Turning DNA into a hard drive

Turning DNA into a hard drive 

Stanford's Drew Endy and his lab figured out a way to turn DNA into a rewriteable data storage device that can operate within a cell.




Stanford engineers have designed rewritable memory modules made out of DNA. Here, E. coli bacteria glow different colors depending on what information is stored in their memory modules. (Norbert von der Groeben, Stanford School of Engineering / May 10, 2012)


Silicon-based computers are fine for typing term papers and surfing the Web, but scientists want to make devices that can work on a far smaller scale, recording data within individual cells. One way to do that is to create a microscopic hard drive out of DNA, the molecule that already stores the genetic blueprints of all living things.

Stanford University bioengineer Drew Endy is a pioneer in the field of synthetic biology, which aims to turn the basic building blocks of nature into tools for designing living machines. This week, members of his lab reported in Proceedings of the National Academies of Sciences that they had figured out a way to turn DNA into a rewriteable data storage device that can operate within a cell. He spoke with The Times about the research.

What is synthetic biology?

Synthetic biology is basically a celebration of an engineer's inclination to want to make things using biology. Humans often learn by taking things apart. But an equally powerful way to learn is putting things back together. In synthetic biology, we can begin to put natural biological systems back together at the molecular level to test the understanding of genetics and biology we've accrued over the last 70 years.

So you want to build things using biology — including, in this case, a way to use DNA to store data?

Yes. We wanted to scope out an area where there are grand challenges in bioengineering, and genetically encoded data storage — meaning storing information inside living organisms — fit the bill.

Why would this be useful?

Say I wanted to put a genetically encoded counter to record cell divisions within every cell of my liver. A USB memory stick simply isn't going to fit in there. And even if I could miniaturize such a device with a future silicon-based manufacturing platform, it would be incredibly difficult to connect up to the biochemistry I'm going to want to record information about.

How does your data storage system work?

We engineered a little sequence of DNA and inserted it onto a chromosome in anE. colibacterium. Then we targeted this DNA with enzymes. Under one set of conditions, one of the enzymes cuts the DNA out from the genome, turns it and reinserts it back into the DNA. It would be as if you took a word in a sentence of text, flipped it upside down and backwards, and pasted it back into the sentence. It would look kind of funny.

Under a different set of conditions, a different set of enzymes finds that backwards DNA, cuts it out, flips it back to the normal orientation and glues the chromosome back together.

We encode a binary digit, or bit, within the DNA by mapping a "0" onto the normal orientation of the DNA and a "1" onto the flipped orientation of the DNA. DNA can only exist in one of two orientations, so it gives us a very nice way to store binary digits.

The key development here was that you were able to flip your DNA switch back and forth, right?

Yes, that hadn't been done before. We thought it would be pretty easy, but it took us three years.

The enzyme that flips from state 0 to state 1 is called the integrase. The enzymes that flip it back are integrase and a controlling protein that modifies its behavior called excisionase. Balancing just the right amounts of the two enzymes in the cells took us 750 attempts.

How might people use a technology like this?

I don't know. What we're working on are ideas to turn into tools that would make it possible to design, build and test things faster, more times or more smartly.

By analogy, the way we got from a room filled by one computer in 1952 to the "cloud" as it exists today was because of investments in tools. We got a lot better at silicon wafer manufacturing. We automated computer design so that human beings didn't have to do it manually. Somebody invested in some programming languages along the way. C++ didn't get discovered under a rock and Java wasn't grown on a tree. You have to work on tools.

But certainly there are ideas for end uses out there.

Sure. My dreams for synthetic biology would include using tools we build to reinvent manufacturing, so that everything now sourced from fossil fuels could be manufactured on a sustainable basis. We could have a much richer partnership with nature. That's quite a big task.

People could use DNA data storage to control processes in sewage treatment plants. If there's a storm and a whole bunch of weird, oil-based runoff from the streets comes into the sewage treatment plant, the system could adapt automatically to better process those oils. You could use biobits in medicine, too. For example, if you wanted to target a tumor inside the body, you might need an engineered immune cell to replicate within the patient — but you wouldn't want it to replicate too many times, otherwise you'd trigger an autoimmune response.

I'm certain I don't know all the applications.

What's next for your data storage module?

We're trying to scale this up. We want to get from one bit to a byte, which is eight bits. These systems don't need to be very big. If I had eight bits I could count up to 256, and I could start to study the development of an organism from a fertilized egg to a differentiated adult.

Another new dimension in the research is demonstrating that it will be possible to make this work in many organisms. We will support others who are working on that.

