DNA could store all of the world’s data in one room | Science | AAAS

DNA could store all of the world’s data in one room

Humanity has a data storage problem: More data were created in the past 2 years than in all of preceding history. And that torrent of information may soon outstrip the ability of hard drives to capture it. Now, researchers report that they’ve come up with a new way to encode digital data in DNA to create the highest-density large-scale data storage scheme ever invented. Capable of storing 215 petabytes (215 million gigabytes) in a single gram of DNA, the system could, in principle, store every bit of datum ever recorded by humans in a container about the size and weight of a couple of pickup trucks. But whether the technology takes off may depend on its cost.

DNA has many advantages for storing digital data. It’s ultracompact, and it can last hundreds of thousands of years if kept in a cool, dry place. And as long as human societies are reading and writing DNA, they will be able to decode it. “DNA won’t degrade over time like cassette tapes and CDs, and it won’t become obsolete,” says Yaniv Erlich, a computer scientist at Columbia University. And unlike other high-density approaches, such as manipulating individual atoms on a surface, new technologies can write and read large amounts of DNA at a time, allowing it to be scaled up.

Scientists have been storing digital data in DNA since 2012. That was when Harvard University geneticists George Church, Sri Kosuri, and colleagues encoded a 52,000-word book in thousands of snippets of DNA, using strands of DNA’s four-letter alphabet of A, G, T, and C to encode the 0s and 1s of the digitized file. Their particular encoding scheme was relatively inefficient, however, and could store only 1.28 petabytes per gram of DNA. Other approaches have done better. But none has been able to store more than half of what researchers think DNA can actually handle, about 1.8 bits of data per nucleotide of DNA. (The number isn’t 2 bits because of rare, but inevitable, DNA writing and reading errors.)

Erlich thought he could get closer to that limit. So he and Dina Zielinski, an associate scientist at the New York Genome Center, looked at the algorithms that were being used to encode and decode the data. They started with six files, including a full computer operating system, a computer virus, an 1895 French film called Arrival of a Train at La Ciotat, and a 1948 study by information theorist Claude Shannon. They first converted the files into binary strings of 1s and 0s, compressed them into one master file, and then split the data into short strings of binary code. They devised an algorithm called a DNA fountain, which randomly packaged the strings into so-called droplets, to which they added extra tags to help reassemble them in the proper order later. In all, the researchers generated a digital list of 72,000 DNA strands, each 200 bases long.

They sent these as text files to Twist Bioscience, a San Francisco, California–based startup, which then synthesized the DNA strands. Two weeks later, Erlich and Zielinski received in the mail a vial with a speck of DNA encoding their files. To decode them, the pair used modern DNA sequencing technology. The sequences were fed into a computer, which translated the genetic code back into binary and used the tags to reassemble the six original files. The approach worked so well that the new files contained no errors, they report today in Science. They were also able to make a virtually unlimited number of error-free copies of their files through polymerase chain reaction, a standard DNA copying technique. What’s more, Erlich says, they were able to encode 1.6 bits of data per nucleotide, 60% better than any group had done before and 85% the theoretical limit.

“I love the work,” says Kosuri, who is now a biochemist at the University of California, Los Angeles. “I think this is essentially the definitive study that shows you can [store data in DNA] at scale.”

However, Kosuri and Erlich note the new approach isn’t ready for large-scale use yet. It cost $7000 to synthesize the 2 megabytes of data in the files, and another $2000 to read it. The cost is likely to come down over time, but it still has a long ways to go, Erlich says. And compared with other forms of data storage, writing and reading to DNA is relatively slow. So the new approach isn’t likely to fly if data are needed instantly, but it would be better suited for archival applications. Then again, who knows? Perhaps those giant Facebook and Amazon data centers will one day be replaced by a couple of pickup trucks of DNA.

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doi:10.1126/science.aal0852

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Warm for the Holidays

Meet Veronika Scott. As a 22 year old Product Design student at the College for Creative Studies in Detroit, Veronica took professor Steve Schock‘s class on Design Activism and it changed her life.

As her class project, Veronika spent hours at a homeless shelter and with the help of their residents, developed a coat that also doubles as a sleeping bag at night and a shoulder bag when not in use.  The Element S (survival),  now called the EMPWR Coat, is self heated, and waterproof .  The coat not only filled a need in the community, but became a way for Scott to improve the lives of others.

Ms. Scott stepped up and decided to do more than help the homeless stay warm in the cold Michigan winters, she began to hire people from local shelters and help them work their way out of homelessness. Her nonprofit organization, “The Empowerment Plan“,  centers around lifting single parents out of homelessness by providing them with training and work making coats.

