us MDs were proud of our old system. It valued our autonomy, our individual practice styles, our resistance to the kind of corporate-style HMO systems in which doctors are told what to do–and which many of us had deliberately avoided (or fled).

Over time, most of us have gotten used to the new procedures, and even come to appreciate them. Some still grumble silently (or not so silently) and some, the practice manager recently told me, still ask the medical assistants to make exceptions for them so they can stick with their old habits.

Why does any of this matter? Because my tales of Pap bottles, gowns, and chart racks hint at a major conundrum in attempts to fix the current crisis in American medicine: skyrocketing costs combined with less than ideal outcomes–or, as New Yorker staff writer and Brigham and Women’s surgeon Atul Gawande put it in a fascinating essay, “greasy-spoon fare at four-star prices.”

The conundrum is that medicine attracts people who generally value autonomy over money (I know, we make a comfortable living, but there are smarter ways to get rich than incurring an average of $160,000 of post-college debt and then starting out with a job in which you work 80+ hours a week for an average of $43,000 per year)–and yet surrendering some of that autonomy may be necessary in order to save a system heading for bankruptcy.

In Gawande’s essay, “Big Med,” he describes visiting the kitchen of a Cheesecake Factory, a chain which produces uniformly good quality food with relatively little waste. Their secret? Strict adherence to protocols. A manager inspects every plate before it leaves the kitchen to make sure that, say, your wasabi tuna looks exactly like that of the guy at the next table.

Gawande also visited a telemedical center in the Boston area in which doctors and nurses monitor ICU patients in several hospitals by camera and computer and alert doctors and nurses on the scene about abnormal lab values, loose breathing tubes, and other problems.

Not surprisingly, there’s more push back from the doctors and nurses in the ICUs than from the line cooks at the Cheesecake Factory. Gawande describes clinicians so resentful of being watched and advised that they cover cameras or even yank them out of the wall. But he also describes doctors and nurses grateful for extra sets of eyes and ears to help them take better care of patients.

Of course patients aren’t wasabi tuna–or cheesecakes–and no protocol will ever replace the intangible and–may I say it?–sacred interaction that occurs between clinician and patient behind a closed door.

I’m sure there are many bureaucrats who don’t understand that–and this misunderstanding will be an ongoing cause of tension with clinicians.

But our practice manager understands it. She told me that she believes all standardization should end when the exam room door closes. Many would disagree with her, and feel that standardization should extend to medical decision-making, with algorithms and protocols to cover every symptom and disease.

I’m ambivalent about this, myself, torn between the desire to deliver the best and most cost efficient care–often determined in large studies and overseen by large organizations– and the desire not to trample what I believe is the most valuable part of medicine: the relationship between individual patients and their caregivers.

But I have come around to seeing the real benefit of systematizing the little things–improved efficiency can lead to more precious time behind that closed door.

“So,” I recently asked our practice manager, “all these protocols about Pap smears and charts, etc. are really meant to protect that sacred doctor-patient space?”

“Yes,” she said, tapping the desk in front of her for emphasis.

“That’s just what they’re meant to do.”

Suzanne Koven is an internal medicine physician who blogs at In Practice at Boston.com, where this article originally appeared. She is the author of Say Hello To A Better Body: Weight Loss and Fitness For Women Over 50.