What we're likely to end up with will not look like classical electronics. Biology is beginning to teach us how to be a little bit more sophisticated in our engineering designs, which is a lot of fun.

 

 

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Mars has life's building blocks

 

Mars 'has life's building blocks'

 

 
 

The researchers suggest Mars has "been undertaking organic chemistry for most of its history"


New evidence from meteorites suggests that the basic building blocks of life are present on Mars.

The study found that carbon present in 10 meteorites, spanning more than four billion years of Martian history, came from the planet and was not the result of contamination on Earth.

Details of the work have been published in the journal Science.

But the research also shows the Martian carbon did not come from life forms.

A team of scientists based at the Carnegie Institution for Science, based in Washington DC, found "reduced carbon" in the meteorites and says it was created by volcanic activity on Mars.


Scientists are looking for clues as to how chemistry evolved to create a "common ancestor" of all life on earth

Reduced carbon is carbon that is chemically bonded to hydrogen or itself.

They argue this is evidence "that Mars has been undertaking organic chemistry for most of its history."

The team's leader Dr Andrew Steele told BBC News: "For about the last 40 years we have been looking for a pool of what is called 'reduced carbon' on Mars, trying to find where it is, if it's there, asking "does it exist?"

"Without carbon, the building blocks of life cannot exist... So it is reduced carbon that, with hydrogen, with oxygen, with nitrogen make up the organic molecules of life."

He says the new analysis has answered the first question.

"This research shows, yes - it does exist on Mars and now we are moving to the next set of questions.
 

 

The Mars Science Laboratory (Curiosity rover) will be next to land on Mars

"What happened to it, what was its fate, did it take the next step of creating life on Mars?"

He hopes the next mission to land on the Red Planet - the Mars Science Laboratory, also known as the "Curiosity" rover - will shed more light on the big question.

"The question 'are we alone' has been a big driver of science but it relates back to our own origins on this planet. If there is no life on Mars why? It allow us to make a more informed hypothesis about why life is here."

So does Dr Steele think there was, or is, life on Mars?

He laughs: "Get me some rocks back, I'll have a look and let you know."

 

 

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Watch rare 'ring of fire' solar eclipse on 21/5/2012

Watch rare 'Ring of Fire' solar eclipse on Monday !!


 

 

Washington: A partial solar eclipse, which will see the moon completely block out the sun except for a ‘ring of fire’ around the moon’s edge, is set to offer a spectacular site for observers on May 21.

The eclipse will occur in the late afternoon or early evening of May 20 throughout the continent of North America while in Asia the date gets switched to May 21.

However, the other parts of the United States and Canada will be able to see only a partial solar eclipse, without being treated to the ring of fire effect.

The East Coast will miss the event since the sun will have set before the eclipse begins.

The event known as an annular solar eclipse originating from the Latin "annulus," meaning "little ring” should be visible in its full glory from much of Asia, the Pacific region and some of western North America, provided the weather stays clear. 

 

At its peak, the eclipse will block out about 94 percent of the sun's light.

Solar eclipses occur when the moon comes in between the Earth and the sun, casting a shadow on our planet. When the moon lines up perfectly with the sun and blots out all of its light it results into a total eclipse.

Annular eclipses are similar to total eclipses in that the moon lines up with the sun.

Like other types of solar eclipses, annular eclipses are spectacular but a potentially hazardous sky watching events.




Care must be taken while observing them otherwise it can cause serious and permanent eye damage including blindness.

To safely observe the May 21 annular eclipse, special solar filters can be bought to fit over the equipment or No. 14 welder's glass to wear over the eyes.

However the safest and simplest technique is perhaps to watch the eclipse indirectly with the solar projection method.

This technique uses projects a magnified image of the sun's disk onto a shaded white piece of cardboard.

The image on the cardboard will be thus is safe to view and photograph.

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Mark Zuckerberg marries long time girlfriend !!

Mark Zuckerberg marries long time girlfriend Priscilla Chan


Facebook's billionaire founder Mark Zuckerberg updated his relationship status on his social networking site to 'married' - he has tied the knot with his long time girlfriend 27 year old Priscilla Chan in a private ceremony at his California home.

 

 

The surprising move came just a day after Facebook went public through one of the largest initial public offerings and its shares began trading on the Nasdaq.
Zuckerberg wrote about the big event in his life on his Facebook timeline, with a status update that read, "Married Priscilla Chan" on May 19.

