Scanner spies document secrets
Source: Isis Innovation
13 Sep 11
The Oxford Multi Spectral scanner was developed for imaging ancient papyri. Photo: OMS
A scanner which combines the convenience of a desktop scanner with the functionality of a powerful laboratory imaging device has been developed at the University of Oxford’s Faculty of Classics, and is now being commercialised by a new company Oxford Multi Spectral Limited which was today spun out by the University’s technology transfer company Isis Innovation.
The scanner was developed for imaging ancient papyri and the technology has been used to successfully scan, restore and archive over a quarter of a million historically significant manuscripts.
Oxford Multi Spectral Limited (OMS) will focus on the applications in restoring manuscripts and art, as well as the huge potential market for detecting forged security and border control documents, bank notes and forensic evidence.
More...
http://www.ox.ac.uk/media/news_stories/2011/130911.html
TECHNOLOGY AND DEVELOPMENT
September 29, 2011, 7:55 pm
Making Change Happen, on a Deadline
By TINA ROSENBERG
Rapid Results, a strategy designed for corporations, is helping communities in Africa set goals and solve problems in 100 days or less.
Excerpt:
"PreFabricated surpassed its goal using a strategy called Rapid Results, in which a group of people choose a project and carry it out in 100 days. Companies in Addis that used Rapid Results got their H.I.V. testing rates up to about 75 percent — triple the norm. The same method has been used in Nicaragua to help pig farmers raise fatter pigs and to improve dairy farms’ milk quality. In Rwanda, two villages doubled the number of attended births in less than 100 days, and the Rapid Results team went on to work on other projects to protect mothers’ health. In Madagascar, four districts quintupled the use of family planning services in 50 days, and the Health Ministry then began the program on a national scale. Kenya is using Rapid Results in virtually all its ministries; one campaign in the province of Nyanza circumcised 40,000 men in two months — a crucial achievement for AIDS prevention. Rapid Results has made Kenya by far the leader in Africa in scaling up circumcision. Villages in Ghana, Sierra Leone, Sudan, Eritrea and other countries have used Rapid Results to improve local infrastructure as well — digging wells, constructing bridges and roads, building schools.
Rapid Results is an eccentric idea. Nadim Matta, a management consultant who is president of the Rapid Results Institute in Stamford, Conn., likes to say that what’s missing to turn poor places into rich places isn’t more information, money, technology, workshops, programs, evaluation or any of the other things that development organizations normally provide. What’s missing are motivation and confidence.
At first glance, this seems crazy — can we cheerlead our way into the middle class?"
http://opinionator.blogs.nytimes.com/20 ... n&emc=tya1
Making Change Happen, on a Deadline
By TINA ROSENBERG
Rapid Results, a strategy designed for corporations, is helping communities in Africa set goals and solve problems in 100 days or less.
Excerpt:
"PreFabricated surpassed its goal using a strategy called Rapid Results, in which a group of people choose a project and carry it out in 100 days. Companies in Addis that used Rapid Results got their H.I.V. testing rates up to about 75 percent — triple the norm. The same method has been used in Nicaragua to help pig farmers raise fatter pigs and to improve dairy farms’ milk quality. In Rwanda, two villages doubled the number of attended births in less than 100 days, and the Rapid Results team went on to work on other projects to protect mothers’ health. In Madagascar, four districts quintupled the use of family planning services in 50 days, and the Health Ministry then began the program on a national scale. Kenya is using Rapid Results in virtually all its ministries; one campaign in the province of Nyanza circumcised 40,000 men in two months — a crucial achievement for AIDS prevention. Rapid Results has made Kenya by far the leader in Africa in scaling up circumcision. Villages in Ghana, Sierra Leone, Sudan, Eritrea and other countries have used Rapid Results to improve local infrastructure as well — digging wells, constructing bridges and roads, building schools.
Rapid Results is an eccentric idea. Nadim Matta, a management consultant who is president of the Rapid Results Institute in Stamford, Conn., likes to say that what’s missing to turn poor places into rich places isn’t more information, money, technology, workshops, programs, evaluation or any of the other things that development organizations normally provide. What’s missing are motivation and confidence.
At first glance, this seems crazy — can we cheerlead our way into the middle class?"
http://opinionator.blogs.nytimes.com/20 ... n&emc=tya1
October 3, 2011, 2:30 pm
Disrupters and Adapters, Continued: Will the Internet Save Newspapers?
The two visions of higher education’s future I described in my column this week – Stanford Professor Sebastian Thrun’s mission of a virtual university and Stanford President John Hennessy’s devotion to a flesh-and-blood campus – intrigued me because of the larger context. So much of the debate about the impact of new technology tends to be polarizing. The utopians versus the skeptics, the idealists versus the realists, those who throw themselves headlong into the great mosh pit of the new, and those who cherish the familiar and time-honored.
To the champions of the new, those who hesitate are Luddites and curmudgeons and reactionaries, destined to be left behind in the march of civilization. (I speak from some experience. The response to recent columns, in which I suggested that social media and news aggregation have their downsides, taught me that, whatever limitations Twitter may have as a vehicle for discussion, it is an excellent medium for name-calling.) To those who have not chosen to move their social lives to Facebook and Google+, or who believe that maybe content doesn’t necessarily want to be free, the digiphiles can sometimes feel a little like a cult of scolds.
What struck me about the rival views of higher education is that it is not so much a stark choice as a kind of tense synergy between old and new. As digital access continues to spread and technologies like telepresence and virtual reality improve, the Web will offer ever better education to wider and wider audiences at lower and lower prices. Education, to borrow a Tom Friedmanism, will be flatter. But there will still be nodes of excellence, actual campuses offering actual human contact.
Hennessy, not surprisingly, stresses the virtues of the non-virtual, especially for undergraduates, and especially in liberal arts. Proximity has real advantages in refining the skills of thought and expression, and nothing quite matches the experience of coexisting with people of diverse backgrounds. Thrun concedes a residential campus is “a fantastic experience.” “Many people find their life partner,” he added. “You hang out with people who are pre-selected to be successful people.” And the extraordinary alliance Stanford has forged with the city of Palo Alto has proven that, sometimes, location can generate explosive creativity. Technology will surely supplant some of the expensive infrastructure of a top college degree, but it is a long, long way from replicating the experience.
You may find yourself more drawn more to Thrun’s status-quo-disrupting mission of delivering education to the masses, or you may find your heart is with Hennessy’s not-quite-so-fast defense of a university system that has produced generations of great scholars. But it is entirely plausible to find them both indispensable.
I think the same thing can be said of many industries, including my own. What doesn’t kill you makes you stronger.
Technology upended the music business – except that today there are more musical choices, more widely accessible, at a reasonable price. (And you can still buy your music on vinyl if you like.) Technology was supposed to render books irrelevant – until eBooks came along to save them. (And you can still buy books in print.)
I think the same may well prove true of the newspaper business – that, having assisted in the death of many newspapers, technology will save those that adapt.
By the way, to digress for a minute, those who say the Internet killed newspapers should review their history. For one thing, nobody has killed more newspapers than newspaper publishers, who culled competition to create monopoly markets. When I left the staff of The Oregonian in 1979, Portland had two daily newspapers. Three years later the Newhouse chain (which owned both of them) closed the afternoon paper. When I left the staff of the Dallas Times Herald in 1985, it was one of two good newspapers jostling for primacy in that city. In 1991, the Belo Corporation, owner of the rival Dallas Morning News, bought the Times Herald for $55 million, and shut it down the next day. It’s no surprise that many of the cities that had newspapers die in recent years have been two-paper cities where the papers had been kept on life support by joint operating agreements. Their demise is sad, but it was a long time coming.
Nor can the Internet be blamed for the Great Recession, which did its part for the newspaper mortality rate. Advertisers hunkered down, cutting off the financial oxygen that most newspapers depend on.
The Internet did its part by siphoning off classified ad revenue that, for many major dailies, was 40 percent of their income; by breaking down the barriers to entry, allowing anyone to start a news site on line; and by nurturing a belief that newspaper content was free. The Great Disrupter did its damage, and some newspapers that had survived monopolist newspaper companies and the recession could not endure.
But for some newspapers that have embraced the opportunities created by the Internet, there is real cause for optimism. The Internet has given us new ways of gathering news, and new ways of telling stories. It has enlarged our audience many fold. It has tapped into the creative energy of good journalists and engendered – at The Times, and elsewhere – an openness to experimentation.
And it holds real promise of rescuing our business model. The New York Times and the Times-owned Boston Globe, the Financial Times and the Wall Street Journal, to cite a few of the most prominent examples, have all persuaded readers to pay for their content on line.
It’s not divulging any dark secret to say that, when The Times began grappling with its digital future, we were not immune from that utopian-realist divide that has emerged at Stanford. There were partisans of scale, who argued for the primacy of an immense audience to drive ad revenues, and partisans of quality, who argued that people would pay for gold-standard journalism. What we discovered – at least, what we hope and believe we have discovered – is that it’s a false choice. If you build it, they will come.
Maybe it’s not too early to start drafting the new narrative: How the Internet Saved the Newspaper.
http://keller.blogs.nytimes.com/2011/10 ... n&emc=tyb1
Disrupters and Adapters, Continued: Will the Internet Save Newspapers?
The two visions of higher education’s future I described in my column this week – Stanford Professor Sebastian Thrun’s mission of a virtual university and Stanford President John Hennessy’s devotion to a flesh-and-blood campus – intrigued me because of the larger context. So much of the debate about the impact of new technology tends to be polarizing. The utopians versus the skeptics, the idealists versus the realists, those who throw themselves headlong into the great mosh pit of the new, and those who cherish the familiar and time-honored.
To the champions of the new, those who hesitate are Luddites and curmudgeons and reactionaries, destined to be left behind in the march of civilization. (I speak from some experience. The response to recent columns, in which I suggested that social media and news aggregation have their downsides, taught me that, whatever limitations Twitter may have as a vehicle for discussion, it is an excellent medium for name-calling.) To those who have not chosen to move their social lives to Facebook and Google+, or who believe that maybe content doesn’t necessarily want to be free, the digiphiles can sometimes feel a little like a cult of scolds.
What struck me about the rival views of higher education is that it is not so much a stark choice as a kind of tense synergy between old and new. As digital access continues to spread and technologies like telepresence and virtual reality improve, the Web will offer ever better education to wider and wider audiences at lower and lower prices. Education, to borrow a Tom Friedmanism, will be flatter. But there will still be nodes of excellence, actual campuses offering actual human contact.
Hennessy, not surprisingly, stresses the virtues of the non-virtual, especially for undergraduates, and especially in liberal arts. Proximity has real advantages in refining the skills of thought and expression, and nothing quite matches the experience of coexisting with people of diverse backgrounds. Thrun concedes a residential campus is “a fantastic experience.” “Many people find their life partner,” he added. “You hang out with people who are pre-selected to be successful people.” And the extraordinary alliance Stanford has forged with the city of Palo Alto has proven that, sometimes, location can generate explosive creativity. Technology will surely supplant some of the expensive infrastructure of a top college degree, but it is a long, long way from replicating the experience.
You may find yourself more drawn more to Thrun’s status-quo-disrupting mission of delivering education to the masses, or you may find your heart is with Hennessy’s not-quite-so-fast defense of a university system that has produced generations of great scholars. But it is entirely plausible to find them both indispensable.
I think the same thing can be said of many industries, including my own. What doesn’t kill you makes you stronger.
Technology upended the music business – except that today there are more musical choices, more widely accessible, at a reasonable price. (And you can still buy your music on vinyl if you like.) Technology was supposed to render books irrelevant – until eBooks came along to save them. (And you can still buy books in print.)
I think the same may well prove true of the newspaper business – that, having assisted in the death of many newspapers, technology will save those that adapt.
By the way, to digress for a minute, those who say the Internet killed newspapers should review their history. For one thing, nobody has killed more newspapers than newspaper publishers, who culled competition to create monopoly markets. When I left the staff of The Oregonian in 1979, Portland had two daily newspapers. Three years later the Newhouse chain (which owned both of them) closed the afternoon paper. When I left the staff of the Dallas Times Herald in 1985, it was one of two good newspapers jostling for primacy in that city. In 1991, the Belo Corporation, owner of the rival Dallas Morning News, bought the Times Herald for $55 million, and shut it down the next day. It’s no surprise that many of the cities that had newspapers die in recent years have been two-paper cities where the papers had been kept on life support by joint operating agreements. Their demise is sad, but it was a long time coming.
Nor can the Internet be blamed for the Great Recession, which did its part for the newspaper mortality rate. Advertisers hunkered down, cutting off the financial oxygen that most newspapers depend on.
The Internet did its part by siphoning off classified ad revenue that, for many major dailies, was 40 percent of their income; by breaking down the barriers to entry, allowing anyone to start a news site on line; and by nurturing a belief that newspaper content was free. The Great Disrupter did its damage, and some newspapers that had survived monopolist newspaper companies and the recession could not endure.
But for some newspapers that have embraced the opportunities created by the Internet, there is real cause for optimism. The Internet has given us new ways of gathering news, and new ways of telling stories. It has enlarged our audience many fold. It has tapped into the creative energy of good journalists and engendered – at The Times, and elsewhere – an openness to experimentation.
And it holds real promise of rescuing our business model. The New York Times and the Times-owned Boston Globe, the Financial Times and the Wall Street Journal, to cite a few of the most prominent examples, have all persuaded readers to pay for their content on line.
It’s not divulging any dark secret to say that, when The Times began grappling with its digital future, we were not immune from that utopian-realist divide that has emerged at Stanford. There were partisans of scale, who argued for the primacy of an immense audience to drive ad revenues, and partisans of quality, who argued that people would pay for gold-standard journalism. What we discovered – at least, what we hope and believe we have discovered – is that it’s a false choice. If you build it, they will come.
Maybe it’s not too early to start drafting the new narrative: How the Internet Saved the Newspaper.
http://keller.blogs.nytimes.com/2011/10 ... n&emc=tyb1
5 October 2011
India launches Aakash tablet computer priced at $35
Indian students pose with Aakash computer tablet, 5 October 2011 Millions of students will have access to the tablets, officials hope
India has launched what it says is the world's cheapest touch-screen tablet computer, priced at just $35 (£23).
Costing a fraction of Apple's iPad, the subsidised Aakash is aimed at students.
