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Museum scientist Professor Sara Russell says the discovery could mean that organic material, including water, is widespread in the outer reaches of our solar system.
Newly released colour images of Pluto reveal blue skies and small areas of bright red water ice on the surface.
The pictures were taken by NASA's New Horizons probe, which flew past Pluto in July and has been beaming tens of gigabytes worth of images back to Earth since 5 September.
Prof Sara Russell, who heads the Museum's Mineral and Planetary Sciences Division, says the presence of blue skies and water ice means that 'organic materials, including water, may be widespread in the outer solar system, and objects from this region may in fact have provided the early Earth with the elements and compounds needed for life to flourish'.
Data from New Horizons and other space probes is being used to produce spectacular images for the Museum's upcoming Otherworlds exhibition, which explores the landscapes of our solar system through six decades of space exploration photography.
Artist, writer and curator of the exhibition Michael Benson says, 'the new images are really interesting to see, as we've rarely seen blue in the atmospheres of other planets'.
Pluto is one of a family of bodies in the Kuiper Belt - a region of the solar system beyond Neptune's orbit that is thought to include comets, asteroids and other small bodies made largely of ice.
Because it is so far away from the Sun (the distance is on average 40 times the distance between the Earth and the Sun), the dwarf planet is in a near-permanent state of twilight.
NASA scientists say Pluto's blue skies are probably caused by clouds of soot-like 'haze particles', which scatter sunlight, turning it blue. This is similar to what happens on Earth, where tiny nitrogen molecules make the sky blue.
'Who would have expected a blue sky in the Kuiper Belt? It is gorgeous,' says Alan Stern, New Horizons Principal Investigator from Southwest Research Institute in Colorado in the USA.
In what the team called a 'second significant finding', the New Horizons images also detected numerous small, exposed regions of water ice.
Much of Pluto's water ice is covered by other types of frozen substances, including nitrogen and methane snow. Curiously, the areas of exposed water ice correspond closely to areas that were coloured bright red in recent colour photos.
Team member Jason Cook, also of the Southwest Research Institute, said that 'understanding why water appears exactly where it does, and not in other places, is a challenge that we are digging into'.
NASA hopes that future image data from the New Horizons probe will help to unravel the mystery.
The colour pictures of Pluto are the latest in a series of images taken by spacecraft from NASA and the European Space Agency (ESA) that have led to significant discoveries about the solar system.
NASA announced last week that its Curiosity Rover found evidence suggesting that ancient lakes on Mars existed long enough to foster life. The news followed on from the announcement at the end of September that scientists had used photos from the Mars Reconnaissance Orbiter to detect evidence of flowing water on the Red Planet.
Prof Russell says it's no accident that these image-led projects have resulted in important discoveries.
'Much of planetary science is very visual. Remote-sensing missions provide global information about the composition of other planets.
'Here at the Museum we also look at planetary materials on a much smaller scale. This can complement the global picture by telling us how the materials formed,' she says.