New organisms have been formed using the first ever 6-letter genetic code

New organisms have been formed using the first ever 6-letter genetic code
This could be the beginning of a whole new life form.
By Bec Crew
Jan 24 2017
http://www.sciencealert.com/new-organisms-have-been-formed-using-the-first-ever-6-letter-genetic-code

Scientists have engineered the first ever ‘semi-synthetic’ organisms, by breeding E. coli bacteria with an expanded, six-letter genetic code.

While every living thing on Earth is formed according to a DNA code made up of four bases (represented by the letters G, T, C and A), these modified E. coli carry an entirely new type of DNA, with two additional DNA bases, X and Y, nestled in their genetic code.

The team, led by Floyd Romesberg from the Scripps Research Institute in California, engineered synthetic nucleotides – molecules that serve as the building blocks of DNA and RNA – to create an additional base pair, and they’ve successfully inserted this into the E. coli’s genetic code.

Now we have the world’s first semi-synthetic organism, with a genetic code made up of two natural base pairs and an additional ‘alien’ base pair, and Romesberg and his team suspect that this is just the beginning for this new form of life.

“With the virtually unrestricted ability to maintain increased information, the optimised semi-synthetic organism now provides a suitable platform [to] … create organisms with wholly unnatural attributes and traits not found elsewhere in nature,” the researchers report.

“This semi-synthetic organism constitutes a stable form of semi-synthetic life, and lays the foundation for efforts to impart life with new forms and functions.”

Back in 2014, the team announced that they had successfully engineered a synthetic DNA base pair – made from molecules referred to as X and Y – and it could be inserted into a living organism.

Since then, they’ve been working on getting their modified E. coli bacteria to not only take the synthetic base pair into their DNA code, but hold onto it for their entire lifespan.

Initially, the engineered bacteria were weak and sickly, and would die soon after they received their new base pair, because they couldn’t hold onto it as they divided.

“Your genome isn’t just stable for a day,” says Romesberg. “Your genome has to be stable for the scale of your lifetime. If the semisynthetic organism is going to really be an organism, it has to be able to stably maintain that information.”

Over the next couple of years, the team devised three methods to engineer a new version of the E. coli bacteria that would hold onto their new base pair indefinitely, allowing them to live normal, healthy lives.

The first step was to build a better version of a tool called a nucleotide transporter, which transports pieces of the synthetic base pair into the bacteria’s DNA, and inserts it into the right place in the genetic code.

“The transporter was used in the 2014 study, but it made the semisynthetic organism very sick,” explains one of the team, Yorke Zhang.

Once they’d altered the transporter to be less toxic, the bacteria no longer had an adverse reaction to it.

[snip]

The merging of humans and machines is happening now

The merging of humans and machines is happening now
Her organisation invented the internet. It gave us the self-driving car. And now DARPA’s former boss sees us crossing a new technological boundary
By ARATI PRABHAKAR
Jan 28 2017
http://www.wired.co.uk/article/darpa-arati-prabhakar-humans-machines

The merging of machine capability and human consciousness is already happening. Writing exclusively for WIRED, DARPA director Arati Prabhkar outlines the potential rewards we face in the future – and the risks we face

Peter Sorger and Ben Gyori are brainstorming with a computer in a laboratory at Harvard Medical School. Their goal is to figure out why a powerful melanoma drug stops helping patients after a few months. But if their approach to human-computer collaboration is successful, it could generate a new approach to fundamentally understanding complexities that may change not only how cancer patients are treated, but also how innovation and discovery are pursued in countless other domains.

At the heart of their challenge is the crazily complicated hairball of activity going on inside a cancer cell – or in any cell. Untold thousands of interacting biochemical processes, constantly morphing, depending on which genes are most active and what’s going on around them. Sorger and Gyori know from studies of cells taken from treated patients that the melanoma drug’s loss of efficacy over time correlates with increased activity of two genes. But with so many factors directly or indirectly affecting those genes, and only a relatively crude model of those global interactions available, it’s impossible to determine which actors in the cell they might want to target with additional drugs.