It supports web browsing and video conferencing, has a three-hour battery life and two USB ports, but questions remain over how it will perform.
Officials hope the computer will give digital access to students in small towns and villages across India, which lags behind its rivals in connectivity.
More...
http://www.bbc.co.uk/news/world-south-asia-15180831
India launches Aakash tablet computer priced at $35
Indian students pose with Aakash computer tablet, 5 October 2011 Millions of students will have access to the tablets, officials hope
India has launched what it says is the world's cheapest touch-screen tablet computer, priced at just $35 (£23).
Costing a fraction of Apple's iPad, the subsidised Aakash is aimed at students.
It supports web browsing and video conferencing, has a three-hour battery life and two USB ports, but questions remain over how it will perform.
Officials hope the computer will give digital access to students in small towns and villages across India, which lags behind its rivals in connectivity.
More...
http://www.bbc.co.uk/news/world-south-asia-15180831
TECHNOLOGY AND BEAUTY
October 8, 2011
Up From Ugliness
By ROSS DOUTHAT
FROM the 1960s through the 1980s, the United States of America conducted a long experiment in ugliness. Our architects grew bored with beauty, our designers tired of elegance, our urban planners decided that function should trump form. We bulldozed row houses and threw up housing projects. We built public buildings out of raw concrete. We wore leisure suits and shoulder pads, buried heart-of-pine floors under shag carpeting, and paneled our automobiles with artificial wood.
This is the world in which Steve Jobs came of age. It was, not coincidentally, a world in which it became easy to believe that the United States was in decline. Our churches looked like recreation centers, and our rec centers looked like re-education camps. Our campuses and civic spaces were defaced by ziggurats of cement. Our cities had crime-ridden towers and white elephant shopping centers where the neighborhoods used to be. Our suburbs were filled with what James Howard Kunstler described as the “junk architecture” of strip malls and ranch houses.
Then, gradually and haltingly, beauty began to make a comeback. A “new urbanist” movement championed a return to walkable neighborhoods, human-scale housing, and pleasant public spaces. Our clothes became less garish, our cars more curvaceous, our civic architecture less offensive. And most remarkably, our machines ceased to be utilitarian boxes, and became something beautiful instead.
When we think about what Jobs meant to turn-of-the-millennium America, this is the place to start: not just with the technical wizardry behind Macs and iPhones and iPads, but with the Apple founder’s eye for grace and style, and his recognition of the deep connection between beauty and civilization.
There would have been some sort of desktop computer without the Macintosh, some sort of popular smartphone without the iPhone, some kind of big-screen computer animation without Pixar. But there was no guarantee that any of these technological wonders would be so exquisite, or that the age of information would also be an age of artistry.
Jobs wasn’t an artist himself. But he was a curator, a critic and a patron. Whether he was deciding that the first Macintosh computer would feature beautiful typography or telling Pixar’s animators to “make it great,” he played a decisive role in restoring a kind of defiant aestheticism to American life.
Like the glories of Art Deco and the allure of the “Mad Men” era, his products were a rebuke to the idea that the aesthetics of modern life needed to be utilitarian and blah. From the Apple store to “The Incredibles,” Jobs revived the romance of modernity — the assumption, shared by Victorian science-fiction writers and space-age dreamers alike, that the world of the future should be more glamorous than the present.
The question is whether this revival has staying power. The age of architectural Brutalism is past, but between the travails of planning-by-committee and the red tape of bureaucracy, our civic projects still tend to be uninspired in design and interminable in execution. (The newest additions to the Washington Mall, the World War II and Martin Luther King Jr. memorials, look like rejected rough drafts for monuments rather than inspiring finished products.) For all its successes, the new urbanism sometimes feels more like a reclamation project than a renaissance: it’s saved the row houses of yesterday without building the neighborhoods of tomorrow.
So too with technology, where some of the eulogies for Jobs have highlighted the gulf between the computer revolution’s rapid progress and the lack of advancement in fields like medicine and transportation. The iPhone and the iPad may be aesthetically perfect, but in an otherwise stagnant society their charms can be an invitation to solipsism — holding up mirrors to our vanity, instead of opening windows to breakthroughs more impressive than the latest app.
You can see a version of this peril in our politics as well. In a sense, Barack Obama’s 2008 march to the White House was the iPhone of political campaigns: a perfect marriage of aesthetics, spectacle and social media, a revival of the old New Frontier excitement, the natural culmination of glamour’s post-1970s comeback in American life. But three years later much of that looks like an illusion — a temporary echo of liberalism’s golden age, evoking successes that today’s Democratic Party can’t recapture.
Right now, Steve Jobs’s legacy seems more secure than President Obama’s. (Certainly his fan base is less fickle.) But there’s still a danger that we’ll look back on Apple’s golden age and see it as a fleeting creative spike in a larger story of cultural decline.
Whether that happens is up to tomorrow’s innovators. If they learn anything from Jobs, it should be that their vocation isn’t just about uniting commerce and technology. It’s about making the modern world more beautiful as well.
http://www.nytimes.com/2011/10/09/opini ... emc=tha212
October 8, 2011
Up From Ugliness
By ROSS DOUTHAT
FROM the 1960s through the 1980s, the United States of America conducted a long experiment in ugliness. Our architects grew bored with beauty, our designers tired of elegance, our urban planners decided that function should trump form. We bulldozed row houses and threw up housing projects. We built public buildings out of raw concrete. We wore leisure suits and shoulder pads, buried heart-of-pine floors under shag carpeting, and paneled our automobiles with artificial wood.
This is the world in which Steve Jobs came of age. It was, not coincidentally, a world in which it became easy to believe that the United States was in decline. Our churches looked like recreation centers, and our rec centers looked like re-education camps. Our campuses and civic spaces were defaced by ziggurats of cement. Our cities had crime-ridden towers and white elephant shopping centers where the neighborhoods used to be. Our suburbs were filled with what James Howard Kunstler described as the “junk architecture” of strip malls and ranch houses.
Then, gradually and haltingly, beauty began to make a comeback. A “new urbanist” movement championed a return to walkable neighborhoods, human-scale housing, and pleasant public spaces. Our clothes became less garish, our cars more curvaceous, our civic architecture less offensive. And most remarkably, our machines ceased to be utilitarian boxes, and became something beautiful instead.
When we think about what Jobs meant to turn-of-the-millennium America, this is the place to start: not just with the technical wizardry behind Macs and iPhones and iPads, but with the Apple founder’s eye for grace and style, and his recognition of the deep connection between beauty and civilization.
There would have been some sort of desktop computer without the Macintosh, some sort of popular smartphone without the iPhone, some kind of big-screen computer animation without Pixar. But there was no guarantee that any of these technological wonders would be so exquisite, or that the age of information would also be an age of artistry.
Jobs wasn’t an artist himself. But he was a curator, a critic and a patron. Whether he was deciding that the first Macintosh computer would feature beautiful typography or telling Pixar’s animators to “make it great,” he played a decisive role in restoring a kind of defiant aestheticism to American life.
Like the glories of Art Deco and the allure of the “Mad Men” era, his products were a rebuke to the idea that the aesthetics of modern life needed to be utilitarian and blah. From the Apple store to “The Incredibles,” Jobs revived the romance of modernity — the assumption, shared by Victorian science-fiction writers and space-age dreamers alike, that the world of the future should be more glamorous than the present.
The question is whether this revival has staying power. The age of architectural Brutalism is past, but between the travails of planning-by-committee and the red tape of bureaucracy, our civic projects still tend to be uninspired in design and interminable in execution. (The newest additions to the Washington Mall, the World War II and Martin Luther King Jr. memorials, look like rejected rough drafts for monuments rather than inspiring finished products.) For all its successes, the new urbanism sometimes feels more like a reclamation project than a renaissance: it’s saved the row houses of yesterday without building the neighborhoods of tomorrow.
So too with technology, where some of the eulogies for Jobs have highlighted the gulf between the computer revolution’s rapid progress and the lack of advancement in fields like medicine and transportation. The iPhone and the iPad may be aesthetically perfect, but in an otherwise stagnant society their charms can be an invitation to solipsism — holding up mirrors to our vanity, instead of opening windows to breakthroughs more impressive than the latest app.
You can see a version of this peril in our politics as well. In a sense, Barack Obama’s 2008 march to the White House was the iPhone of political campaigns: a perfect marriage of aesthetics, spectacle and social media, a revival of the old New Frontier excitement, the natural culmination of glamour’s post-1970s comeback in American life. But three years later much of that looks like an illusion — a temporary echo of liberalism’s golden age, evoking successes that today’s Democratic Party can’t recapture.
Right now, Steve Jobs’s legacy seems more secure than President Obama’s. (Certainly his fan base is less fickle.) But there’s still a danger that we’ll look back on Apple’s golden age and see it as a fleeting creative spike in a larger story of cultural decline.
Whether that happens is up to tomorrow’s innovators. If they learn anything from Jobs, it should be that their vocation isn’t just about uniting commerce and technology. It’s about making the modern world more beautiful as well.
http://www.nytimes.com/2011/10/09/opini ... emc=tha212
October 30, 2011
Concerns Are Raised About Genetically Engineered Mosquitoes
By ANDREW POLLACK
These mosquitoes are genetically engineered to kill — their own children.
Researchers on Sunday reported initial signs of success from the first release into the environment of mosquitoes engineered to pass a lethal gene to their offspring, killing them before they reach adulthood.
The results, and other work elsewhere, could herald an age in which genetically modified insects will be used to help control agricultural pests and insect-borne diseases like dengue fever and malaria.
More.....
http://www.nytimes.com/2011/10/31/scien ... &emc=tha25
Concerns Are Raised About Genetically Engineered Mosquitoes
By ANDREW POLLACK
These mosquitoes are genetically engineered to kill — their own children.
Researchers on Sunday reported initial signs of success from the first release into the environment of mosquitoes engineered to pass a lethal gene to their offspring, killing them before they reach adulthood.
The results, and other work elsewhere, could herald an age in which genetically modified insects will be used to help control agricultural pests and insect-borne diseases like dengue fever and malaria.
More.....
http://www.nytimes.com/2011/10/31/scien ... &emc=tha25
October 31, 2011
Decoding the Brain’s Cacophony
By BENEDICT CAREY
ST. HELENA, Calif. — The scientists exchanged one last look and held their breath.
Everything was ready. The electrode was in place, threaded between the two hemispheres of a living cat’s brain; the instruments were tuned to pick up the chatter passing from one half to the other. The only thing left was to listen for that electronic whisper, the brain’s own internal code.
The amplifier hissed — the three scientists expectantly leaning closer — and out it came, loud and clear.
“We all live in a yellow submarine, yellow submarine, yellow submarine ....”
“The Beatles’ song! We somehow picked up the frequency of a radio station,” recalled Michael S. Gazzaniga, chuckling at the 45-year-old memory. “The brain’s secret code. Yeah, right!”
Dr. Gazzaniga, 71, now a professor of psychology at the University of California, Santa Barbara, is best known for a dazzling series of studies that revealed the brain’s split personality, the division of labor between its left and right hemispheres. But he is perhaps next best known for telling stories, many of them about blown experiments, dumb questions and other blunders during his nearly half-century career at the top of his field.
Now, in lectures and a new book, he is spelling out another kind of cautionary tale — a serious one, about the uses of neuroscience in society, particularly in the courtroom.
Brain science “will eventually begin to influence how the public views justice and responsibility,” Dr. Gazzaniga said at a recent conference here sponsored by the Edge Foundation.
And there is no guarantee, he added, that its influence will be a good one.
More.....
http://www.nytimes.com/2011/11/01/scien ... emc=tha210
******
October 29, 2011
Addicted to Exercise?
By NICHOLAS D. KRISTOF
FOR decades, scientists have studied areas deep within the brain that seem associated with pleasure and addiction.
Put an electrode in that part of a rat’s brain, and it will become obsessed with stimulating those areas. When rats are allowed to push a lever in exchange for a mild current that produces a “high” in the “pleasure centers,” they will press the lever up to 7,000 times per hour.
These rats forget to eat or drink, and they must be unhooked to prevent self-starvation. Male rats ignore females in heat to get a fix, and nursing mothers ignore their babies.
“Pressing that lever became their entire world,” David J. Linden, a neuroscientist at Johns Hopkins University medical school, writes in his fascinating new book, “The Compass of Pleasure.”
Professor Linden explains how drugs such as cocaine that light up these pleasure centers (there are several interconnected areas) actually rewire the brain to increase cravings. You can look at magnified photos of rat brains and tell which animal was given cocaine and which wasn’t.
Yet it’s not just drugs. Brain scans suggest that everything from sugar to sex lights up the brain’s pleasure circuitry. These all can have neurological consequences that correspond to what we think of as addiction. For example: exercise.
More....
http://www.nytimes.com/2011/10/30/opini ... rcise.html
Decoding the Brain’s Cacophony
By BENEDICT CAREY
ST. HELENA, Calif. — The scientists exchanged one last look and held their breath.
Everything was ready. The electrode was in place, threaded between the two hemispheres of a living cat’s brain; the instruments were tuned to pick up the chatter passing from one half to the other. The only thing left was to listen for that electronic whisper, the brain’s own internal code.
The amplifier hissed — the three scientists expectantly leaning closer — and out it came, loud and clear.
“We all live in a yellow submarine, yellow submarine, yellow submarine ....”
“The Beatles’ song! We somehow picked up the frequency of a radio station,” recalled Michael S. Gazzaniga, chuckling at the 45-year-old memory. “The brain’s secret code. Yeah, right!”
Dr. Gazzaniga, 71, now a professor of psychology at the University of California, Santa Barbara, is best known for a dazzling series of studies that revealed the brain’s split personality, the division of labor between its left and right hemispheres. But he is perhaps next best known for telling stories, many of them about blown experiments, dumb questions and other blunders during his nearly half-century career at the top of his field.
Now, in lectures and a new book, he is spelling out another kind of cautionary tale — a serious one, about the uses of neuroscience in society, particularly in the courtroom.
Brain science “will eventually begin to influence how the public views justice and responsibility,” Dr. Gazzaniga said at a recent conference here sponsored by the Edge Foundation.
And there is no guarantee, he added, that its influence will be a good one.
More.....
http://www.nytimes.com/2011/11/01/scien ... emc=tha210
******
October 29, 2011
Addicted to Exercise?