Over 34 families now have permanent housing thanks to a 20-something with a good idea, and a good heart. Together they have made over 15.000 EMPWR coats distributed across North America.

Good for you Veronika!  Thanks for keeping us all warm for the holidays.

 

Camille A. Brown: A visual history of social dance in 25 moves

Lovely (only 4 minutes) TED Studio Talk with
Camille A. Brown, Choreographer and educator
Camille A. Brown leads her dance company through excavations of ancestral stories, both timeless and traditional, that connect history with contemporary culture. Full bio
Why do we dance? African-American social dances started as a way for enslaved Africans to keep cultural traditions alive and retain a sense of inner freedom. They remain an affirmation of identity and independence. In this electric demonstration, packed with live performances, choreographer, educator and TED Fellow Camille A. Brown explores what happens when communities let loose and express themselves by dancing together.

Learning From Data: An Intiguing Link between Police Shootings and Black Voter Registration

To understand how black Americans are impacted by fatal police shootings in each state, we defined an “over-representation ratio”: the percentage of fatal police shootings in which a black American was killed divided by percentage of black Americans in a state. The number one determinant of over-representation in fatal police shootings is the percentage of eligible black Americans registered to vote.

WIRED/MAIMUNA SHAHNAZ MAJUMDER

I found a very interesting piece in Wired Magazine, demonstrating a link between police shootings and voter registration, written by an equally interesting person.  I encourage you to read more about Maia Majumder and her article.

aaeaaqaaaaaaaahxaaaajdiwndc5yzixltyxztitndy4my05mdm2lwnlyjy3zju2ntmwzgMaimuna (Maia) Majumder is an Engineering Systems PhD candidate at MIT and computational epidemiology research fellow at HealthMap. Before coming to MIT, she earned a Bachelors of Science in Engineering Science and a Masters of Public Health in Epidemiology and Biostatistics at Tufts University. Her research interests involve probabilistic modeling, Bayesian statistics, and “systems epidemiology” in the context of emerging infectious diseases. She also enjoys exploring novel techniques for data procurement, writing about data for the general public, and creating meaningful data visualizations. When taking a break from work, Maia moonlights as a jazz vocalist, budding chef, and primal wellness enthusiast who loves Bikram yoga, Zumba, & lifting heavy objects with her awesome husband, Imran Malek.

An Intriguing Link Between Police Shootings and Black Voter Registration

Since January 1, 2016, there have been 714 fatal police shootings in the United States. That comes to 79 deaths a month, 18 a week, and three a day. For context, the US recorded 43 cases of locally transmitted Zika virus and 25 deaths from West Nile in the same time frame.

For most, if not all, public health issues, some segments of the population are more vulnerable than others. Americans who engage in unprotected sex are more likely to contract Zika virus, while older people are more likely to die from West Nile.

Read the full article here


 

 

University professor and students save lives with their inventions

2016 MacArthur Fellow, Rebecca Richards-Kortum is amazing.  The Rice University bioengineering professor has inspired her students to invent  new low cost medical technologies for the third world that are remarkable.

New medical technologies created by BTB students include an LED-based phototherapy light for treating jaundice in newborns that can be made for less than $100, and a bubble continuous positive airway pressure machine (bCPAP) for premature infants unable to breathe on their own. The bCPAP decreased mortality rates in a Malawi neonatal ward by 46 percent at a cost of nearly 38 times lower than the standard model.

Committed to improving access to quality health care for all the world’s people, Richards-Kortum is not only developing novel solutions but also training and inspiring the next generation of engineers and scientists to address our shared global challenges.

For more about the work of the good professor and her students at Rice University in Houston, see the following:

MacArthur Foundation:  https://www.macfound.org/fellows/970/

NPR Morning Edition segment:  ‘Genius Grant’ Winner Is A Genius At Inspiring Students

“THE RECYCLED ORCHESTRA” EXHIBIT AT MIM

On exhibit now at the Musical Instrument Museum

Exhibit displays instruments from remarkable group

Amid a massive landfill in Cateura, Paraguay, children find hope by making music on instruments built from recycled trash. In a slum town where families survive by collecting and reselling garbage (and where a violin can cost more than a house), a visionary music teacher gathered a small team to plunder the landfill for materials and construct an ensemble of “recycled” instruments. In just a few years, their innovation has led to a thriving music school in Cateura and a youth orchestra that performs internationally. For members of the Recycled Orchestra, material poverty is not an obstacle to a life rich with music. They have each learned to value greatly how music impacts their lives, helping them express creativity, build self-confidence, and strengthen community.

