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On Tuesday morning, the federal government made a big mistake.

The Centers for Disease Control and Prevention and the Food and Drug Administration jointly announced that they are investigating six cases of rare blood clots that may be linked to Johnson & Johnson’s coronavirus vaccine — and recommended temporarily halting its use.

Public intellectuals piled onto social media, incredulously asking what the government was doing shutting down a vaccine amid a pandemic over an extremely rare side effect. Longtime FDA watchers, however, saw the agency doing what it almost always does: erring on the side of caution, no matter what.

To be fair to the government, the reported clotting problems are of an unusual type, and heparin, a standard treatment for blood clots, may make these cases worse. Officials are understandably worried that doctors could unintentionally harm their patients.

So one could argue that the government is doing what it should: pausing to assess the extent of the problem and give doctors time to absorb new treatment guidelines. And if a few days’ delay were the only side effect, this would be a strong argument.

The Johnson & Johnson vaccine is a small fraction of the U.S. stock and and even that supply was already being temporarily disrupted by production problems at a Baltimore plant. While it’s nice to have more options — particularly ones that don’t have the exacting refrigeration requirements of the messenger RNA vaccines from Pfizer and Moderna — this is probably not going to slow the pace of vaccination nationwide much, especially since we’re quickly approaching the point where vaccine hesitancy is going to be a bigger problem than shortages.

But that’s exactly why the pause is likely to do more harm than good. Europe’s experience suggests that when regulators halt vaccinations even temporarily, it sends a negative signal about the vaccine’s safety that lingers in the public mind. And even if the clots are a real side effect of Johnson & Johnson’s vaccine, in context, this vaccine still appears very safe.

So far we know that six women who got the Johnson & Johnson vaccine experienced a rare form of blood clot, and one died. But more than 7 million people have received this vaccine, which means that if the vaccine is causing this problem, it appears to be a less than one-in-a-million side effect. Extrapolating that out: If everyone in America received this vaccine and it caused clots at the same rate, there would be around 330 such cases, and perhaps some fatalities. By comparison, almost 500 Americans died of covid-19 Monday.

Of course, people make distinctions between passive risks, like catching covid-19, and active risks, such as taking a vaccine. But other common medications and activities can cause blood clots, notably birth control and flying. Most people aren’t deterred, because it’s a tiny risk against a great gain. That’s also true of protecting ourselves and our neighbors from a deadly pandemic.

This announcement does not vindicate the vaccine hesitaters who worry that drug companies and regulators took shortcuts; paradoxically, it’s almost a good sign that we’re discovering rare side effects.

No pharmaceutical trial is powered to reliably detect one-in-a-million side effects, because that would take millions of trial subjects, which would be less like a trial and more like . . . injecting a substance into millions of people without studying it first. And even if we had possessed data showing such a rare effect, it shouldn’t have stopped regulators from approving a vaccine for covid-19, which kills a lot more than one in every million people who catch it.

Based on what we know right now, the math still strongly favors using this vaccine. Unfortunately, the FDA’s action has probably made people less likely to take it, or any coronavirus vaccine, even if regulators ultimately pronounce it safe. Even more unfortunately, this is a pattern: When faced with a difficult decision, the FDA almost always chooses the more restrictive option.

The defense of this institutional conservatism is generally that it has prevented the approval of drugs with awful side effects, such as thalidomide. That’s true. But economist Alex Tabarrok points out that excess caution has an equally real price, which he calls “the invisible graveyard.” It’s full of people who died waiting for the FDA to be extra sure about a good treatment.

Only in a global pandemic, when we are all watching the deaths pile up, do we see the grim outline of all those invisible tombstones we’ve been paying for. And having seen them, we need to do more than just shout at the FDA about this one case; we need to decide right now whether we’re willing to pay such costs — and if not, how we’re going to stop overcautious regulators from digging more graves.

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