By NICHOLAS D. KRISTOF
FOR decades, scientists have studied areas deep within the brain that seem associated with pleasure and addiction.
Put an electrode in that part of a rat’s brain, and it will become obsessed with stimulating those areas. When rats are allowed to push a lever in exchange for a mild current that produces a “high” in the “pleasure centers,” they will press the lever up to 7,000 times per hour.
These rats forget to eat or drink, and they must be unhooked to prevent self-starvation. Male rats ignore females in heat to get a fix, and nursing mothers ignore their babies.
“Pressing that lever became their entire world,” David J. Linden, a neuroscientist at Johns Hopkins University medical school, writes in his fascinating new book, “The Compass of Pleasure.”
Professor Linden explains how drugs such as cocaine that light up these pleasure centers (there are several interconnected areas) actually rewire the brain to increase cravings. You can look at magnified photos of rat brains and tell which animal was given cocaine and which wasn’t.
Yet it’s not just drugs. Brain scans suggest that everything from sugar to sex lights up the brain’s pleasure circuitry. These all can have neurological consequences that correspond to what we think of as addiction. For example: exercise.
More....
http://www.nytimes.com/2011/10/30/opini ... rcise.html
February 19, 2012
Physicists Create a Working Transistor From a Single Atom
By JOHN MARKOFF
Australian and American physicists have built a working transistor from a single phosphorus atom embedded in a silicon crystal.
The group of physicists, based at the University of New South Wales and Purdue University, said they had laid the groundwork for a futuristic quantum computer that might one day function in a nanoscale world and would be orders of magnitude smaller and quicker than today’s silicon-based machines.
In contrast to conventional computers that are based on transistors with distinct “on” and “off” or “1” and “0” states, quantum computers are built from devices called qubits that exploit the quirky properties of quantum mechanics. Unlike a transistor, a qubit can represent a multiplicity of values simultaneously.
That might make it possible to factor large numbers more quickly than with conventional machines, thereby undermining modern data-scrambling systems that are the basis of electronic commerce and data privacy. Quantum computers might also make it possible to simulate molecular structures with great speed, an advance that holds promise for designing new drugs and other materials.
More...
http://www.nytimes.com/2012/02/20/scien ... &emc=tha23
Physicists Create a Working Transistor From a Single Atom
By JOHN MARKOFF
Australian and American physicists have built a working transistor from a single phosphorus atom embedded in a silicon crystal.
The group of physicists, based at the University of New South Wales and Purdue University, said they had laid the groundwork for a futuristic quantum computer that might one day function in a nanoscale world and would be orders of magnitude smaller and quicker than today’s silicon-based machines.
In contrast to conventional computers that are based on transistors with distinct “on” and “off” or “1” and “0” states, quantum computers are built from devices called qubits that exploit the quirky properties of quantum mechanics. Unlike a transistor, a qubit can represent a multiplicity of values simultaneously.
That might make it possible to factor large numbers more quickly than with conventional machines, thereby undermining modern data-scrambling systems that are the basis of electronic commerce and data privacy. Quantum computers might also make it possible to simulate molecular structures with great speed, an advance that holds promise for designing new drugs and other materials.
More...
http://www.nytimes.com/2012/02/20/scien ... &emc=tha23
Sometimes simpler is better
UW researcher’s X-ray device could help to “knock out” tuberculosis in developing countries
Karim Karim University of Waterloo associate professor Karim S. Karim is developing a low-cost digital x-ray tool to detect TB in developing countries.
Philip Walker/Record staff
WATERLOO — It only takes an inexpensive digital X-ray detector to help stamp out a disease that is killing millions of people in developing countries, an award-winning University of Waterloo researcher says.
Karim S. Karim is developing a $1,000 digital X-ray device to screen for tuberculosis, a killer disease that affects a third of the world’s population and claims 1.8-million lives annually, most of them in Asia and Africa.
Karim, who was born in Pakistan, has seen the devastation that tuberculosis can do. He vividly recalls being a child in Pakistan and seeing patients with tuberculosis cough up blood. Both of his parents were doctors, he says, and he heard about the disease a lot at home.
“Tuberculosis is something that I have seen, and it’s bad . . . . It was a big thing there. In fact, I’d say it’s more prevalent than heart disease. It’s in all ages, but the worst segment that’s affected is the young ones. It’s the biggest tragedy there.”
As a scientist, Karim made a key discovery that led him to challenge the disease.
And that is that you don’t need to come up with the best advancement, the highest-performing technology or the most-talked-about solution in order to make a difference in the world, he says.
This month, the associate professor in the UW department of electrical and computer engineering was named one of 15 “rising star” researchers by Grand Challenges Canada.
Grand Challenges is an independent not-for-profit organization funded through a federal government program that urges the best minds to find solutions to the world’s health problems.
Karim received a $100,000 seed grant to develop his digital X-ray detector further. He could receive $1 million to continue the work if his innovation is judged to have the highest potential of the proposals. Other winners include a scientist who is using chicken feathers as a filter to remove arsenic in water supplies and a researcher who is developing a medical records system for use in the worst slum in Nairobi.
Digital X-ray detectors currently cost about $100,000 and are produced for general use in hospitals in developing countries, Karim says. But because there are too few hospitals, they aren’t very accessible, he says.
So Karim is developing a low-cost digital X-ray detector that will screen for tuberculosis only. He’s using existing detectors and modifying them so that they’re smaller — since the detector will only be used to examine the lungs, not the full chest. Then they can be used in tuberculosis screening clinics in developing countries, he says.
“The technology is out there,” he says. “The larger the panel, the larger the cost. You cut the area in half and you’ve taken half the cost out.” Karim is working with Aga Khan University in Pakistan, which is providing him with images of patients with tuberculosis in order to help him build a prototype. “I want to build a system that I can now ship to Aga Khan University in Pakistan for them to test,” he says.
“The ultimate vision would be a network of low-cost health care clinics in developing countries.” Screening would help detect the disease so people can be cured. Besides saving lives, the diagnostic tool has the potential to help change a country’s prosperity, he says.
“Right now, the problem that grips a lot of developing countries is their workforce gets decimated by preventable diseases like tuberculosis. If you can find a way to screen and knock out tuberculosis, now you’ve got a massive improvement in the workforce, therefore the economy and positive change comes about.”
During his research career, Karim says, he experienced a series of eureka moments that made him realize that aiming for the ultimate in scientific discovery isn’t always the most useful approach.
But that’s a different way of thinking for many researchers, whose culture it is to continue to raise the bar by developing faster, newer, better technology than anything that exists, says Karim, adding that he’s “not knocking fundamental science.”
He had to give his own head a shake before he accepted his own conclusions, he says.
“I think it’s a bizarre thing for a researcher to say . . . but I actually think this is a key point,” Karim says.
“I’ve been developing all this wonderful technology that is an inch better or an ounce better or a per cent better. We’re constantly pushing that envelope of performance, but what does it really mean to get it out there?”
Karim says he learned this lesson after trying to commercialize technology he developed while working on his PhD in Waterloo, then at Simon Fraser University in Vancouver where he taught from 2003 to 2007.
One project he developed was a low-dose, real-time X-ray camera.
“I had developed something improved, but not necessarily what was needed.”
He decided that he needed to learn from businesspeople. They “always have the end use in mind because if you don’t have the end use in mind, you’re going to fail in business,” he says.
He applied for a Science to Business fellowship that was offered by a federal health research funding agency and would pay the cost for him to obtain a master of business administration degree.
He got the funding, and was on the road, twice a week, for 7 a.m. classes at the Rotman School of Management at the University of Toronto.
With full teaching responsibilities at UW and two young daughters, he couldn’t have managed the work and study load without the help of his wife, Tasreen Charania, who is also working on her PhD, he says. He will finish the MBA program in April.
Karim has learned to think of the consumer, rather than taking “the deep dive into technology.” As a result, he says, he took old technology and low-cost materials and made them perform better to produce a fast, low-dose X-ray camera with good image quality. A Canadian company is now interested in the results of that research, he says.
What he learned at business school also led him to enter the Grand Challenges Canada competition with his idea for a revised screening technology for tuberculosis. If his idea is used, “it’s huge,” he says.
“We’d be giving people a chance at a better life . . . or at life, period.” He says he views the research as a fulfilling way to give back to the community. “It tends to meet the needs of the spirit.”
Video:
http://www.guelphmercury.com/living/art ... -is-better
UW researcher’s X-ray device could help to “knock out” tuberculosis in developing countries
Karim Karim University of Waterloo associate professor Karim S. Karim is developing a low-cost digital x-ray tool to detect TB in developing countries.
Philip Walker/Record staff
WATERLOO — It only takes an inexpensive digital X-ray detector to help stamp out a disease that is killing millions of people in developing countries, an award-winning University of Waterloo researcher says.
Karim S. Karim is developing a $1,000 digital X-ray device to screen for tuberculosis, a killer disease that affects a third of the world’s population and claims 1.8-million lives annually, most of them in Asia and Africa.
Karim, who was born in Pakistan, has seen the devastation that tuberculosis can do. He vividly recalls being a child in Pakistan and seeing patients with tuberculosis cough up blood. Both of his parents were doctors, he says, and he heard about the disease a lot at home.
“Tuberculosis is something that I have seen, and it’s bad . . . . It was a big thing there. In fact, I’d say it’s more prevalent than heart disease. It’s in all ages, but the worst segment that’s affected is the young ones. It’s the biggest tragedy there.”
As a scientist, Karim made a key discovery that led him to challenge the disease.
And that is that you don’t need to come up with the best advancement, the highest-performing technology or the most-talked-about solution in order to make a difference in the world, he says.
This month, the associate professor in the UW department of electrical and computer engineering was named one of 15 “rising star” researchers by Grand Challenges Canada.
Grand Challenges is an independent not-for-profit organization funded through a federal government program that urges the best minds to find solutions to the world’s health problems.
Karim received a $100,000 seed grant to develop his digital X-ray detector further. He could receive $1 million to continue the work if his innovation is judged to have the highest potential of the proposals. Other winners include a scientist who is using chicken feathers as a filter to remove arsenic in water supplies and a researcher who is developing a medical records system for use in the worst slum in Nairobi.
Digital X-ray detectors currently cost about $100,000 and are produced for general use in hospitals in developing countries, Karim says. But because there are too few hospitals, they aren’t very accessible, he says.
So Karim is developing a low-cost digital X-ray detector that will screen for tuberculosis only. He’s using existing detectors and modifying them so that they’re smaller — since the detector will only be used to examine the lungs, not the full chest. Then they can be used in tuberculosis screening clinics in developing countries, he says.
“The technology is out there,” he says. “The larger the panel, the larger the cost. You cut the area in half and you’ve taken half the cost out.” Karim is working with Aga Khan University in Pakistan, which is providing him with images of patients with tuberculosis in order to help him build a prototype. “I want to build a system that I can now ship to Aga Khan University in Pakistan for them to test,” he says.
“The ultimate vision would be a network of low-cost health care clinics in developing countries.” Screening would help detect the disease so people can be cured. Besides saving lives, the diagnostic tool has the potential to help change a country’s prosperity, he says.
“Right now, the problem that grips a lot of developing countries is their workforce gets decimated by preventable diseases like tuberculosis. If you can find a way to screen and knock out tuberculosis, now you’ve got a massive improvement in the workforce, therefore the economy and positive change comes about.”
During his research career, Karim says, he experienced a series of eureka moments that made him realize that aiming for the ultimate in scientific discovery isn’t always the most useful approach.
But that’s a different way of thinking for many researchers, whose culture it is to continue to raise the bar by developing faster, newer, better technology than anything that exists, says Karim, adding that he’s “not knocking fundamental science.”
He had to give his own head a shake before he accepted his own conclusions, he says.
“I think it’s a bizarre thing for a researcher to say . . . but I actually think this is a key point,” Karim says.
“I’ve been developing all this wonderful technology that is an inch better or an ounce better or a per cent better. We’re constantly pushing that envelope of performance, but what does it really mean to get it out there?”
Karim says he learned this lesson after trying to commercialize technology he developed while working on his PhD in Waterloo, then at Simon Fraser University in Vancouver where he taught from 2003 to 2007.
One project he developed was a low-dose, real-time X-ray camera.
“I had developed something improved, but not necessarily what was needed.”
He decided that he needed to learn from businesspeople. They “always have the end use in mind because if you don’t have the end use in mind, you’re going to fail in business,” he says.
He applied for a Science to Business fellowship that was offered by a federal health research funding agency and would pay the cost for him to obtain a master of business administration degree.
He got the funding, and was on the road, twice a week, for 7 a.m. classes at the Rotman School of Management at the University of Toronto.
With full teaching responsibilities at UW and two young daughters, he couldn’t have managed the work and study load without the help of his wife, Tasreen Charania, who is also working on her PhD, he says. He will finish the MBA program in April.
Karim has learned to think of the consumer, rather than taking “the deep dive into technology.” As a result, he says, he took old technology and low-cost materials and made them perform better to produce a fast, low-dose X-ray camera with good image quality. A Canadian company is now interested in the results of that research, he says.
What he learned at business school also led him to enter the Grand Challenges Canada competition with his idea for a revised screening technology for tuberculosis. If his idea is used, “it’s huge,” he says.
“We’d be giving people a chance at a better life . . . or at life, period.” He says he views the research as a fulfilling way to give back to the community. “It tends to meet the needs of the spirit.”
Video:
http://www.guelphmercury.com/living/art ... -is-better
March 7, 2012
Cost of Gene Sequencing Falls, Raising Hopes for Medical Advances
By JOHN MARKOFF
MOUNTAIN VIEW, Calif. — In Silicon Valley, the line between computing and biology has begun to blur in a way that could have enormous consequences for human longevity.
Bill Banyai, an optical physicist at Complete Genomics, has helped make that happen. When he began developing a gene sequencing machine, he relied heavily on his background at two computer networking start-up companies. His digital expertise was essential in designing a factory that automated and greatly lowered the cost of mapping the three billion base pairs that form the human genome.
The promise is that low-cost gene sequencing will lead to a new era of personalized medicine, yielding new approaches for treating cancers and other serious diseases. The arrival of such cures has been glacial, however, although the human genome was originally sequenced more than a decade ago.
