But if the government's goal is to lower the cost of health care, it might start requiring doctors to use the "winning" drug, especially if it’s a generic. And then you can take that a step further and figure the government might try to put a price tag on the incremental benefit a drug brings. How much is the extra 1.6 months of extended survival -- or whatever it turns out to be in a true head-to-head trial -- worth for Dendreon 's (Nasdaq: DNDN) Provenge compared to sanofi-aventis ' Taxotere? And is that worth the likely price difference in treatments?

Slippery slope indeed.

The end result of the added risk -- a company not only has to show that the drug works, but that it works better -- might stifle innovation. Companies may avoid developing drugs for fear of marketing failure due to comparative studies, which would be a shame for both patients and investors. After all, the world's best selling drug, Pfizer 's (NYSE: PFE) Lipitor, was essentially a "me-too" drug, following fellow statins made by Merck (NYSE: MRK) and Bristol-Myers Squibb (NYSE: BMY).

What's a Foolish investor to do?
The best thing is probably to do nothing, for now. We're likely a ways away from seeing the full impact of comparative medicine. But, because it’s a big unknown with huge potential to move toward socialized medicine, investors need to be extremely careful and be willing to jump ship if it comes to that.

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