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One oddity is the amount of oxygen. There are more oxygen atoms floating freely in the solar system than in the immediate interstellar space, or the vast region between stars.
Scientists were unsure why, but they said it's possible some of the life-supporting element could be hidden in dust or ice.
"We discovered this big puzzle -- that the matter just outside of our solar system doesn't look like the material inside," said David McComas of the Southwest Research Institute in San Antonio, Texas.
The discovery came from NASA's Interstellar Boundary Explorer spacecraft, which launched in 2008 to study the chaotic boundary where the solar wind from the sun clashes with cold gases from interstellar space.
Circling 200,000 miles above Earth, the Ibex spacecraft spots particles streaming into the solar system. A protective bubble surrounding around the sun and planets prevents dangerous cosmic radiation from seeping through, but neutral particles can pass freely, allowing Ibex to map their distribution.
The presence of less oxygen outside the solar system should not have any bearing on the search for Earth-like planets, scientists involved in the exoplanet hunt said.
There's plenty of oxygen in all the stars in the galaxy and in the material out of which stars and planets form, Geoff Marcy of University of California, Berkeley said in an email.
While Ibex probes the edge of the solar system from Earth orbit, NASA's long-running, nuclear-powered twin Voyager spacecraft are at the fringes. Launched in 1977, the spacecraft have been exploring the solar system boundary since 2004.
Scientists have said it'll be months or years before Voyager 1 exits the solar system and becomes the first manmade probe to cross into interstellar space.
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