Now that is changing, in large part because of the same semiconductor industry manufacturing trends that opened up consumer devices like the PC and the smartphone: exponential increases in processing power and transistor density are accompanied by costs that fall at an accelerating rate.
As a result, both new understanding and new medicines will arrive at a quickening pace, according to the biologists and computer scientists.
“For all of human history, humans have not had the readout of the software that makes them alive,” said Larry Smarr, director of the California Institute of Telecommunications and Information Technology, a research center that is jointly operated by the University of California, San Diego, and the University of California, Irvine, who is a member of the Complete Genomics scientific advisory board. “Once you make the transition from a data poor to data rich environment, everything changes.”
Complete Genomics, based in Mountain View, is one of more than three dozen firms hastening to push the cost of sequencing an entire human genome below $1,000. The challenge is part biology, part chemistry, part computing, and in Complete Genomics’ case, part computer networking.
Complete Genomics is a classic Silicon Valley start-up story. Even the gene sequencing machines, which are housed in a 4,000-square-foot room bathed in an eerie blue light, appear more like a traditional data center than a biology lab.
In 2005 ,when Clifford Reid, a successful Silicon Valley software entrepreneur, began to assemble his team, he approached Dr. Banyai and asked if he was interested in joining a gene sequencing start-up. Dr. Reid, who was also trained in physics and math, had spent a year as an entrepreneur-in-residence at the Massachusetts Institute of Technology, where he had become a convert to bioinformatics, the application of computer science and information technologies to biology and medicine.
Dr. Banyai had even less experience in biology.
Formerly with the Internet networking start-ups GlimmerGlass and Silicon Light Machines, he in turn began by reading a pioneering 2005 article in the journal Science in which a group of researchers in George Church’s genetics laboratory at Harvard describe a new technique intended to speed gene sequencing.
Today Dr. Banyai is finishing the second generation of a machine that blends robotics, chemistry, optics and computing. It is emblematic of the serendipitous changes that take place when a manufacturing process is transformed: performance increases and cost falls at an accelerating rate.
“Genomes are now being sequenced incredibly cheaply,” said Russ B. Altman, who is a founder of Personalis, a start-up based in Palo Alto, Calif., that is developing software to interpret genomes. “On the discovery and science side we will be able to do clinical trials. We’ll be able to check the entire genome.”
Recently, on the company’s Web site, Dr. Reid predicted that the cost of gene sequencing could eventually be as low as that of a blood test: “I believe that the impact on the medical community of whole human genome sequencing at a cost comparable to a comprehensive blood test will be profound, and it will raise a host of public policy issues (privacy, security, disclosure, reimbursement, interpretation, counseling, etc.), all important topics for future discussions,” he wrote.
Dr. Banyai said he had found that Silicon Valley start-up ideas tracked well. “There is this remarkable thing that happens in start-ups. You make up this plan and then you step off a cliff and magically a little bridge appears,” he noted, as new technologies appear in the nick of time.
In the case of Complete Genomics, the company is riding in part on big advances being made in industrial digital cameras that are capable of capturing the fluorescent molecules that are used to “read” small sequences of DNA.
In the last half-year, a new generation of cameras, more frequently used for factory inspection systems, has made it possible to speed up the Complete Genomics sequencing process tenfold. That, the company has said, will drive its capacity to 100,000 genomes annually from 10,000.
The parallels between the evolution of the nascent gene sequencing industry and the Valley’s chip makers are striking. By placing more circuits on a silicon wafer at an exponentially increasing pace since the early 1960s, the semiconductor industry transformed the cost of computing. As a result, today the world’s most powerful supercomputer from the 1980s nestles comfortably in your hand and costs several hundred dollars.
Complete Genomics’ competitors are also exploiting designs to drive costs down. For example, Life Technologies, based in Carlsbad, Calif. uses a direct approach to read the bases in the genome from an array of sensors on the surface of a semiconductor chip. As more sensors are packed onto each successive generation of technology, the cost of sequencing will also fall sharply.
Last month, Oxford Nanopore Technologies created an industry sensation when it introduced a machine that sequenced genes using an alternative approach called nanopore sequencing, in which a strand of DNA is read as it is pulled through a microscopic hole.
The system is scheduled to be available later this year. However, it has an error rate much higher than that of the Complete Genomics system, which has independently been given high marks for accuracy.
Because there is no clear winner yet, all of the companies are pushing hard to get down the cost curve as fast as possible
In 2011, Complete Genomics became one of the market leaders. This year, it has produced more than 3,000 sequences at a cost of about $5,000 each. Dr. Banyai’s higher capacity second generation system is now being installed and will begin production during the first half of this year. A third generation design has been completed.
What initially set Complete Genomics apart from the field was its strategy of offering gene sequencing as a service, rather than selling a machine to laboratories. More recently, Illumina, one of its crucial competitors, has also begun offering sequencing as a service, in addition to selling its machines.
“Our competitors have to supply kits that can be executed by a graduate student rolling out of bed with a hangover,” said Dr. Reid. “We don’t live with that standard, and that can be tremendously liberating. Ours can be horrifically complex as long as it can be executed by a robot.”
The company also began with the business intent of sequencing only the human genome, rather than those of other species, too — a strategy that was heresy in 2005, when the founders set out to raise money. At that time, only two human genomes had been sequenced. However, Complete Genomics founders argue that focusing just on the human genome has given them a leg up.
“You make a whole bunch of decisions that don’t work well for corn or bacteria, but they work very well for humans,” Dr. Reid said.
http://www.nytimes.com/2012/03/08/techn ... h_20120308
Cost of Gene Sequencing Falls, Raising Hopes for Medical Advances
By JOHN MARKOFF
MOUNTAIN VIEW, Calif. — In Silicon Valley, the line between computing and biology has begun to blur in a way that could have enormous consequences for human longevity.
Bill Banyai, an optical physicist at Complete Genomics, has helped make that happen. When he began developing a gene sequencing machine, he relied heavily on his background at two computer networking start-up companies. His digital expertise was essential in designing a factory that automated and greatly lowered the cost of mapping the three billion base pairs that form the human genome.
The promise is that low-cost gene sequencing will lead to a new era of personalized medicine, yielding new approaches for treating cancers and other serious diseases. The arrival of such cures has been glacial, however, although the human genome was originally sequenced more than a decade ago.
Now that is changing, in large part because of the same semiconductor industry manufacturing trends that opened up consumer devices like the PC and the smartphone: exponential increases in processing power and transistor density are accompanied by costs that fall at an accelerating rate.
As a result, both new understanding and new medicines will arrive at a quickening pace, according to the biologists and computer scientists.
“For all of human history, humans have not had the readout of the software that makes them alive,” said Larry Smarr, director of the California Institute of Telecommunications and Information Technology, a research center that is jointly operated by the University of California, San Diego, and the University of California, Irvine, who is a member of the Complete Genomics scientific advisory board. “Once you make the transition from a data poor to data rich environment, everything changes.”
Complete Genomics, based in Mountain View, is one of more than three dozen firms hastening to push the cost of sequencing an entire human genome below $1,000. The challenge is part biology, part chemistry, part computing, and in Complete Genomics’ case, part computer networking.
Complete Genomics is a classic Silicon Valley start-up story. Even the gene sequencing machines, which are housed in a 4,000-square-foot room bathed in an eerie blue light, appear more like a traditional data center than a biology lab.
In 2005 ,when Clifford Reid, a successful Silicon Valley software entrepreneur, began to assemble his team, he approached Dr. Banyai and asked if he was interested in joining a gene sequencing start-up. Dr. Reid, who was also trained in physics and math, had spent a year as an entrepreneur-in-residence at the Massachusetts Institute of Technology, where he had become a convert to bioinformatics, the application of computer science and information technologies to biology and medicine.
Dr. Banyai had even less experience in biology.
Formerly with the Internet networking start-ups GlimmerGlass and Silicon Light Machines, he in turn began by reading a pioneering 2005 article in the journal Science in which a group of researchers in George Church’s genetics laboratory at Harvard describe a new technique intended to speed gene sequencing.
Today Dr. Banyai is finishing the second generation of a machine that blends robotics, chemistry, optics and computing. It is emblematic of the serendipitous changes that take place when a manufacturing process is transformed: performance increases and cost falls at an accelerating rate.
“Genomes are now being sequenced incredibly cheaply,” said Russ B. Altman, who is a founder of Personalis, a start-up based in Palo Alto, Calif., that is developing software to interpret genomes. “On the discovery and science side we will be able to do clinical trials. We’ll be able to check the entire genome.”
Recently, on the company’s Web site, Dr. Reid predicted that the cost of gene sequencing could eventually be as low as that of a blood test: “I believe that the impact on the medical community of whole human genome sequencing at a cost comparable to a comprehensive blood test will be profound, and it will raise a host of public policy issues (privacy, security, disclosure, reimbursement, interpretation, counseling, etc.), all important topics for future discussions,” he wrote.
Dr. Banyai said he had found that Silicon Valley start-up ideas tracked well. “There is this remarkable thing that happens in start-ups. You make up this plan and then you step off a cliff and magically a little bridge appears,” he noted, as new technologies appear in the nick of time.
In the case of Complete Genomics, the company is riding in part on big advances being made in industrial digital cameras that are capable of capturing the fluorescent molecules that are used to “read” small sequences of DNA.
In the last half-year, a new generation of cameras, more frequently used for factory inspection systems, has made it possible to speed up the Complete Genomics sequencing process tenfold. That, the company has said, will drive its capacity to 100,000 genomes annually from 10,000.
The parallels between the evolution of the nascent gene sequencing industry and the Valley’s chip makers are striking. By placing more circuits on a silicon wafer at an exponentially increasing pace since the early 1960s, the semiconductor industry transformed the cost of computing. As a result, today the world’s most powerful supercomputer from the 1980s nestles comfortably in your hand and costs several hundred dollars.
Complete Genomics’ competitors are also exploiting designs to drive costs down. For example, Life Technologies, based in Carlsbad, Calif. uses a direct approach to read the bases in the genome from an array of sensors on the surface of a semiconductor chip. As more sensors are packed onto each successive generation of technology, the cost of sequencing will also fall sharply.
Last month, Oxford Nanopore Technologies created an industry sensation when it introduced a machine that sequenced genes using an alternative approach called nanopore sequencing, in which a strand of DNA is read as it is pulled through a microscopic hole.
The system is scheduled to be available later this year. However, it has an error rate much higher than that of the Complete Genomics system, which has independently been given high marks for accuracy.
Because there is no clear winner yet, all of the companies are pushing hard to get down the cost curve as fast as possible
In 2011, Complete Genomics became one of the market leaders. This year, it has produced more than 3,000 sequences at a cost of about $5,000 each. Dr. Banyai’s higher capacity second generation system is now being installed and will begin production during the first half of this year. A third generation design has been completed.
What initially set Complete Genomics apart from the field was its strategy of offering gene sequencing as a service, rather than selling a machine to laboratories. More recently, Illumina, one of its crucial competitors, has also begun offering sequencing as a service, in addition to selling its machines.
“Our competitors have to supply kits that can be executed by a graduate student rolling out of bed with a hangover,” said Dr. Reid. “We don’t live with that standard, and that can be tremendously liberating. Ours can be horrifically complex as long as it can be executed by a robot.”
The company also began with the business intent of sequencing only the human genome, rather than those of other species, too — a strategy that was heresy in 2005, when the founders set out to raise money. At that time, only two human genomes had been sequenced. However, Complete Genomics founders argue that focusing just on the human genome has given them a leg up.
“You make a whole bunch of decisions that don’t work well for corn or bacteria, but they work very well for humans,” Dr. Reid said.
http://www.nytimes.com/2012/03/08/techn ... h_20120308
Vijay Kumar: Robots that fly ... and cooperate
http://www.youtube.com/watch?feature=pl ... ErEBkj_3PY#!
http://www.youtube.com/watch?feature=pl ... ErEBkj_3PY#!
32 Innovations That Will Change Your Tomorrow
The electric light was a failure.
Invented by the British chemist Humphry Davy in the early 1800s, it spent nearly 80 years being passed from one initially hopeful researcher to another, like some not-quite-housebroken puppy. In 1879, Thomas Edison finally figured out how to make an incandescent light bulb that people would buy. But that didn’t mean the technology immediately became successful. It took another 40 years, into the 1920s, for electric utilities to become stable, profitable businesses. And even then, success happened only because the utilities created other reasons to consume electricity. They invented the electric toaster and the electric curling iron and found lots of uses for electric motors. They built Coney Island. They installed electric streetcar lines in any place large enough to call itself a town. All of this, these frivolous gadgets and pleasurable diversions, gave us the light bulb.
We tend to rewrite the histories of technological innovation, making myths about a guy who had a great idea that changed the world. In reality, though, innovation isn’t the goal; it’s everything that gets you there. It’s bad financial decisions and blueprints for machines that weren’t built until decades later. It’s the important leaps forward that synthesize lots of ideas, and it’s the belly-up failures that teach us what not to do.
When we ignore how innovation actually works, we make it hard to see what’s happening right in front of us today. If you don’t know that the incandescent light was a failure before it was a success, it’s easy to write off some modern energy innovations — like solar panels — because they haven’t hit the big time fast enough.
Worse, the fairy-tale view of history implies that innovation has an end. It doesn’t. What we want and what we need keeps changing. The incandescent light was a 19th-century failure and a 20th- century success. Now it’s a failure again, edged out by new technologies, like LEDs, that were, themselves, failures for many years.
That’s what this issue is about: all the little failures, trivialities and not-quite-solved mysteries that make the successes possible. This is what innovation looks like. It’s messy, and it’s awesome. Maggie Koerth-Baker
More.....
http://www.nytimes.com/interactive/2012 ... h_20120602
The electric light was a failure.
Invented by the British chemist Humphry Davy in the early 1800s, it spent nearly 80 years being passed from one initially hopeful researcher to another, like some not-quite-housebroken puppy. In 1879, Thomas Edison finally figured out how to make an incandescent light bulb that people would buy. But that didn’t mean the technology immediately became successful. It took another 40 years, into the 1920s, for electric utilities to become stable, profitable businesses. And even then, success happened only because the utilities created other reasons to consume electricity. They invented the electric toaster and the electric curling iron and found lots of uses for electric motors. They built Coney Island. They installed electric streetcar lines in any place large enough to call itself a town. All of this, these frivolous gadgets and pleasurable diversions, gave us the light bulb.
