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Methane is the source of the gas we burn in stoves. You can also use it to make everything from plastics and anti-freeze to fertilizer. It comes out of underground deposits. But it also comes from swamps, landfills, even the stomachs of cows. While methane is valuable, a lot of it gets away into the atmosphere, where it becomes a damaging greenhouse gas. Scientists have been trying to find out how much of this climate-warming gas gets into the atmosphere, with varying success.

NPR's Christopher Joyce reports on a new study that says there's much more up there than we thought.

CHRISTOPHER JOYCE, BYLINE: The U.S. Environmental Protection Agency tries to keep track of methane that goes up into the atmosphere. But a new study says they've got it wrong, on average by 50 percent.

SCOT MILLER: Our numbers for the entire United States are about a factor of 1.5 larger than the United States Environmental Protection Agency.

JOYCE: Scot Miller is a PhD candidate at Harvard University and co-author of a new study on methane published this week in the Proceedings of the National Academy of Sciences. He says 1.5 times the EPA estimate is serious because you're talking about hundreds of millions of tons of a very potent greenhouse gas going up every year. And in some parts of the atmosphere, over Texas, Kansas and Oklahoma, the new study found more than 2.5 times the methane that EPA and other groups have measured. Miller says he's not that surprised at these higher numbers.

MILLER: It's a really, really difficult problem to try and estimate greenhouse gas emissions.

JOYCE: The EPA calculates how much to expect from all the nation's gas drilling sites and swamps and refineries, even individual cows that burp it up. But it's mostly a bottom-up approach, looking at sources of methane by using computer models and adding them all up. The new study, by scientists from universities, the federal government and Europe, took almost 13,000 measurements in 2007 and 2008.

They collected them from cell towers as high as the Empire State Building, as well as from airplanes. It was a top-down study, looking at what's actually up in the air. And they found that what's airborne is more than the sum of the ground measurements. Now, the top down approach does have its weaknesses.

MILLER: It's very difficult to desegregate, you know, how much methane came from a well site or a particular feed-lot, et cetera.

JOYCE: On the other hand, it's based on actual measurements, not just computer models and calculations. Environmental scientist Rob Jackson says bottom up measurements usually come up with lower numbers for methane leakage than measurements in the air. This has been a problem for people trying to get a handle on emissions from the country's natural gas boom, for example.

ROB JACKSON: I think bottom up measurements are lower because we miss the few percent of sites that are really leaking a lot of gases. We probably have 90 percent of oil and gas operations that are pretty clean, and a few percent that leak like a sieve.

JOYCE: And those few aren't necessarily easy to find when you're talking about tens of thousands of sites in the country.

JACKSON: It's like trying to find that needle in the haystack. The needle's there but you've got to do a lot of on-the-ground sampling to find that needle and most times, people don't do that.

JOYCE: Jackson, from Duke University, also says the higher emissions found in the South Central U.S. suggests that oil and gas operations are emitting more methane than previously thought. Miller and Jackson say it's important to get these numbers right. Some states have or are contemplating limits on methane emissions from industry and agriculture. If the current estimates of what's actually going up in the air are off by half, that could make those limits meaningless. Christopher Joyce, NPR News.

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