Sunday, January 9, 2011

A Gene Sequencing Machine To Look For Life On Mars


The DNA Sequencer That Could Go To Mars

Dec. 14 2010 - 7:39 am | 7,048 views | 1 recommendation | 1 comment
Mars with polar ice caps visible.
Image via Wikipedia
Did life begin on Earth?
Maybe not. For more than a hundred years, some scientists have believed the first living things evolved elsewhere, perhaps on Mars, and then stowed away on rocks that made their way here.
This idea is known as ‘panspermia.’ Lord Kelvin, the British physicist who formulated the first and second laws of thermodynamics, proposed it in 1871, though he was neither the first nor the last to do so.
For more than a century, panspermia has fallen into the large category of scientific ideas that capture the imagination but are completely unverifiable. Gary Ruvkun, a Harvard molecular biologist, has been trying to figure out ways of designing space probes that could test the idea for years. Now, he thinks he has found the perfect tool: a new DNA sequencing device called the Ion Torrent Personal Genome Machine, made by Life Technologies of Carlsbad, Calif. The device is launching commercially today.
DNA sequencing has been undergoing a revolution, decreasing in price and increasing power at a speed unmatched by any other technology since the microchip. Decoding a human genome cost more than $1 billion a decade ago, but can be done for less than $10,000 now, a rate of decrease that beats the computer industry’s famous Moore’s law. But you wouldn’t think of sending these existing machines, which contain complicated high tech cameras and robotics and are operated by highly trained scientists, to another planet.
“Anything you’re proposing to fly in space, it should be in eighth grade science classes,” says Ruvkun. He believes that with advances like the Ion Torrent machine “sequencing will be done in eighth grade science classes very soon.”
The promise of the Ion Torrent PGM is that it is based entirely on the kind of silicon chips the microprocessor industry has used for decades. It sequences DNA by measuring the electrical charges produced as DNA molecules are copied; it does this by testing for each of the four possible DNA letters in sequence, catching a whiff of charge every time it hits the right code. Right now, it is far more expensive on a DNA-letter by DNA-letter basis, but it also delivers results faster – in hours, not a week. Moreover, the machine costs just $50,000, about a tenth as much as the more expensive machines made by Illumina, Life Technologies, and, coming soon, Pacific Biosciences.
Ruvkun became excited when he heard about the PGM because it sounded so much sturdier than existing machines. For years, he had been making the case that polymerase chain reaction (PCR) would be the best way to test for the existence of Earth-like DNA on Mars. His argument was that the technique, which makes many copies of a piece of DNA, would be so cheap to put on a Mars probe that it would be silly not to. But PCR doesn’t tell you what genetic code is written on a DNA strand. And without that information, it would be impossible to know for sure that the DNA didn’t hitch a ride to Mars from Earth. It could be dandruff from the guys who put together the probe, or a hardy virus.
But being able to get even a tiny bit of sequence from DNA found on Mars would allow scientists to know for sure that they’re not looking at a run-of-the-mill earthling. The current version of the PGM is capable of sequencing 10 million DNA bases; Ruvkun hopes to modify the device to make it simpler, and says that he could make do with as little as a thousand bases. His work is funded by the National Aeronautics and Space Administration, but he is first to admit the chances of actually making it onto a space probe are slim.
Here on Earth, the promise of the PGM is that it will allow scientists to verify their results more quickly and sequence microbes more easily. In the future, it might form the basis for diagnostic tests. Jonathan Rothberg, who led the development of the device and is chief executive of Life’s Ion Torrent division, says he hopes it will open up DNA sequencing to thousands more labs. Chad Nusbaum, co-director of the Genome Sequencing and Analysis Program at the Broad Institute, says that he thinks of the technology as being akin to digital photography: it was adopted because it was small and fast, but there was always the potential that it would replace film. Either way, it shows how quickly the field of DNA decoding is advancing.
“It has changed everything about what I do,” says Ruvkun. “There’s nothing more fun than living through a revolution. Genomics is just the best. It’s so much better to be a scientist now that it was 20 years ago.”

1 comment:

  1. DNA testing by way of oral swabs is by far the standard procedure of sample collection as it's really quick to perform; nevertheless DNA tests, such as paternity testing.

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