We tend to rewrite the histories of technological innovation, making myths about a guy who had a great idea that changed the world. In reality, though, innovation isn’t the goal; it’s everything that gets you there. It’s bad financial decisions and blueprints for machines that weren’t built until decades later. It’s the important leaps forward that synthesize lots of ideas, and it’s the belly-up failures that teach us what not to do.
When we ignore how innovation actually works, we make it hard to see what’s happening right in front of us today. If you don’t know that the incandescent light was a failure before it was a success, it’s easy to write off some modern energy innovations — like solar panels — because they haven’t hit the big time fast enough.
Worse, the fairy-tale view of history implies that innovation has an end. It doesn’t. What we want and what we need keeps changing. The incandescent light was a 19th-century failure and a 20th- century success. Now it’s a failure again, edged out by new technologies, like LEDs, that were, themselves, failures for many years.
That’s what this issue is about: all the little failures, trivialities and not-quite-solved mysteries that make the successes possible. This is what innovation looks like. It’s messy, and it’s awesome. Maggie Koerth-Baker
More.....
http://www.nytimes.com/interactive/2012 ... h_20120602
June 6, 2012
DNA Blueprint for Fetus Built Using Tests of Parents
By ANDREW POLLACK
For the first time, researchers have determined virtually the entire genome of a fetus using only a blood sample from the pregnant woman and a saliva specimen from the father.
The accomplishment heralds an era in which parents might find it easier to know the complete DNA blueprint of a child months before it is born.
That would allow thousands of genetic diseases to be detected prenatally. But the ability to know so much about an unborn child is likely to raise serious ethical considerations as well. It could increase abortions for reasons that have little to do with medical issues and more to do with parental preferences for traits in children.
“It’s an extraordinary piece of technology, really quite remarkable,” said Peter Benn, professor of genetics and developmental biology at the University of Connecticut, who was not involved in the work. “What I see in this paper is a glance into the future.”
The paper, published Wednesday in the journal Science Translational Medicine, was written by genome scientists at the University of Washington. They took advantage of new high-speed DNA sequencing and some statistical and computational acrobatics to deduce the DNA sequence of the fetus with about 98 percent accuracy.
The process is not practical, affordable or accurate enough for use now, experts said. The University of Washington researchers estimated that it would cost $20,000 to $50,000 to do one fetal genome today.
But the cost of DNA sequencing is falling at a blistering pace, and accuracy is improving as well. The researchers estimated that the procedure could be widely available in three to five years. Others said it would take somewhat longer.
It is already possible to determine the DNA sequence of a fetus by acquiring fetal cells through amniocentesis or chorionic villus sampling, which involves testing the placental tissue. But these procedures are invasive and carry a slight risk of inducing a miscarriage.
For couples worried about passing on a genetic disease, it is also possible to use in vitro fertilization and have an embryo genetically tested before implantation into the womb.
http://www.nytimes.com/2012/06/07/healt ... h_20120607
DNA Blueprint for Fetus Built Using Tests of Parents
By ANDREW POLLACK
For the first time, researchers have determined virtually the entire genome of a fetus using only a blood sample from the pregnant woman and a saliva specimen from the father.
The accomplishment heralds an era in which parents might find it easier to know the complete DNA blueprint of a child months before it is born.
That would allow thousands of genetic diseases to be detected prenatally. But the ability to know so much about an unborn child is likely to raise serious ethical considerations as well. It could increase abortions for reasons that have little to do with medical issues and more to do with parental preferences for traits in children.
“It’s an extraordinary piece of technology, really quite remarkable,” said Peter Benn, professor of genetics and developmental biology at the University of Connecticut, who was not involved in the work. “What I see in this paper is a glance into the future.”
The paper, published Wednesday in the journal Science Translational Medicine, was written by genome scientists at the University of Washington. They took advantage of new high-speed DNA sequencing and some statistical and computational acrobatics to deduce the DNA sequence of the fetus with about 98 percent accuracy.
The process is not practical, affordable or accurate enough for use now, experts said. The University of Washington researchers estimated that it would cost $20,000 to $50,000 to do one fetal genome today.
But the cost of DNA sequencing is falling at a blistering pace, and accuracy is improving as well. The researchers estimated that the procedure could be widely available in three to five years. Others said it would take somewhat longer.
It is already possible to determine the DNA sequence of a fetus by acquiring fetal cells through amniocentesis or chorionic villus sampling, which involves testing the placental tissue. But these procedures are invasive and carry a slight risk of inducing a miscarriage.
For couples worried about passing on a genetic disease, it is also possible to use in vitro fertilization and have an embryo genetically tested before implantation into the womb.
http://www.nytimes.com/2012/06/07/healt ... h_20120607
July 3, 2012
Rapid H.I.V. Home Test Wins Federal Approval
By DONALD G. McNEIL Jr.
After decades of controversy, the Food and Drug Administration approved a new H.I.V. test on Tuesday that for the first time makes it possible for Americans to learn in the privacy of their homes whether they are infected.
The availability of an H.I.V. test as easy to use as a home-pregnancy kit is yet another step in the normalization of a disease that was once seen as a mark of shame and a death sentence.
The OraQuick test, by OraSure Technologies, uses a mouth swab and gives results in 20 to 40 minutes. A previous test sold over the counter required a user to prick a finger and mail a drop of dried blood to a lab.
Dr. Anthony S. Fauci, the longtime AIDS researcher and director of the National Institute of Allergy and Infectious Diseases, called the new test a “positive step forward” and one that could help bring the 30-year-old epidemic under control.
Getting an infected person onto antiretroviral drugs lowers by as much as 96 percent the chance that he or she will transmit the virus to someone else, so testing and treatment have become crucial to prevention. About 20 percent of the 1.2 million infected Americans do not know they have the disease, the Centers for Disease Control and Prevention estimates, and about 50,000 more get infected each year.
Dr. Robert Gallo, who headed the National Institutes of Health lab that developed the first American blood test for the virus in 1984, called the F.D.A. approval “wonderful because it will get more people into care.”
The idea of a home test has long been mired in controversy. The first application for one was made in 1987, and the F.D.A. has been considering OraSure’s simple mouth-swab test since 2005.
But the history of AIDS and the human immunodeficiency virus that causes it are unique. AIDS emerged in the 1980s wrapped in a shroud of stigma. It was spread by sex, drug injections and blood transfusions. Along with hemophiliacs, heroin users and Haitians, the most vocal group of early victims was gay men, who were then in the throes of a loud and defiant liberation movement.
Because merely being tested for H.I.V. was seen as tantamount to being publicly revealed as gay or addicted to drugs, and because an H.I.V.-positive result was a death sentence, groups like the Gay Men’s Health Crisis and newspapers like The New York Native advised their members and readers to shun testing until ironclad guarantees of anonymity were put in place.
Alarmists predicted a wave of suicides if home tests were made available. At hearings, advocates for AIDS patients handed out copies of an obituary of a San Francisco man who jumped off the Golden Gate Bridge after learning he was infected. C.D.C. officials warned their F.D.A. counterparts that home testing could lead to a surge of new patients that would swamp overburdened health clinics, according to an F.D.A. document.
So, even as tests for other stigmatized diseases like syphilis were once part of getting a marriage license and home pregnancy kits became available at every corner pharmacy, H.I.V. tests lived in a special limbo, usually requiring a counseling session and the signing of a consent form, adding to the air of dread.
Even when antiretroviral drugs emerged in the mid-1990s, states were slow to rewrite laws governing testing.
Mark Harrington, the executive director of the Treatment Action Group, an AIDS advocacy organization, said in an interview that he thought such fears were “a thing of the past” now that it is clear that early treatment saves lives. “Any tool that speeds up diagnosis is really needed,” he said.
The new test has some drawbacks. While it is extremely accurate when administered by medical professionals, it is less so when used by consumers. Researchers found the home test accurate 99.98 percent of the time for people who do not have the virus. By comparison, they found it to be accurate 92 percent of the time in detecting people who do. One concern is the “window period” between the time someone gets the virus and begins to develop the antibodies to it, which the test detects. That can take up to three months.
So, while only about one person in 5,000 would get a false negative test, about one person in 12 could get a false positive.
Any positive test needs confirmation in a doctor’s office, the F.D.A. said, and people engaged in high-risk sex should test themselves regularly.
The agency does not intend for the home test to replace medical testing, but instead to provide another way for people to find out their H.I.V. status, said Dr. Karen Midthun, director of the F.D.A.’s Center for Biologics Evaluation and Research.
The home test should be available in 30,000 pharmacies, grocery stores and online retailers by October, said Douglas Michels, OraSure’s chief executive. The price has not yet been set. But he said it would be higher than the $17.50 now charged to medical professionals because the company will do more complicated packaging for the home kit, open a 24-hour question line, and advertise to high-risk groups, including gay men, blacks and Hispanics, and sexually active adults. Still, he said, it will be kept inexpensive enough to appeal to people who might want to buy several a year.
Because the F.D.A. approved the home test only for people 17 and older, retail stores may ask customers to show ID, he said. The restriction is not for medical reasons, but because only a few subjects age 14 to 16 were tested, he said, “so that was the deal we worked out with the F.D.A.”
Whether having to show identification would deter teenagers or young-looking people from buying a test is unclear. Mr. Harrington said he thought it might.
In contrast, teenage girls are not legally required to show identification to buy pregnancy tests.
http://www.nytimes.com/2012/07/04/healt ... h_20120704
Rapid H.I.V. Home Test Wins Federal Approval
By DONALD G. McNEIL Jr.
After decades of controversy, the Food and Drug Administration approved a new H.I.V. test on Tuesday that for the first time makes it possible for Americans to learn in the privacy of their homes whether they are infected.
The availability of an H.I.V. test as easy to use as a home-pregnancy kit is yet another step in the normalization of a disease that was once seen as a mark of shame and a death sentence.
The OraQuick test, by OraSure Technologies, uses a mouth swab and gives results in 20 to 40 minutes. A previous test sold over the counter required a user to prick a finger and mail a drop of dried blood to a lab.
Dr. Anthony S. Fauci, the longtime AIDS researcher and director of the National Institute of Allergy and Infectious Diseases, called the new test a “positive step forward” and one that could help bring the 30-year-old epidemic under control.
Getting an infected person onto antiretroviral drugs lowers by as much as 96 percent the chance that he or she will transmit the virus to someone else, so testing and treatment have become crucial to prevention. About 20 percent of the 1.2 million infected Americans do not know they have the disease, the Centers for Disease Control and Prevention estimates, and about 50,000 more get infected each year.
Dr. Robert Gallo, who headed the National Institutes of Health lab that developed the first American blood test for the virus in 1984, called the F.D.A. approval “wonderful because it will get more people into care.”
The idea of a home test has long been mired in controversy. The first application for one was made in 1987, and the F.D.A. has been considering OraSure’s simple mouth-swab test since 2005.
But the history of AIDS and the human immunodeficiency virus that causes it are unique. AIDS emerged in the 1980s wrapped in a shroud of stigma. It was spread by sex, drug injections and blood transfusions. Along with hemophiliacs, heroin users and Haitians, the most vocal group of early victims was gay men, who were then in the throes of a loud and defiant liberation movement.
Because merely being tested for H.I.V. was seen as tantamount to being publicly revealed as gay or addicted to drugs, and because an H.I.V.-positive result was a death sentence, groups like the Gay Men’s Health Crisis and newspapers like The New York Native advised their members and readers to shun testing until ironclad guarantees of anonymity were put in place.
Alarmists predicted a wave of suicides if home tests were made available. At hearings, advocates for AIDS patients handed out copies of an obituary of a San Francisco man who jumped off the Golden Gate Bridge after learning he was infected. C.D.C. officials warned their F.D.A. counterparts that home testing could lead to a surge of new patients that would swamp overburdened health clinics, according to an F.D.A. document.
So, even as tests for other stigmatized diseases like syphilis were once part of getting a marriage license and home pregnancy kits became available at every corner pharmacy, H.I.V. tests lived in a special limbo, usually requiring a counseling session and the signing of a consent form, adding to the air of dread.
Even when antiretroviral drugs emerged in the mid-1990s, states were slow to rewrite laws governing testing.
Mark Harrington, the executive director of the Treatment Action Group, an AIDS advocacy organization, said in an interview that he thought such fears were “a thing of the past” now that it is clear that early treatment saves lives. “Any tool that speeds up diagnosis is really needed,” he said.
The new test has some drawbacks. While it is extremely accurate when administered by medical professionals, it is less so when used by consumers. Researchers found the home test accurate 99.98 percent of the time for people who do not have the virus. By comparison, they found it to be accurate 92 percent of the time in detecting people who do. One concern is the “window period” between the time someone gets the virus and begins to develop the antibodies to it, which the test detects. That can take up to three months.
So, while only about one person in 5,000 would get a false negative test, about one person in 12 could get a false positive.
Any positive test needs confirmation in a doctor’s office, the F.D.A. said, and people engaged in high-risk sex should test themselves regularly.
The agency does not intend for the home test to replace medical testing, but instead to provide another way for people to find out their H.I.V. status, said Dr. Karen Midthun, director of the F.D.A.’s Center for Biologics Evaluation and Research.
The home test should be available in 30,000 pharmacies, grocery stores and online retailers by October, said Douglas Michels, OraSure’s chief executive. The price has not yet been set. But he said it would be higher than the $17.50 now charged to medical professionals because the company will do more complicated packaging for the home kit, open a 24-hour question line, and advertise to high-risk groups, including gay men, blacks and Hispanics, and sexually active adults. Still, he said, it will be kept inexpensive enough to appeal to people who might want to buy several a year.
Because the F.D.A. approved the home test only for people 17 and older, retail stores may ask customers to show ID, he said. The restriction is not for medical reasons, but because only a few subjects age 14 to 16 were tested, he said, “so that was the deal we worked out with the F.D.A.”
Whether having to show identification would deter teenagers or young-looking people from buying a test is unclear. Mr. Harrington said he thought it might.
In contrast, teenage girls are not legally required to show identification to buy pregnancy tests.
http://www.nytimes.com/2012/07/04/healt ... h_20120704
July 20, 2012
In First, Software Emulates Lifespan of Entire Organism
By JOHN MARKOFF
STANFORD, Calif. — Scientists at Stanford University and the J. Craig Venter Institute have developed the first software simulation of an entire organism, a humble single-cell bacterium that lives in the human genital and respiratory tracts.