That’s where the team’s novel computer system comes in. All Sorger and Gyori have to do is type in a new idea they have about the interactions among three proteins, based on a mix of clinical evidence, their deep scientific expertise, and good old human intuition. The system instantly considers the team’s thinking and generates hundreds of new differential equations, enriching and improving its previous analytical model of the myriad activities inside drug-treated cells. And then it spits out new results.

These don’t predict all the relevant observations from tumour cells, but it gives the researchers another idea involving two more proteins – which they shoot back on their keyboard. The computer churns and responds with a new round of analysis, producing a model that, it turns out, predicts exactly what happens in patients and offers new clues about how to prevent some cases of melanoma recurrence.

In a sense, Sorger and Gyori do what scientists have done for centuries with one another: engage in ideation and a series of what-ifs. But in this case, their intellectual partner is a machine that builds, stores, computes and iterates on all those hundreds of equations and connections.

The combination of insights from the researchers and their computer creates a model that does not simply document correlations – “When you see more of this, you’ll likely see more of that” – but rather starts to unveil the all-important middle steps and linkages of cause and effect, the how and why of molecular interactions, instead of just the what. In doing so, they make a jump from big data to deep understanding.

More than 3,220km away, another kind of human-machine collaboration unfolds at the University of Utah as Greg Clark asks Doug Fleenor to reach out and touch the image of a wooden door on a computer monitor.

Clark knows that Fleenor cannot physically touch this or any other object; Fleenor lost both his hands in a near-fatal electrical accident 25 years ago. But Fleenor’s arm has a chip in it that communicates with the computer, so when he moves his arm the image of a hand on the monitor also moves. He’s done this before – raising his arm, watching the cartoon hand move in sync and seemingly stroke
the face of the door – but this time it’s different. He lurches back and gasps. “That is so cool!” he blurts.

What’s so cool is that as he guides his virtual hand across that virtual plank, he literally, biologically and neurologically, feels its wooden surface. Thanks to some new software and an array of fine electrical connections between another embedded chip and the nerves running up his arm to his brain, he experiences a synthesised sensation of touch and texture indistinguishable from a tactile event.

For someone who hasn’t actually touched anything with his hands for a quarter of a century, this is a transcendent moment – one that points to a remarkable future that is now becoming real… and in Fleenor’s case, even tangible.

In ways as diverse as a shared understanding of causal complexity as in Peter Sorger’s lab and the seamless commingling of software and wetware as in Greg Clark’s lab, it’s a future in which humans and machines will not just work side by side, but rather will interact and collaborate with such a degree of intimacy that the distinction between us and them will become almost imperceptible.

[snip]

The Human Toll of Protecting the Internet from the Worst of Humanity

The Human Toll of Protecting the Internet from the Worst of Humanity
By Adrian Chen
Jan 28 2017
http://www.newyorker.com/tech/elements/the-human-toll-of-protecting-the-internet-from-the-worst-of-humanity

Henry Soto worked for Microsoft’s online-safety team, in Seattle, for eight years. He reviewed objectionable material on Microsoft’s products—Bing, the cloud-storage service OneDrive, and Xbox Live among them—and decided whether to delete it or report it to the police. Each day, Soto looked at thousands of disturbing images and videos, which included depictions of killings and child abuse. Particularly traumatic was a video of a girl being sexually abused and then murdered. The work took a heavy toll. He developed symptoms of P.T.S.D., including insomnia, nightmares, anxiety, and auditory hallucinations. He began to have trouble spending time around his son, because it triggered traumatic memories. In February, 2015, he went on medical leave.