The Musical Instrument Museum features the inspiring story and the innovative instruments of the Recycled Orchestra through a Latin America gallery exhibit and docent mini-tours. The Recycled Orchestra exhibit features eight recycled instruments from Paraguay as well as video and images of the youth orchestra and the environment of Cateura.

The Hottest Year on Record … 2016

The scorching temperatures mean 2016 is all but certain to be the hottest year ever recorded, beating the previous hottest year in 2015, which itself beat 2014. This run of three record years is also unprecedented and, without climate change, would be a one in a million chance. Scaife says: “Including this year so far, 16 of the 17 warmest years on record have been since 2000 – it’s a shocking statistic.”

Shattered records show climate change is an emergency today, scientists warn

Unprecedented temperature levels mean more heatwaves, flooding, wildfires and hurricanes as experts say global warming is here and affecting us now

Read more about the science and realities of climate change in this article by Damian Carrington of The Guardian.

New Gecko-Inspired Adhesive

From The Scientist:  http://www.the-scientist.com/?articles.view/articleNo/45741/title/New-Gecko-Inspired-Adhesive/

By Jef Akst | April 6, 2016

New Gecko-Inspired Adhesive

Flexible patches of silicone that stick to skin and conduct electricity could serve as the basis for a new, reusable electrode for medical applications.

For years, researchers have recreated the microscopic hair-like pillars on gecko feet that, through atomic forces known as van der Waals’ interactions, allow the animals to scurry up walls and across ceilings. Such gecko-inspired adhesives could have a variety of applications, including medical bandages, but materials scientist Seokwoo Jeon at the Korea Advanced Institute of Science and Technology (KAIST) and colleagues wanted to apply these materials to create a novel wearable electrode.

Read more of Jef’s article in The Scientist here:

 

Italy rules that stealing food not a crime if desperately hungry

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The right to survival prevails over property,” Italy’s highest court of appeals ruled this week when reviewing the case of a homeless man who had been given a six month jail sentence and a €100 euro fine for stealing cheese and sausages.

The man was caught before leaving the store and returned the goods, so the state prosecutor argued for the sentence to be reduced from “theft” to “attempted theft.”

But when the court of appeals heard the case, they radically upended the decision. This wasn’t worthy of punishment, they argued. In fact, taking food to stave off hunger should not even be considered a crime.

The judges wrote that the food had been taken “in the face of the immediate and essential need for nourishment.”

They also rebuked the entire process that brought this case before them–an attempt to take less than €5 of food went through 3 rounds of court hearings.

Italy, like large parts of the world, is coping with a recession. Each day, 615 people in Italy fall into poverty, according an op-ed in response to the ruling, many of whom struggle to find housing and food. Forgetting about these people is not an option, the piece argued.

Another op-ed argued that the ruling aligned with one of the most fundamental pillars of Western legal thinking–the concept of humanity that says a person’s dignity should be protected and that dignity rises when basic needs like food, water, housing and security are met.

On one level, this ruling attempts to return sense, discretion and an appreciation of context to criminal justice. Why, after all, was it necessary to spend so many resources to punish a man suffering from hunger, especially when this punishment will only deepen his poverty? Why not, instead, provide food for this person?

On another level, this ruling is a radical rethinking of human rights. Sure, it connects to ancient ideas of “humanity,” but these ideas have never fully been practiced on a large scale. The thought of a homeless person walking into a grocery store and just taking food without paying for it is, in a way, a radical affront to the market-based logic that rules most societies. If you want food, you pay for it just like everyone else, right?

Then there’s a more mundane explanation to all of this. Recently, Italy passed a law requiring all sellers of food to donate unsold food to charities rather than throw it away. So this decision may have been made under the aegis of the new legislation.

But even still–in a world of abundance, should the vagaries of circumstance–job loss, illness, traumas–ever leave a person without the ability to get food?

When grocery stores around the world are stuffed with food, is it moral to allow someone to suffer from hunger?

These are challenging questions that strike at the core of many societal arrangements. But they’re questions that are worth asking, and finding some compromise for, in a time when inequality is rising and more people find themselves in economically distressed situations.

Globally, 795 million people do not have enough food to lead normal, healthy lives. Many more people struggle to buy and find food every day.

It’s unlikely that this ruling in Italy will lead to widespread theft from grocery stores and it’s cynical to suggest that a breakdown in the rule of law will follow (as some critics have suggested).

The more likely result will be an evaluation of what really matters in life and how much another person’s humanity should be respected.

In an ideal world, there would be consensus that a person’s dignity is the top priority in any situation and from there other rules based on other, secondary considerations would apply.

Read More @ Global Citizen