The scientists and other experts said the work was a giant step toward developing computerized laboratories that could carry out many thousands of experiments much faster than is possible now, helping scientists penetrate the mysteries of diseases like cancer and Alzheimer’s.
“You read in the paper just about every week, ‘Cancer gene discovered’ or ‘Alzheimer gene discovered,’ ” said the leader of the new research, Markus W. Covert, an assistant professor of bioengineering at Stanford. “A lot of the public wonders, ‘Why haven’t we cured all these things?’ The answer, of course, is that cancer is not a one-gene problem; it’s a many-thousands-of-factors problem.”
For medical researchers and biochemists, simulation software will vastly speed the early stages of screening for new compounds. And for molecular biologists, models that are of sufficient accuracy will yield new understanding of basic cellular principles.
This kind of modeling is already in use to study individual cellular processes like metabolism. But Dr. Covert said: “Where I think our work is different is that we explicitly include all of the genes and every known gene function. There’s no one else out there who has been able to include more than a handful of functions or more than, say, one-third of the genes.”
The simulation of the complete life cycle of the pathogen, Mycoplasma genitalium, was presented on Friday in the journal Cell. The scientists called it a “first draft” but added that the effort was the first time an entire organism had been modeled in such detail — in this case, all of its 525 genes.
The simulation, which runs on a cluster of 128 computers, models the complete life span of the cell at the molecular level, charting the interactions of 28 categories of molecules — including DNA, RNA, proteins and small molecules known as metabolites, which are generated by cell processes.
“The model presented by the authors is the first truly integrated effort to simulate the workings of a free-living microbe, and it should be commended for its audacity alone,” wrote two independent commentators, Peter L. Freddolino and Saeed Tavazoie, both of Columbia University, in an editorial accompanying the article. “This is a tremendous task, involving the interpretation and integration of a massive amount of data.”
They called the simulation an important advance in the new field of computational biology, which has recently yielded such achievements as the creation of a synthetic life form — an entire bacterial genome created by a team led by the genome pioneer J. Craig Venter. The scientists used it to take over an existing cell.
Efforts to build computer models of cell behavior are not new. A decade ago, scientists developed simulations of metabolism that are now being used to study a wide array of cells, including bacteria, yeast and photosynthetic organisms. Other models exist for processes like protein synthesis.
“These models are now in routine use around the world to study the metabolic properties of many organisms,” said Bernhard O. Palsson, a professor of bioengineering at the University of California, San Diego, who added that they were used commercially to formulate commodity chemicals and biofuels.
For the new computer simulation, the researchers had the advantage of extensive scientific literature on the bacterium. They were able to use data taken from more than 900 scientific papers to validate the accuracy of their software model.
Still, they said, the model of the simplest biological system was pushing the limits of their computers.
“Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data,” Dr. Covert wrote. “I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds. We often think of the DNA as the storage medium, but clearly there is more to it than that.”
In designing their model, the scientists chose an approach called object-oriented programming, which parallels the design of modern software systems. Software designers organize their programs in modules, which communicate with one another by passing data and instructions back and forth.
Similarly, the simulated bacterium is a series of modules that mimic the various functions of the cell.
“The major modeling insight we had a few years ago was to break up the functionality of the cell into subgroups, which we could model individually, each with its own mathematics, and then to integrate these submodels together into a whole,” Dr. Covert said. “It turned out to be a very exciting idea.”
M. genitalium, a parasite that causes sexually transmitted disease, has the smallest genome of any independent organism. It played a role in 2008 in the Venter Institute‘s synthesis of the first artificial chromosome; the researchers were able to stitch together the entire genome of the bacterium.
The bacterium, with its 525 genes, is far less complex than E. coli, another bacterium widely used in laboratory experiments; E. coli has 4,288 genes. The researchers said that more complex cells would present significant challenges. Currently it takes about 9 to 10 hours of computer time to simulate a single division of the smallest cell — about the same time the cell takes to divide in its natural environment.
“The real question on our minds is: what happens when we bring this to a bigger organism, like E. coli, yeast or even eventually a human cell?” Dr. Covert said. He noted that E. coli divided every 20 to 30 minutes and that the number of molecular interactions in E. coli was a much higher multiple, which would significantly extend the time required to run the simulation.
“I’ll have the answer in a couple of years,” he wrote.
http://www.nytimes.com/2012/07/21/scien ... h_20120721
********
July 20, 2012
European Agency Backs Approval of a Gene Therapy
By ANDREW POLLACK
After more than two decades of dashed expectations, the field of gene therapy appears close to reaching a milestone: a regulatory approval.
The European Medicines Agency has recommended approval of a gene therapy to treat a rare genetic disease, according to the agency’s Web site.
If the European Commission follows the advice, as it usually does, this would be the first regulatory approval of a gene therapy drug in the Western world. That could give a boost to the field, which at times has struggled for credibility and financing.
An approval “is really potentially going to change the way the field is looked at,” said Jeffrey Ostrove, chief executive of Ceregene, a gene therapy company in San Diego. Some pharmaceutical companies have been reluctant to invest in the field, he said, because “there are no approved products in the major markets they sell in.”
Gene therapy involves providing the body with genes it needs, like correct copies of defective genes that cause genetic disorders. Its use in the West so far has been confined to clinical trials.
The therapy recommended for approval in Europe, called Glybera, was developed by uniQure, a Dutch company. It treats lipoprotein lipase deficiency, a disease that affects only several hundred people in the European Union and a similar number in North America.
People with the disease have a genetic mutation that prevents them from producing an enzyme needed to break down certain fat-carrying particles that circulate in the bloodstream after meals. Without the enzyme, so much fat can accumulate that the blood looks white rather than red.
“It’s the equivalent of having a 10 percent cream in your bloodstream,” said Dr. Daniel Gaudet, a professor of medicine at the University of Montreal, who led the clinical trials of the drug. People with the disease are prone to severe bouts of inflammation of the pancreas. There is no good treatment except an extremely low-fat diet.
Glybera provides correct copies of the lipoprotein lipase gene, which allows patients to make some of the needed enzyme. A single treatment, consisting of injections into multiple spots on the leg muscles on the same day, is expected to last for several years, if not longer, said Jorn Aldag, chief executive of uniQure.
Mr. Aldag said the company hoped to apply for approval of the gene therapy in the United States eventually, but he was not certain of the timing.
Gene therapy has long been seen as a promising way to treat numerous diseases. But hundreds of clinical trials have been conducted since 1990 and most have failed, in part because it has been difficult to deliver the genes and get them to work for a long time. The field has also been set back by some safety issues, particularly the death of a teenager in a 1999 clinical trial at the University of Pennsylvania.
But researchers have been slowly overcoming the obstacles and in the last few years there have been reports of successes in attempts to treat cancer, hemophilia B, certain immune diseases and a condition that causes blindness.
“It didn’t occur as rapidly, I think, as people had kind of promised or suggested 15 or 20 years ago, but we are starting to see success,” said Dr. Mark A. Kay, a professor of pediatrics and genetics at Stanford.
A gene therapy to treat cancer won approval in China in 2003. But some Western experts have questions about the rigor of the regulatory review in that country.
How effective Glybera is might still be open to some question, in part because the company tested the drug in only 27 patients, and without rigorous controlled clinical trials.
The Committee for Medicinal Products for Human Use, which recommends whether new drugs should be approved in Europe, rejected Glybera three times in the last year or so.
After its third rejection, in April, the committee said that the company had “not provided sufficient evidence” that blood lipids were lowered in a persistent manner and that there was also insufficient evidence of a reduction of the incidence of pancreatitis, the inflammation of the pancreas.
But the committee has now reversed itself. It said that the approved population had been narrowed to those with the most severe disease and that the company would be required to monitor the outcomes of patients treated with Glybera and provide that data to regulators.
Dr. Gaudet, who has been a paid adviser to uniQure, said the trials showed that after the treatment, patients had fewer bouts of pancreatitis and those bouts tended to be less intense and painful.
The repeated setbacks took its toll on the company, which was once known as Amsterdam Molecular Therapeutics. That company ran out of money this year and is now being liquidated. UniQure, which is privately held, was formed with new investment and took on the people and assets of Amsterdam Molecular.
http://www.nytimes.com/2012/07/21/healt ... h_20120721
In First, Software Emulates Lifespan of Entire Organism
By JOHN MARKOFF
STANFORD, Calif. — Scientists at Stanford University and the J. Craig Venter Institute have developed the first software simulation of an entire organism, a humble single-cell bacterium that lives in the human genital and respiratory tracts.
The scientists and other experts said the work was a giant step toward developing computerized laboratories that could carry out many thousands of experiments much faster than is possible now, helping scientists penetrate the mysteries of diseases like cancer and Alzheimer’s.
“You read in the paper just about every week, ‘Cancer gene discovered’ or ‘Alzheimer gene discovered,’ ” said the leader of the new research, Markus W. Covert, an assistant professor of bioengineering at Stanford. “A lot of the public wonders, ‘Why haven’t we cured all these things?’ The answer, of course, is that cancer is not a one-gene problem; it’s a many-thousands-of-factors problem.”
For medical researchers and biochemists, simulation software will vastly speed the early stages of screening for new compounds. And for molecular biologists, models that are of sufficient accuracy will yield new understanding of basic cellular principles.
This kind of modeling is already in use to study individual cellular processes like metabolism. But Dr. Covert said: “Where I think our work is different is that we explicitly include all of the genes and every known gene function. There’s no one else out there who has been able to include more than a handful of functions or more than, say, one-third of the genes.”
The simulation of the complete life cycle of the pathogen, Mycoplasma genitalium, was presented on Friday in the journal Cell. The scientists called it a “first draft” but added that the effort was the first time an entire organism had been modeled in such detail — in this case, all of its 525 genes.
The simulation, which runs on a cluster of 128 computers, models the complete life span of the cell at the molecular level, charting the interactions of 28 categories of molecules — including DNA, RNA, proteins and small molecules known as metabolites, which are generated by cell processes.
“The model presented by the authors is the first truly integrated effort to simulate the workings of a free-living microbe, and it should be commended for its audacity alone,” wrote two independent commentators, Peter L. Freddolino and Saeed Tavazoie, both of Columbia University, in an editorial accompanying the article. “This is a tremendous task, involving the interpretation and integration of a massive amount of data.”
They called the simulation an important advance in the new field of computational biology, which has recently yielded such achievements as the creation of a synthetic life form — an entire bacterial genome created by a team led by the genome pioneer J. Craig Venter. The scientists used it to take over an existing cell.
Efforts to build computer models of cell behavior are not new. A decade ago, scientists developed simulations of metabolism that are now being used to study a wide array of cells, including bacteria, yeast and photosynthetic organisms. Other models exist for processes like protein synthesis.
“These models are now in routine use around the world to study the metabolic properties of many organisms,” said Bernhard O. Palsson, a professor of bioengineering at the University of California, San Diego, who added that they were used commercially to formulate commodity chemicals and biofuels.
For the new computer simulation, the researchers had the advantage of extensive scientific literature on the bacterium. They were able to use data taken from more than 900 scientific papers to validate the accuracy of their software model.
Still, they said, the model of the simplest biological system was pushing the limits of their computers.
“Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data,” Dr. Covert wrote. “I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds. We often think of the DNA as the storage medium, but clearly there is more to it than that.”
In designing their model, the scientists chose an approach called object-oriented programming, which parallels the design of modern software systems. Software designers organize their programs in modules, which communicate with one another by passing data and instructions back and forth.
Similarly, the simulated bacterium is a series of modules that mimic the various functions of the cell.
“The major modeling insight we had a few years ago was to break up the functionality of the cell into subgroups, which we could model individually, each with its own mathematics, and then to integrate these submodels together into a whole,” Dr. Covert said. “It turned out to be a very exciting idea.”
M. genitalium, a parasite that causes sexually transmitted disease, has the smallest genome of any independent organism. It played a role in 2008 in the Venter Institute‘s synthesis of the first artificial chromosome; the researchers were able to stitch together the entire genome of the bacterium.
The bacterium, with its 525 genes, is far less complex than E. coli, another bacterium widely used in laboratory experiments; E. coli has 4,288 genes. The researchers said that more complex cells would present significant challenges. Currently it takes about 9 to 10 hours of computer time to simulate a single division of the smallest cell — about the same time the cell takes to divide in its natural environment.
“The real question on our minds is: what happens when we bring this to a bigger organism, like E. coli, yeast or even eventually a human cell?” Dr. Covert said. He noted that E. coli divided every 20 to 30 minutes and that the number of molecular interactions in E. coli was a much higher multiple, which would significantly extend the time required to run the simulation.
“I’ll have the answer in a couple of years,” he wrote.
http://www.nytimes.com/2012/07/21/scien ... h_20120721
********
July 20, 2012
European Agency Backs Approval of a Gene Therapy
By ANDREW POLLACK
After more than two decades of dashed expectations, the field of gene therapy appears close to reaching a milestone: a regulatory approval.
The European Medicines Agency has recommended approval of a gene therapy to treat a rare genetic disease, according to the agency’s Web site.
If the European Commission follows the advice, as it usually does, this would be the first regulatory approval of a gene therapy drug in the Western world. That could give a boost to the field, which at times has struggled for credibility and financing.
An approval “is really potentially going to change the way the field is looked at,” said Jeffrey Ostrove, chief executive of Ceregene, a gene therapy company in San Diego. Some pharmaceutical companies have been reluctant to invest in the field, he said, because “there are no approved products in the major markets they sell in.”
Gene therapy involves providing the body with genes it needs, like correct copies of defective genes that cause genetic disorders. Its use in the West so far has been confined to clinical trials.
The therapy recommended for approval in Europe, called Glybera, was developed by uniQure, a Dutch company. It treats lipoprotein lipase deficiency, a disease that affects only several hundred people in the European Union and a similar number in North America.
People with the disease have a genetic mutation that prevents them from producing an enzyme needed to break down certain fat-carrying particles that circulate in the bloodstream after meals. Without the enzyme, so much fat can accumulate that the blood looks white rather than red.
“It’s the equivalent of having a 10 percent cream in your bloodstream,” said Dr. Daniel Gaudet, a professor of medicine at the University of Montreal, who led the clinical trials of the drug. People with the disease are prone to severe bouts of inflammation of the pancreas. There is no good treatment except an extremely low-fat diet.