This story is laid out in a lawsuit filed against Microsoft, late last year, by Soto and a colleague named Greg Blauert, and first reported by Courthouse News Service. Soto and Blauert claim that the company did not prepare them for the stress of the job, nor did it offer adequate counselling and other measures to mitigate the psychological harm. Microsoft disputes Soto’s story, telling the Guardian in a statement that it “takes seriously its responsibility to remove and report imagery of child sexual exploitation and abuse being shared on its services, as well as the health and resiliency of the employees who do this important work.”

The lawsuit offers a rare look into a little-known field of digital work known as content moderation. Even technology that seems to exist only as data on a server rests on tedious and potentially dangerous human labor. Although algorithms and artificial intelligence have helped streamline the process of moderation, most technology companies that host user-generated content employ moderators like Soto to screen video, text, and images, to see if they violate company guidelines. But the labor of content moderators is pretty much invisible, since it manifests not in flashy new features or viral videos but in a lack of filth and abuse. Often, the moderators are workers in developing countries, like the Philippines or India, or low-paid contractors in the United States. There’s no reliable figure for how many people are employed in this line of work, but it’s certainly in the tens of thousands. Content moderators are recent college graduates and stay-at-home mothers, remote workers in Morocco and employees sitting in giant outsourcing companies in Manila. The number of moderators will only increase, as more of our lives are lived online, requiring more and more policing. Whenever I share on Twitter an article about content moderation, I’m always struck by the number of people who tell me that they’ve done the work and how psychologically difficult they found it.

Regardless of the merits of Soto’s specific case, constant exposure to the worst of humanity on a daily basis takes an undeniable toll. One former moderator for Facebook described it to me: “Think like that there is a sewer channel and all of the mess/dirt/waste/shit of the world flow towards you and you have to clean it.” A former moderator for YouTube told me that constant exposure to brutal combat and animal-abuse videos sent him into a depression. Studies that examine the impact that exposure to disturbing content has on moderators are rare, but there have been a number of studies of law-enforcement officers who investigate computer crimes. A study, conducted by the U.S. Marshals Service, of six hundred employees of the Justice Department’s Internet Crimes Against Children task force, suggested that a quarter of the investigators surveyed displayed symptoms of secondary traumatic-stress disorder, which is akin to P.T.S.D., but is caused by indirect exposure to trauma.

Tech companies don’t like to talk about the details of content moderation, so it’s difficult to judge how well they’re caring for the psychological health of moderators. Silicon Valley’s optimistic brand does not fit well with frank discussions of beheading videos and child-molestation images. Social-media companies are also not eager to highlight the extent to which they set limits on our expression in the digital age—think of the recurring censorship controversies involving deleted Facebook pages and Twitter accounts. In 2013, an internal Facebook moderation document was leaked, revealing that Facebook moderators were instructed to flag all attacks on Kemal Atatürk, the founder of modern Turkey. Kurdish users critical of the Turkish government protested the company’s actions. Leaving the moderation process opaque offers a degree of flexibility and plausible deniability when dealing with politically sensitive issues.

[snip]

The Rise (And Possible Untimely Fall) Of Rogue Government Twitter

The Rise (And Possible Untimely Fall) Of Rogue Government Twitter
The resistance may not be tweeted after all
By Allee Manning
Jan 26 2017
http://www.vocativ.com/396847/rogue-government-twitter/

Over 40 “rogue” Twitter accounts sprang up earlier this week after the Trump administration reportedly imposed gag orders on several federal agencies. The users behind some of these accounts, such as AltYellowstoneNatPark and AltEPA, claim to be employees of the agencies and sites they are representing, while others acknowledged that they were not associated with the entities they have decided to represent.

The accounts quickly became a viral sensation, sending out sassy messages of dissent, underscoring the truth about climate change, sharing support for the people of Standing Rock in the face of the now imminent Dakota Access Pipeline, and promoting the planned Scientists’ March On Washington.

In the short time that these accounts have sprung up, they’ve amassed massive followings. @AltNatParkSer, he largest “unofficial ‘resistance’” account for the National Parks Service has over one million followers as of Thursday morning, more than two and a half times that of the actual agency account.