The ceremony took place in Zuckerberg's backyard at his Palo Alto home in California before fewer than 100 guests yesterday. An accompanying picture shows a smiling Zuckerberg dressed in a simple dark blue suit, white shirt and wearing a tie. Chan is in an elegant sleeveless laced white wedding gown with a veil falling over her shoulders. A string of bulbs are hung in the background which is Zuckerberg's backyard.

The picture got over 131,000 likes within the first 30 minutes of Zuckerberg posting the status update.

The couple met at Harvard and have been together for more than nine years. Chan's Facebook page also had the updated relationship status with the message "married to Mark Zuckerberg."

The marriage capped an extremely eventful week for the couple. Zuckerberg celebrated his 28th birthday on Monday, May 14. Days later Facebook, which was founded by Zuckerberg in 2004 in his Harvard dorm, became went public through an IPO that pegged the value of the world's most popular social network site at 104 billion dollars.

The same week Chan graduated from the University of California, San Francisco. Chan studied medicine and is now a doctor of pediatrician. On her graduation day, Zuckerberg had written on his Facebook page, "I am so proud of you Dr Chan."

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Asteroid can narrowly miss Earth in February 2013

Asteroid can narrowly miss Earth in February 2013, but may destroy satellites




Madrid, May 20: Astronomers at the LaSagra Observatory in Spain have disclosed that a newly discovered 150-foot-wide asteroid may come so close to the Earth in February that it might hit satellites, Daily Mail reported.
The asteroid named 2012 DA14 can come close enough to Earth to potentially disrupt geosynchronous satellites on February 15, 2013.

However, NASA says the chance of the asteroid hitting Earth is 0.031 percent.

But if it did, it would hit with the force of a 2.4 megaton explosion, similar to the mysterious Tunguska event of 1908 which leveled hundreds of square miles of Siberian forest.

The path of 2012 DA14 as projected through February 15, 2013 shows the asteroid falling inside the orbit of geosynchronous satellites

It is not expected that the path of 2012 DA14 will come anywhere near to hitting Earth in 2013, but scientists have added it to the list of near-Earth objects to examine for its flypast in 2020



At the moment, the exact orbital path of the asteroid is being determined by NASA and astronomers are erring on the side of caution in case it does come in contact with a satellite.

'That's very unlikely, but we can't rule it out,' said Paul Chodas, a planetary astronomer at NASA's Jet Propulsion Laboratory (JPL) in Pasadena California.

While the the asteroid is currently a 'fuzzy little blob', as seen through telescopes, 2012 DA14 may eventually come to pass 21,000 miles away from the Earth putting synchronous satellites in the firing line.

'The orbit for 2012 DA14 is currently very Earth-like, which means it will be very close to Earth on a regular basis,' said Chodas.

2012 DA14 will pass so close that astronomers will be able to observe it with a telescope, but even though satellites might be in danger, the International Space Station is not.

In the preceding months to February, NASA will try to form a fuller picture of where and how close the satellite will get.



'We don't know exactly where it is, and that uncertainty maps through to an uncertainty in the orbit and predictions,' said Steven Chesley, who also works at JPL.

But for now, no one at NASA is worried that the asteroid will hit but say that 2012 DA14 might be visible from Earth as it flies past.

'It might be visible to people with good binoculars or a small telescope,' said Chodas.

Even if 2012 DA14 did hit Earth it would not cause any long term damage to civilization but would cause massive loss of life if it hit a populated centre

'For such a small object, that's really unusual.'

While astronomers examine their initial estimate of a 0.031 percent chance of 2012 DA14 hitting earth, they cannot rule out the possibility of it hitting in 2020 on its next fly-pass.

That is because they will have to see how close 2012 DA14 gets to Earth in February and how much our gravitational pull affects its course for its next fly by in 2020.

If it does hit, scientist believe that its south-bound approach mean that it will hit Antarctica or the Southern Ocean.

In 1908 an unkown object from space caused hundreds of square miles of forest to flatten in Tunguska in Siberia and it is thought that similar damage would be wreaked by 2012 DA14 if it did hit in 2020

The detonation of the 140,000 ton rock would not end civilization but would potentially cause massive loss of life if it hit a populated centre.

In 1908 it is believed that a comet of an asteroid exploded in the skies above Tunguska in Siberia, causing trees for hundreds of square miles to flatten horizontally.

Regardless of any future dangers, NASA agree that it is good to locate these potential dangers, so that we can add 2012 DA14 to the list of near-Earth asteroids.

'We're now on top of it,' said Chelsey.

 

 

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