The Obama administration and Congress are moving forward with plans to evaluate the strengths and weaknesses of the various medical treatments for common health conditions, despite concerns of some lawmakers and the drug and device industry that it will lead to rationed health care.

But how the government uses this comparative effectiveness research and how it might benefit – or complicate – the decision-making of average people and their doctors are also matters of some debate.

On a human level, it gets down to people like Jay Allen. He does security work for the government and has been an exercise enthusiast all his life. Last year, at the age of 44, he started having problems on his 14-mile bike ride from his suburban Virginia home to his office in Washington, D.C.

“I’d have onset of shortness of breath, and then occasionally I’d get the same shortness of breath just sitting at my desk or waking up in the middle of the night,” Allen says.

A cardiologist diagnosed a condition called atrial fibrillation, or a-fib. It’s a very common condition – 2.2 million Americans have it. In a-fib, the top part of the heart occasionally shivers instead of beats, causing shortness of breath, fatigue and palpitations. In some people, a-fib can lead to heart failure; in others, it can cause blood clots that in turn cause strokes.

There are a lot of treatment options: a lifetime of anti-clotting drugs, which can cause a different kind of stroke and can react with other drugs; there are drugs that slow the heartbeat; there are anti-arrhythmic drugs that have their own side effects, like lung damage.

Doctors can also apply an external shock to the heart to reset the heart’s rhythm, although in about 50 percent of cases, the irregular beating eventually reoccurs. Another option is something called radiofrequency catheter ablation, where doctors thread a catheter through your arm or leg, up to part of the heart that plays a key role in generating the abnormal beats, and use radiofrequency to destroy that part. Earlier this month, the federal Agency for Healthcare Research and Quality concluded that while there’s good data showing the procedure is effective for a year, not much is known about its long-term effects.

The drug regimen is inexpensive, for the most part – dollars a day. The Food and Drug Administration just approved a new anti-arrhythmia drug, but the manufacturer has yet to announce a price. The heart shock technique is about $1,000 or $2,000 in Washington. The surgical procedure is tens of thousands of dollars.

In terms of effectiveness, cardiologist Stuart Seides, a partner of the doctor taking care of Allen, says to think of it like buses, trains and planes. Taking the bus means slowing the heart rate and using blood thinners to prevent clots; taking the train means getting a normal heart rhythm back with drugs or an external shock; the plane is radiofrequency catheter ablation.

“All will probably get you where you’re going reasonably safely,” Seides says. “You can lead a long and active life with atrial fibrillation.”

But he can’t tell his patients which approach will mean the longest life. “There is no data at present to be able to say to a person that one or another treatment is superior in terms of the hard endpoints,” he says.

Right now, Seides and his patients work out treatment decisions based on whether the patients are comfortable with and can afford daily medications, or whether they want to go through anesthesia and surgery for a chance at a quick fix. Allen chose the ablation because he wanted his heartbeat to go back to normal, and he didn’t want to rely on drugs, although he will be on drugs for some period of time. Allen says he is happy with his decision.

Seides would love to be able to give his patients comparative information about longevity and quality of life. But thinking about such a study makes him anxious, as well. He doesn’t want it to result in a set of cookbook rules that will require him to treat all his patients the same way.

“We don’t want to stifle innovation by creating large studies, getting some outcomes and saying this is the way we treat a-fib,” he says. A relatively inactive patient may be happy with just anti-clotting agents; someone very active may want to try getting rid of the a-fib once and for all with the ablation approach.

Carolyn Clancy understands his concern. She is head of the Agency for Healthcare Research and Quality, the government agency that just did the analysis that found that not enough is known about a-fib treatment. “Our intent is to be descriptive, not prescriptive,” she says.

Her agency does not look at the comparative costs, just the risks and benefits. She says the studies won’t get done if left up to the drug and medical device makers – discovering that their approach doesn’t work as well as another one wouldn’t be in their best interest. She says comparative effectiveness should be respected the same way biomedical research is, because it helps doctors determine the best approach for their patients.

Clancy says determining which treatments are the most effective for specific conditions will cut the nation’s health spending, because some of the choices currently made by doctors and patients – some of them quite expensive – aren’t necessarily the best ones.