Glybera provides correct copies of the lipoprotein lipase gene, which allows patients to make some of the needed enzyme. A single treatment, consisting of injections into multiple spots on the leg muscles on the same day, is expected to last for several years, if not longer, said Jorn Aldag, chief executive of uniQure.
Mr. Aldag said the company hoped to apply for approval of the gene therapy in the United States eventually, but he was not certain of the timing.
Gene therapy has long been seen as a promising way to treat numerous diseases. But hundreds of clinical trials have been conducted since 1990 and most have failed, in part because it has been difficult to deliver the genes and get them to work for a long time. The field has also been set back by some safety issues, particularly the death of a teenager in a 1999 clinical trial at the University of Pennsylvania.
But researchers have been slowly overcoming the obstacles and in the last few years there have been reports of successes in attempts to treat cancer, hemophilia B, certain immune diseases and a condition that causes blindness.
“It didn’t occur as rapidly, I think, as people had kind of promised or suggested 15 or 20 years ago, but we are starting to see success,” said Dr. Mark A. Kay, a professor of pediatrics and genetics at Stanford.
A gene therapy to treat cancer won approval in China in 2003. But some Western experts have questions about the rigor of the regulatory review in that country.
How effective Glybera is might still be open to some question, in part because the company tested the drug in only 27 patients, and without rigorous controlled clinical trials.
The Committee for Medicinal Products for Human Use, which recommends whether new drugs should be approved in Europe, rejected Glybera three times in the last year or so.
After its third rejection, in April, the committee said that the company had “not provided sufficient evidence” that blood lipids were lowered in a persistent manner and that there was also insufficient evidence of a reduction of the incidence of pancreatitis, the inflammation of the pancreas.
But the committee has now reversed itself. It said that the approved population had been narrowed to those with the most severe disease and that the company would be required to monitor the outcomes of patients treated with Glybera and provide that data to regulators.
Dr. Gaudet, who has been a paid adviser to uniQure, said the trials showed that after the treatment, patients had fewer bouts of pancreatitis and those bouts tended to be less intense and painful.
The repeated setbacks took its toll on the company, which was once known as Amsterdam Molecular Therapeutics. That company ran out of money this year and is now being liquidated. UniQure, which is privately held, was formed with new investment and took on the people and assets of Amsterdam Molecular.
http://www.nytimes.com/2012/07/21/healt ... h_20120721
July 27, 2012
Imagine a World Without AIDS
By DANIELLE OFRI
THE beginning of the end of AIDS? The article with that title jumped out at me last week, as I did my weekly table-of-contents scan of The New England Journal of Medicine. I wasn’t prepared for the flood of emotion that overcame me. The beginning of the end? Could it really be?
For those of us who did our medical training in the late ’80s and early ’90s, AIDS saturated our lives. The whole era had a medieval feel, with visceral suffering and human decimation all around. Death was vivid, brutal and omnipresent.
Bellevue Hospital, where I trained, was one of those city hospitals that felt like ground zero for the plague. Every third admission seemed to be a patient in his mid-20s who looked as if he’d arrived from Dachau or Biafra, with nary a T-cell to his name. Horrific Kaposi’s sarcoma ulcerated these patients’ bodies. P.C.P., a brutal form of pneumonia, strangled their breathing. Fevers and infections plundered every organ system. What few defenses their bodies mustered were pummeled into insignificance.
The utter relentlessness of the disease pummeled the doctors-in-training as well. It felt as if we were slogging knee-deep in death, with a horizon that was a monochrome of despair. Witnessing your own generation dying off is not for the faint of heart.
The 17 West AIDS ward in Bellevue was always full to capacity, so H.I.V. patients overflowed into the general medical wards, and of course swamped the prison ward, the tuberculosis ward, the pediatric ward and the emergency room. We even had a “spillover” ward, 12 East, reserved for the “actively dying.” The hospital had carved out a ward of private rooms — otherwise unheard-of in a city hospital — so that these patients could have a modicum of privacy in their final days. Needless to say, 12 East was also full to capacity, with a line of patients waiting for a room to “open up.”
If you’d grabbed a random intern toward the end of my residency in 1995, and asked her if she could envision the headline “The Beginning of the End of AIDS” in less than 20 years, she would have simply stared uncomprehendingly at you with bleary eyes. More than 50,000 Americans died of AIDS that year. By 2009, the number had edged under 20,000.
In the worlds of both medicine and metaphor, the narrative arc of AIDS has almost no peer. The transformation from hopelessness to pragmatic optimism is — scientifically speaking — nothing short of miraculous. Potent combinations of antiviral medications that brought patients off their deathbeds and back to life, viral load testing and H.I.V. genotyping that helped tailor treatment regimens, screening of the blood supply, aggressive public health campaigns, prevention of maternal-fetal transmission — we could hardly have envisioned the pace of development.
After years of disappointments, H.I.V. vaccine research is heating up again, as breakthroughs in the understanding of H.I.V. immunology have identified nearly two dozen potential vaccine candidates. The apparent H.I.V. cure as a result of a bone-marrow transplant in a man known as the “Berlin patient” has stimulated tantalizing gene therapy research.
The staggering progress of these past two decades leaves me breathless, and to be honest, almost teary-eyed. For nearly every other category of disease that afflicts my patients, the treatments are largely the same as when I was an intern. Yes, we have fancier stents for our cardiac patients, and more targeted chemotherapy for our cancer patients, but the overall paradigms have shifted only incrementally.
H.I.V. has been easier to target, in part, because it is caused by a single infectious agent — as opposed to the diverse factors that influence cardiovascular disease and cancer. And then there was the avalanche of resources and the galvanizing of public activism that served to concentrate scientific efforts in a manner never seen before. By no means do I wish to belittle the impressive advances in other fields of medicine, but our oncology wards and cardiac wards still do a brisk business.
AIDS patients in the hospital are a rarity now — they are more likely to be admitted for an ulcer or a heart attack than for an H.I.V.-related illness. The overwhelming majority receive their medical care in outpatient settings, like everyone else who is living with a disease rather than dying of a disease. AIDS has settled in next to hypertension and diabetes as one of those chronic conditions that patients deal with over the course of a lifetime.
“Over the course of a lifetime.” Now there’s a concept we never thought about back then.
There is still a long way to go, of course. The 19th annual International AIDS Conference just ended on Friday, and no one is underestimating the gravity of the challenges that remain, particularly in developing countries. But to even contemplate, however tentatively, the beginning of the end is something that my peers and I never imagined happening in our lifetimes.
I often think about grim days we spent doing rounds on 17 West and 12 East. I remember the slow and tortured deaths of our patients, their emaciated bodies disintegrating into nothingness before our eyes. More tears were shed on those wards than any I’ve worked in since.
And what happened? The 17 West AIDS ward became a regular medical ward. The 12 East dying ward was turned into offices. And then, this month, the inpatient AIDS service at Bellevue closed down entirely. If that doesn’t signify the beginning of the end, I don’t know what does.
Danielle Ofri, an associate professor at New York University School of Medicine, is the editor of the Bellevue Literary Review and the author, most recently, of “Medicine in Translation: Journeys With My Patients.”
http://www.nytimes.com/2012/07/28/opini ... h_20120728
Imagine a World Without AIDS
By DANIELLE OFRI
THE beginning of the end of AIDS? The article with that title jumped out at me last week, as I did my weekly table-of-contents scan of The New England Journal of Medicine. I wasn’t prepared for the flood of emotion that overcame me. The beginning of the end? Could it really be?
For those of us who did our medical training in the late ’80s and early ’90s, AIDS saturated our lives. The whole era had a medieval feel, with visceral suffering and human decimation all around. Death was vivid, brutal and omnipresent.
Bellevue Hospital, where I trained, was one of those city hospitals that felt like ground zero for the plague. Every third admission seemed to be a patient in his mid-20s who looked as if he’d arrived from Dachau or Biafra, with nary a T-cell to his name. Horrific Kaposi’s sarcoma ulcerated these patients’ bodies. P.C.P., a brutal form of pneumonia, strangled their breathing. Fevers and infections plundered every organ system. What few defenses their bodies mustered were pummeled into insignificance.
The utter relentlessness of the disease pummeled the doctors-in-training as well. It felt as if we were slogging knee-deep in death, with a horizon that was a monochrome of despair. Witnessing your own generation dying off is not for the faint of heart.
The 17 West AIDS ward in Bellevue was always full to capacity, so H.I.V. patients overflowed into the general medical wards, and of course swamped the prison ward, the tuberculosis ward, the pediatric ward and the emergency room. We even had a “spillover” ward, 12 East, reserved for the “actively dying.” The hospital had carved out a ward of private rooms — otherwise unheard-of in a city hospital — so that these patients could have a modicum of privacy in their final days. Needless to say, 12 East was also full to capacity, with a line of patients waiting for a room to “open up.”
If you’d grabbed a random intern toward the end of my residency in 1995, and asked her if she could envision the headline “The Beginning of the End of AIDS” in less than 20 years, she would have simply stared uncomprehendingly at you with bleary eyes. More than 50,000 Americans died of AIDS that year. By 2009, the number had edged under 20,000.
In the worlds of both medicine and metaphor, the narrative arc of AIDS has almost no peer. The transformation from hopelessness to pragmatic optimism is — scientifically speaking — nothing short of miraculous. Potent combinations of antiviral medications that brought patients off their deathbeds and back to life, viral load testing and H.I.V. genotyping that helped tailor treatment regimens, screening of the blood supply, aggressive public health campaigns, prevention of maternal-fetal transmission — we could hardly have envisioned the pace of development.
After years of disappointments, H.I.V. vaccine research is heating up again, as breakthroughs in the understanding of H.I.V. immunology have identified nearly two dozen potential vaccine candidates. The apparent H.I.V. cure as a result of a bone-marrow transplant in a man known as the “Berlin patient” has stimulated tantalizing gene therapy research.
The staggering progress of these past two decades leaves me breathless, and to be honest, almost teary-eyed. For nearly every other category of disease that afflicts my patients, the treatments are largely the same as when I was an intern. Yes, we have fancier stents for our cardiac patients, and more targeted chemotherapy for our cancer patients, but the overall paradigms have shifted only incrementally.
H.I.V. has been easier to target, in part, because it is caused by a single infectious agent — as opposed to the diverse factors that influence cardiovascular disease and cancer. And then there was the avalanche of resources and the galvanizing of public activism that served to concentrate scientific efforts in a manner never seen before. By no means do I wish to belittle the impressive advances in other fields of medicine, but our oncology wards and cardiac wards still do a brisk business.
AIDS patients in the hospital are a rarity now — they are more likely to be admitted for an ulcer or a heart attack than for an H.I.V.-related illness. The overwhelming majority receive their medical care in outpatient settings, like everyone else who is living with a disease rather than dying of a disease. AIDS has settled in next to hypertension and diabetes as one of those chronic conditions that patients deal with over the course of a lifetime.
“Over the course of a lifetime.” Now there’s a concept we never thought about back then.
There is still a long way to go, of course. The 19th annual International AIDS Conference just ended on Friday, and no one is underestimating the gravity of the challenges that remain, particularly in developing countries. But to even contemplate, however tentatively, the beginning of the end is something that my peers and I never imagined happening in our lifetimes.
I often think about grim days we spent doing rounds on 17 West and 12 East. I remember the slow and tortured deaths of our patients, their emaciated bodies disintegrating into nothingness before our eyes. More tears were shed on those wards than any I’ve worked in since.
And what happened? The 17 West AIDS ward became a regular medical ward. The 12 East dying ward was turned into offices. And then, this month, the inpatient AIDS service at Bellevue closed down entirely. If that doesn’t signify the beginning of the end, I don’t know what does.
Danielle Ofri, an associate professor at New York University School of Medicine, is the editor of the Bellevue Literary Review and the author, most recently, of “Medicine in Translation: Journeys With My Patients.”
http://www.nytimes.com/2012/07/28/opini ... h_20120728
Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role
By GINA KOLATA
Among the many mysteries of human biology is why complex diseases like diabetes, high blood pressure and psychiatric disorders are so difficult to predict and, often, to treat. An equally perplexing puzzle is why one individual gets a disease like cancer or depression, while an identical twin remains perfectly healthy.
Now scientists have discovered a vital clue to unraveling these riddles. The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave. The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches.
The findings, which are the fruit of an immense federal project involving 440 scientists from 32 laboratories around the world, will have immediate applications for understanding how alterations in the non-gene parts of DNA contribute to human diseases, which may in turn lead to new drugs. They can also help explain how the environment can affect disease risk. In the case of identical twins, small changes in environmental exposure can slightly alter gene switches, with the result that one twin gets a disease and the other does not.
More....
http://www.nytimes.com/2012/09/06/scien ... h_20120906
By GINA KOLATA
Among the many mysteries of human biology is why complex diseases like diabetes, high blood pressure and psychiatric disorders are so difficult to predict and, often, to treat. An equally perplexing puzzle is why one individual gets a disease like cancer or depression, while an identical twin remains perfectly healthy.
Now scientists have discovered a vital clue to unraveling these riddles. The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave. The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches.
The findings, which are the fruit of an immense federal project involving 440 scientists from 32 laboratories around the world, will have immediate applications for understanding how alterations in the non-gene parts of DNA contribute to human diseases, which may in turn lead to new drugs. They can also help explain how the environment can affect disease risk. In the case of identical twins, small changes in environmental exposure can slightly alter gene switches, with the result that one twin gets a disease and the other does not.
More....
http://www.nytimes.com/2012/09/06/scien ... h_20120906
November 3, 2012
How Science Can Build a Better You
By DAVID EWING DUNCAN
IF a brain implant were safe and available and allowed you to operate your iPad or car using only thought, would you want one? What about an embedded device that gently bathed your brain in electrons and boosted memory and attention? Would you order one for your children?
In a future presidential election, would you vote for a candidate who had neural implants that helped optimize his or her alertness and functionality during a crisis, or in a candidates’ debate? Would you vote for a commander in chief who wasn’t equipped with such a device?
If these seem like tinfoil-on-the-head questions, consider the case of Cathy Hutchinson. Paralyzed by a stroke, she recently drank a canister of coffee by using a prosthetic arm controlled by thought. She was helped by a device called Braingate, a tiny bed of electrons surgically implanted on her motor cortex and connected by a wire to a computer.