These accounts popped up when Interior Department employees were ordered to stop tweeting to its account after the National Park Service retweeted a side-by-side photo that showed a smaller crowd at Trump’s inauguration compared to Obama’s inauguration in 2009, according to an AP report.

But already, some of those manning the rogue accounts announced that they are relinquishing control to “non-federal workers” for fear of losing their jobs.

Under the Hatch Act, which the “Rogue NASA” account is citing as its reason for passing ownership on to people who are not NASA employees, it is illegal for members of the federal workforce to engage on “partisan political activity on official duty time; on federal property; while wearing a uniform or insignia identifying them as federal officials or employees.” Other concerns have been raised over the fact that many of these “alt” or “resistance” accounts bear the official logo of the department they are identifying without proper authorization.

In an apparent effort to ensure they are not in violation of Twitter’s impersonation policy, many of these account holders have been adding language like “not official” and “not affiliated” to their bios.

“It’s not up to the administration to censor scientific research,” a person claiming to be a writer working in tandem with three mid-level and senior climate change scientists with the EPA for the @ActualEPAFacts told Vocativ over a Twitter Direct Message.

[snip]

How Life (and Death) Spring From Disorder

How Life (and Death) Spring From Disorder
Life was long thought to obey its own set of rules. But as simple systems show signs of lifelike behavior, scientists are arguing about whether this apparent complexity is all a consequence of thermodynamics.
By Philip Ball
Jan 26 2017
https://www.quantamagazine.org/20170126-information-theory-and-the-foundation-of-life/

What’s the difference between physics and biology? Take a golf ball and a cannonball and drop them off the Tower of Pisa. The laws of physics allow you to predict their trajectories pretty much as accurately as you could wish for.

Now do the same experiment again, but replace the cannonball with a pigeon.

Biological systems don’t defy physical laws, of course — but neither do they seem to be predicted by them. In contrast, they are goal-directed: survive and reproduce. We can say that they have a purpose — or what philosophers have traditionally called a teleology — that guides their behavior.

By the same token, physics now lets us predict, starting from the state of the universe a billionth of a second after the Big Bang, what it looks like today. But no one imagines that the appearance of the first primitive cells on Earth led predictably to the human race. Laws do not, it seems, dictate the course of evolution.

The teleology and historical contingency of biology, said the evolutionary biologist Ernst Mayr, make it unique among the sciences. Both of these features stem from perhaps biology’s only general guiding principle: evolution. It depends on chance and randomness, but natural selection gives it the appearance of intention and purpose. Animals are drawn to water not by some magnetic attraction, but because of their instinct, their intention, to survive. Legs serve the purpose of, among other things, taking us to the water.

Mayr claimed that these features make biology exceptional — a law unto itself. But recent developments in nonequilibrium physics, complex systems science and information theory are challenging that view.

Once we regard living things as agents performing a computation — collecting and storing information about an unpredictable environment — capacities and considerations such as replication, adaptation, agency, purpose and meaning can be understood as arising not from evolutionary improvisation, but as inevitable corollaries of physical laws. In other words, there appears to be a kind of physics of things doing stuff, and evolving to do stuff. Meaning and intention — thought to be the defining characteristics of living systems — may then emerge naturally through the laws of thermodynamics and statistical mechanics.

This past November, physicists, mathematicians and computer scientists came together with evolutionary and molecular biologists to talk — and sometimes argue — about these ideas at a workshop at the Santa Fe Institute in New Mexico, the mecca for the science of “complex systems.” They asked: Just how special (or not) is biology?

It’s hardly surprising that there was no consensus. But one message that emerged very clearly was that, if there’s a kind of physics behind biological teleology and agency, it has something to do with the same concept that seems to have become installed at the heart of fundamental physics itself: information.

