All along, Mr. Obama’s aides have said they knew that Congress might pass bills with serious flaws. The White House strategy was to stand back and work with Congressional leaders to fix those flaws once the legislation entered its endgame.

The endgame is here.

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For anyone who cares about reducing medical costs and improving outcomes, there are probably six big issues to follow in the coming weeks. Let’s take them one at a time:

THE EASY STUFF Each year, about 100,000 people die from preventable infections they contract in a hospital. When 108 hospitals in Michigan instituted a simple process to prevent some of these infections, it nearly eliminated them.

If Medicare reduced payments for the treatment of such infections, it would give hospitals a huge financial incentive to prevent them. The Senate bill takes a small step in this direction by cutting payments to hospitals with high infection rates by 1 percent. The House bill merely requires hospitals to report their rates publicly. There are also other basic patient safety areas in which the bills can do much better.

WHAT WORKS? Earlier this year, I used prostate cancer as an example of how our fee-for-service medical system leads to higher costs and worse outcomes. There are a handful of possible treatments for early-stage prostate cancer, and the fastest-growing are the most expensive. But no one knows which ones work best.

Modern medicine is full of such uncertainty. Again, the federal government could make a big difference here by giving Medicare a moderate amount of money for research, which would pay for itself many times over. The stimulus bill began paying for such research, but the health reform bills fail to pick up where the stimulus leaves off.

A FED FOR HEALTH Twice a year, an outside advisory board sends Congress a list of suggestions for Medicare payment rates, based on the available evidence. Congress generally ignores them, in deference to the various industry groups that oppose any cuts to their payments.

We already have a wonderful model for how to avoid such interference. It’s called the Federal Reserve. The Fed is charged with setting interest rates based on economic conditions, not politics. The Senate bill would create such a commission for Medicare. Unfortunately, it initially applies to doctors and home health care providers but not hospitals, thanks to a deal between the hospitals and the White House. It expands to include everyone in 2019. The House bill has no such commission.