As health care reform remains the key issue to debate in the nation’s capital, the media headlines and Twitter chatter have focused on such things as costs and coverage. And rightfully so! After all, those are the pressing bottom-line pieces of the puzzle that must be clarified if a program is to be put in place this year.

Of course, there are many elements involved in crafting legislation that can muster enough votes and land on President Obama’s desk by October, a timeframe he has repeatedly requested. But one component that is certainly causing a good deal of friction is the notion of comparative effectiveness, or CE, as policy wonk insidersrefer to the otherwise stodgy term.

Eye-glazing terminology aside, comparative effectiveness is central to the health care system overhaul, thanks to the $787 billion economic stimulus bill that came about earlier this year. That legislation provides $1.1 billion to compare drugs, devices and other ways to treat health problems, along with a council of federal employees to oversee research and spending.

The purpose is well known: by requiring comparative effectiveness, Congress hopes to address criticisms that there is no easy way to compare treatments that, in some instances, may prove unnecessarily costly. And that resonates far and wide as most everyone – insurer, employer, employee, the uninsured and underinsured – bemoans the rapidly rising cost of health care in this country.

Whether this goal can be achieved remains to be seen. For one thing, comparative effectiveness has always been controversial over concerns about running trials between competing products. “They’re expensive. You need a lot of patients and they take a long time,” said Barton Cobert, an industry consultant who has held drug safety and pharmacovigilance positions at Medidata Solutions, Novartis Consumer Health and Forest Laboratories. “And let’s face it: if your product lost, you’re dead.”

A flashpoint, however, has been the extent to which cost comparisons may be used as the basis for treatment or payment decisions. The pharmaceutical industry has worried that the U.S. will look for comparative effectiveness to determine coverage, an issue that has plagued drug makers in the United Kingdom, where the concept has been used by the government’s National Institute for Health and Clinical Excellence (NICE).

Across the pond, NICE has regularly rejected coverage for medicines, citing high costs and the probability that other drugs that are already available may be equally effective. The practice spooks drug makers, some of which have responded with novel gambits that involve offering refunds if objectives aren’t achieved. And in Washington, Johnson & Johnson asked the Institute of Medicine to run a comparative study between newer and older anti-psychotics. Such moves reveal an industry willingness to play ball and an acknowledgement that comparative effectiveness may offer some advantages. But some maintain this will not be a panacea.

“When you talk about comparative effectiveness, you’d like to get away from the subjective and go to the objective,” says Michael Eckstein of Topaz Clinical Consulting. “And there’s always the question of the metrics being used. When you talk about symptoms, well, what is effectiveness? With diabetes, for instance, we’re not offering cures. It’s a maintenance situation. And what’s a comparative advantage when we talk about asthma? There’ll be more data (with comparative effectiveness), but also the possibility of more confusing endpoints. Nothing is cut and dried.”

In other words, whatever bill Congress sends to the White House, there will likely be continued debate over the virtues of comparative effectiveness. Mr. Cobert, for instance, argues that better results are far from guaranteed. Rather, the drumbeat for comparative studies, in his view, may just as easily yield nuanced findings that fail to move the ball forward but are expensive and inconclusive.

Just the same, the huge amounts of money the federal government is providing will benefit clinical research organizations, because they stand to gain if drug and device makers are compelled to order up more studies. Certainly, that appears to be a consensus view, at least in the short run. After all, somebody has to design and run clinical trials, as well as analyze databases for patient clues.

This would build on the existing trend in which a growing amount of trial work is outsourced. In fact, comparative effectiveness may well be the antidote to recent cutbacks by big drug makers, which have pared their research budgets and eliminated some areas of research altogether, and biotechs that are so starved for cash that they are going out of business in an unusually large numbers.

Yet, there are some who maintain comparative effectiveness will not be a boon for CROs. In fact, the Association of Clinical Research Organizations is trying to dampen impressions that its members are rubbing their collective hands together in glee at the prospect of government-mandated studies that will involve untold numbers of patients for a large number of products.

“Nobody objects, at least not publicly, to the research being done. The sticking point is what to do with the research after it’s done and whether it’s going to be used for reimbursement decisions. Patient advocacy groups and (drug) industry groups say research is important, but it should be up to the doctor and patient about what works best,” said John Lewis, an ACRO point man on Capitol Hill for the issue.

“In the short term, yes, there should be more opportunities for CROs. But I can tell you the long-term implications may not be the same. If research isn’t done correctly or if there’s a mandate for coverage of certain pharmaceuticals as opposed to others, we see that actually shrinking the R&D pipeline and hurting pharma. They’ll have less money put into research as a result, which isn’t good for CROs,” he added.

“If we have a situation where Medicare says it’ll cover one statin and not another because a study showed drug A is more effective, generally, than drug B, the manufacturer of drug B is now going to lose a significant part of its market, because a decision gets made by a major payer. And that trickles through to R&D spending,” he concluded. “That’s what we’re talking about when we say there’s a potential negative implication.”

So will comparative effectiveness be a windfall? The dire warnings may be premature. After all, if more and more drug makers decide that certain studies are worth pursuing because results can be used to influence payers and ring the register, the concept will eventually leech into the corporate mindset. In other words, the real issue may be who decides which studies get done. But like it or not, comparisons are going to get made.

Ed Silverman is a prize-winning journalist who has covered the pharmaceutical industry for The Star-Ledger of New Jersey, one of the nation’s largest daily newspapers, for more than 12 years. During that time, he has closely followed a variety of topics of concern to those who work for, and with, pharmaceutical manufacturers – drug development, mergers and acquisitions, regulatory oversight, safety and pricing controversies, and marketing issues. For the past two years, Ed blogged about the drug industry at Pharmalot. Prior to joining The Star-Ledger, Ed spent six years at New York Newsday and previously worked at Investor’s Business Daily, among other newspapers.