[snip]

In Venezuela, we couldn’t stop Chávez. Don’t make the same mistakes we did.

In Venezuela, we couldn’t stop Chávez. Don’t make the same mistakes we did.
By Andrés Miguel Rondón
Jan 27 2017
https://www.washingtonpost.com/amphtml/posteverything/wp/2017/01/27/in-venezuela-we-couldnt-stop-chavez-dont-make-the-same-mistakes-we-did/

Donald Trump is an avowed capitalist; Hugo Chávez was a socialist with communist dreams. One builds skyscrapers, the other expropriated them. But politics is only one-half policy: The other, darker half is rhetoric. Sometimes the rhetoric takes over. Such has been our lot in Venezuela for the past two decades — and such is yours now, Americans. Because in one regard, Trump and Chávez are identical. They are both masters of populism.

The recipe for populism is universal. Find a wound common to many, find someone to blame for it, and make up a good story to tell. Mix it all together. Tell the wounded you know how they feel. That you found the bad guys. Label them: the minorities, the politicians, the businessmen. Caricature them. As vermin, evil masterminds, haters and losers, you name it. Then paint yourself as the savior. Capture the people’s imagination. Forget about policies and plans, just enrapture them with a tale. One that starts with anger and ends in vengeance. A vengeance they can participate in.

That’s how it becomes a movement. There’s something soothing in all that anger. Populism is built on the irresistible allure of simplicity. The narcotic of the simple answer to an intractable question. The problem is now made simple.

The problem is you.

How do I know? Because I grew up as the “you” Trump is about to turn you into. In Venezuela, the urban middle class I come from was cast as the enemy in the political struggle that followed Chávez’s arrival in 1998. For years, I watched in frustration as the opposition failed to do anything about the catastrophe overtaking our nation. Only later did I realize that this failure was self-inflicted. So now, to my American friends, here is some advice on how to avoid Venezuela’s mistakes.

• Don’t forget who the enemy is.

Populism can survive only amid polarization. It works through the unending vilification of a cartoonish enemy. Never forget that you’re that enemy. Trump needs you to be the enemy, just like all religions need a demon. A scapegoat. “But facts!” you’ll say, missing the point entirely.

What makes you the enemy? It’s very simple to a populist: If you’re not a victim, you’re a culprit.

During the 2007 student-led protests against the government’s closure of RCTV , then the second-biggest TV channel in Venezuela, Chávez continually went on air to frame us students as “pups of the American Empire,” “supporters of the enemy of the country” — spoiled, unpatriotic babies who only wanted to watch soap operas. Using our socioeconomic background as his main accusation, he sought to frame us as the direct inheritors of the mostly imagined “oligarchs” of our fathers’ generation. The students who supported Chavismo were “children of the homeland,” “sons of the people,” “the future of the country.” Not for one moment did the government’s analysis go beyond such cartoons.

[snip]

Inequality and life expectancy

[Note: This item comes from friend David Rosenthal. DLH]

From: “David S. H. Rosenthal” <dshr@abitare.org>
Subject: Inequality and life expectancy
Date: January 28, 2017 at 1:24:39 PM EST
To: dewayne@warpspeed.com

https://www.ft.com/content/80a76f38-e3be-11e6-8405-9e5580d6e5fb

Yves Smith writes:
http://www.nakedcapitalism.com/2017/01/links-12817.html

The huge disparities in US life expectancy in five charts Financial Times. Today’s must read. Clear cookies and Google the headline if you must. Not only has life expectancy fallen for the poor, notice no life expectancy gains for women, even upper middle class women, only for the richest. And in a huge reversal of historical patterns, middle and upper middle class men have longer life expectancies than women.

Also via Yves:

https://theintercept.com/2017/01/27/federal-reserve-bankers-mocked-unemployed-americans-behind-closed-doors/

and:

http://fair.org/home/its-austerity-not-globalization-that-pulls-european-workers-to-the-right/

David.