Working with a team of neuroscientists at Brown University, Ms. Hutchinson, then 58, was asked to imagine that she was moving her own arm. As her neurons fired, Braingate interpreted the mental commands and moved the artificial arm and humanlike hand to deliver the first coffee Ms. Hutchinson had raised to her own lips in 15 years.
Braingate has barely worked on just a handful of people, and it is years away from actually being useful. Yet it’s an example of nascent technologies that in the next two to three decades may transform life not only for the impaired, but also for the healthy.
Other medical technologies that might break through the enhancement barrier range from genetic modifications and stem-cell therapies that might make people cognitively more efficient to nano-bots that could one day repair and optimize molecular structures in cells.
Many researchers, including the Brown neuroscientist John Donoghue, leader of the Braingate team, adamantly oppose the use of their technologies for augmenting the nonimpaired. Yet some healthy Americans are already availing themselves of medical technologies. For years millions of college students and professionals have been popping powerful stimulants like Adderall and Provigil to take exams and to pull all-nighters. These drugs can be highly addictive and may not work for everyone. While more research is needed, so far no evidence has emerged that legions of users have been harmed. The same may be true for a modest use of steroids for athletes.
Which leads us to the crucial question: How far would you go to modify yourself using the latest medical technology?
Over the last couple of years during talks and lectures, I have asked thousands of people a hypothetical question that goes like this: “If I could offer you a pill that allowed your child to increase his or her memory by 25 percent, would you give it to them?”
The show of hands in this informal poll has been overwhelming, with 80 percent or more voting no.
Then I asked a follow-up question. “What if this pill was safe and increased your kid’s grades from a B average to an A average?” People tittered nervously, looked around to see how others were voting as nearly half said yes. (Many didn’t vote at all.)
“And what if all of the other kids are taking the pill?” I asked. The tittering stopped and nearly everyone voted yes.
No pill now exists that can boost memory by 25 percent. Yet neuroscientists tell me that pharmaceutical companies are testing compounds in early stage human trials that may enable patients with dementia and other memory-stealing diseases to have better recall. No one knows if these will work to improve healthy people, but it’s possible that one will work in the future.
More intriguing is the notion that a supermemory or attention pill might be used someday by those with critical jobs like pilots, surgeons, police officers — or the chief executive of the United States. In fact, we may demand that they use them, said the bioethicist Thomas H. Murray. “It might actually be immoral for a surgeon not to take a drug that was safe and steadied his hand,” said Mr. Murray, the former president of the Hastings Center, a bioethics research group. “That would be like using a scalpel that wasn’t sterile.”
HERE is a partial checklist of cutting-edge medical-technology therapies now under way or in an experimental phase that might lead to future enhancements.
More than 200,000 deaf people have had their hearing partially restored by a brain implant that receives sound waves and uses a minicomputer to process and deliver them directly into the brain via the cochlear (audio) nerve. New and experimental technologies could lead to devices that allow people with or possibly without hearing loss to hear better, possibly much better.
The Israel-based company Nano Retina and others are developing early-stage devices and implants that restore partial sight to the blind. Nano Retina uses a tiny sensor backed by electrodes embedded in the back of the eye, on top of the retina. They replace connections damaged by macular degeneration and other diseases. So far images are fuzzy and gray-scale and a long way from restoring functional eyesight. Scientists, however, are currently working on ways to mimic and improve eyesight in people and in robots that could lead to far more sophisticated technologies.
Engineers at companies like Ekso Bionics of Richmond, Calif., are building first-generation exoskeletons that aim to allow patients with paralyzed legs to walk, though the devices are still in the baby-step phase. This summer the sprinter Oscar Pistorius of South Africa proved he could compete at the Olympics using artificial half-leg blades called Cheetahs that some worried might give him an advantage over runners with legs made of flesh and blood. Neuroscientists are developing more advanced prosthetics that may one day be operated from the brain via fiber optic lines embedded under the skin.
For years, scientists have been manipulating genes in animals to make improvements in neural performance, strength and agility, among other augmentations. Directly altering human DNA using “gene therapy” in humans remains dangerous and fraught with ethical challenges. But it may be possible to develop drugs that alter enzymes and other proteins associated with genes for, say, speed and endurance or dopamine levels in the brain connected to improved neural performance.
Synthetic biologists contend that re-engineering cells and DNA may one day allow us to eliminate diseases; a few believe we will be able to build tailor-made people. Others are convinced that stem cells might one day be used to grow fresh brain, heart or liver cells to augment or improve cells in these and other organs.
Not all enhancements are high-tech or invasive. Neuroscientists are seeing boosts from neuro-feedback and video games designed to teach and develop cognition and from meditation and improvements in diet, exercise and sleep. “We may see a convergence of several of these technologies,” said the neurologist Adam Gazzaley of the University of California at San Francisco. He is developing brain-boosting games with developers and engineers who once worked for Lucas Arts, founded by the “Star Wars” director George Lucas.
Which leads to another question: How far would you go to augment yourself? Would you replace perfectly good legs with artificial ones if they made you faster and stronger? What if a United States Agency for Human Augmentation had approved this and other radical enhancements? Would that persuade you?
Ethical challenges for the coming Age of Enhancement include, besides basic safety questions, the issue of who would get the enhancements, how much they would cost, and who would gain an advantage over others by using them. In a society that is already seeing a widening gap between the very rich and the rest of us, the question of a democracy of equals could face a critical test if the well-off also could afford a physical, genetic or bionic advantage. It also may challenge what it means to be human.
Still, the enhancements are coming, and they will be hard to resist. The real issue is what we do with them once they become irresistible.
David Ewing Duncan is a journalist who has contributed to the science section of The New York Times.
http://www.nytimes.com/2012/11/04/sunda ... h_20121104
How Science Can Build a Better You
By DAVID EWING DUNCAN
IF a brain implant were safe and available and allowed you to operate your iPad or car using only thought, would you want one? What about an embedded device that gently bathed your brain in electrons and boosted memory and attention? Would you order one for your children?
In a future presidential election, would you vote for a candidate who had neural implants that helped optimize his or her alertness and functionality during a crisis, or in a candidates’ debate? Would you vote for a commander in chief who wasn’t equipped with such a device?
If these seem like tinfoil-on-the-head questions, consider the case of Cathy Hutchinson. Paralyzed by a stroke, she recently drank a canister of coffee by using a prosthetic arm controlled by thought. She was helped by a device called Braingate, a tiny bed of electrons surgically implanted on her motor cortex and connected by a wire to a computer.
Working with a team of neuroscientists at Brown University, Ms. Hutchinson, then 58, was asked to imagine that she was moving her own arm. As her neurons fired, Braingate interpreted the mental commands and moved the artificial arm and humanlike hand to deliver the first coffee Ms. Hutchinson had raised to her own lips in 15 years.
Braingate has barely worked on just a handful of people, and it is years away from actually being useful. Yet it’s an example of nascent technologies that in the next two to three decades may transform life not only for the impaired, but also for the healthy.
Other medical technologies that might break through the enhancement barrier range from genetic modifications and stem-cell therapies that might make people cognitively more efficient to nano-bots that could one day repair and optimize molecular structures in cells.
Many researchers, including the Brown neuroscientist John Donoghue, leader of the Braingate team, adamantly oppose the use of their technologies for augmenting the nonimpaired. Yet some healthy Americans are already availing themselves of medical technologies. For years millions of college students and professionals have been popping powerful stimulants like Adderall and Provigil to take exams and to pull all-nighters. These drugs can be highly addictive and may not work for everyone. While more research is needed, so far no evidence has emerged that legions of users have been harmed. The same may be true for a modest use of steroids for athletes.
Which leads us to the crucial question: How far would you go to modify yourself using the latest medical technology?
Over the last couple of years during talks and lectures, I have asked thousands of people a hypothetical question that goes like this: “If I could offer you a pill that allowed your child to increase his or her memory by 25 percent, would you give it to them?”
The show of hands in this informal poll has been overwhelming, with 80 percent or more voting no.
Then I asked a follow-up question. “What if this pill was safe and increased your kid’s grades from a B average to an A average?” People tittered nervously, looked around to see how others were voting as nearly half said yes. (Many didn’t vote at all.)
“And what if all of the other kids are taking the pill?” I asked. The tittering stopped and nearly everyone voted yes.
No pill now exists that can boost memory by 25 percent. Yet neuroscientists tell me that pharmaceutical companies are testing compounds in early stage human trials that may enable patients with dementia and other memory-stealing diseases to have better recall. No one knows if these will work to improve healthy people, but it’s possible that one will work in the future.
More intriguing is the notion that a supermemory or attention pill might be used someday by those with critical jobs like pilots, surgeons, police officers — or the chief executive of the United States. In fact, we may demand that they use them, said the bioethicist Thomas H. Murray. “It might actually be immoral for a surgeon not to take a drug that was safe and steadied his hand,” said Mr. Murray, the former president of the Hastings Center, a bioethics research group. “That would be like using a scalpel that wasn’t sterile.”
HERE is a partial checklist of cutting-edge medical-technology therapies now under way or in an experimental phase that might lead to future enhancements.
More than 200,000 deaf people have had their hearing partially restored by a brain implant that receives sound waves and uses a minicomputer to process and deliver them directly into the brain via the cochlear (audio) nerve. New and experimental technologies could lead to devices that allow people with or possibly without hearing loss to hear better, possibly much better.
The Israel-based company Nano Retina and others are developing early-stage devices and implants that restore partial sight to the blind. Nano Retina uses a tiny sensor backed by electrodes embedded in the back of the eye, on top of the retina. They replace connections damaged by macular degeneration and other diseases. So far images are fuzzy and gray-scale and a long way from restoring functional eyesight. Scientists, however, are currently working on ways to mimic and improve eyesight in people and in robots that could lead to far more sophisticated technologies.
Engineers at companies like Ekso Bionics of Richmond, Calif., are building first-generation exoskeletons that aim to allow patients with paralyzed legs to walk, though the devices are still in the baby-step phase. This summer the sprinter Oscar Pistorius of South Africa proved he could compete at the Olympics using artificial half-leg blades called Cheetahs that some worried might give him an advantage over runners with legs made of flesh and blood. Neuroscientists are developing more advanced prosthetics that may one day be operated from the brain via fiber optic lines embedded under the skin.
For years, scientists have been manipulating genes in animals to make improvements in neural performance, strength and agility, among other augmentations. Directly altering human DNA using “gene therapy” in humans remains dangerous and fraught with ethical challenges. But it may be possible to develop drugs that alter enzymes and other proteins associated with genes for, say, speed and endurance or dopamine levels in the brain connected to improved neural performance.
Synthetic biologists contend that re-engineering cells and DNA may one day allow us to eliminate diseases; a few believe we will be able to build tailor-made people. Others are convinced that stem cells might one day be used to grow fresh brain, heart or liver cells to augment or improve cells in these and other organs.
Not all enhancements are high-tech or invasive. Neuroscientists are seeing boosts from neuro-feedback and video games designed to teach and develop cognition and from meditation and improvements in diet, exercise and sleep. “We may see a convergence of several of these technologies,” said the neurologist Adam Gazzaley of the University of California at San Francisco. He is developing brain-boosting games with developers and engineers who once worked for Lucas Arts, founded by the “Star Wars” director George Lucas.
Which leads to another question: How far would you go to augment yourself? Would you replace perfectly good legs with artificial ones if they made you faster and stronger? What if a United States Agency for Human Augmentation had approved this and other radical enhancements? Would that persuade you?
Ethical challenges for the coming Age of Enhancement include, besides basic safety questions, the issue of who would get the enhancements, how much they would cost, and who would gain an advantage over others by using them. In a society that is already seeing a widening gap between the very rich and the rest of us, the question of a democracy of equals could face a critical test if the well-off also could afford a physical, genetic or bionic advantage. It also may challenge what it means to be human.
Still, the enhancements are coming, and they will be hard to resist. The real issue is what we do with them once they become irresistible.
David Ewing Duncan is a journalist who has contributed to the science section of The New York Times.
http://www.nytimes.com/2012/11/04/sunda ... h_20121104
This GE technology is out to change and advance our medical knowledge for ever as described by Doctor Topol.
THIS SOUNDS LIKE A HUGE REVOLUTION IN MEDICINE
IT IS VERY INTERESTING
Something new to ask your Doctor about on your next visit. This is our future in medicine. very cool!!
(Just wait until the commercial finishes and the interview starts.)
http://www.msnbc.msn.com/id/21134540/vp ... 2#50582822
THIS SOUNDS LIKE A HUGE REVOLUTION IN MEDICINE
IT IS VERY INTERESTING
Something new to ask your Doctor about on your next visit. This is our future in medicine. very cool!!
(Just wait until the commercial finishes and the interview starts.)
http://www.msnbc.msn.com/id/21134540/vp ... 2#50582822
Truly amazing! Operation rooms as we know them might not be needed any longer ... sometime in the not too distant future
7 min video
http://youtu.be/IfJemqkby_0
7 min video
http://youtu.be/IfJemqkby_0
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mominmomin103
- Posts: 8
- Joined: Thu Feb 14, 2013 1:50 am
Ginans are loaded about future Technology, developments and future predictions, while Quran is silents about this, you can not find many answers of modern time questions arising now a days in "Quran" for a example subbogate mother, who rent her womb is allowed or not? donate Kidney or eyes are allowed or not? what will happen after thousand and thousand years latter? Quran is silent about these any many other topics, it may possible that scholars still has not understand these information from quran, but you can find these and many other answers in ginans I don't say that Ginans are "superior" than Quran, BUT LET ME MAKE IT CLEAR HERE THAT GINANS ARE TAFSIR OF "QURAN" But interpretations made of Qur'an are does not have much information on these and many other questions so far also interpretation made by different scholars does not match with each others. so obviously we Ismailis have to stick with Ginans.hey can any one reply acout TECHNOLOGY and DEVELOPMENT acorrding to holy ginan and Quran...
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shiraz.virani
- Posts: 1256
- Joined: Thu May 28, 2009 2:52 pm
Agakhani bhai, Just because you cannot understand quran or use your intellect that doesnt mean quran is silent on technology and development.
If you read quran H.Solomen [as] communicated with ants...We humans can only hear upto certain frequency....Please refer to holy quran verse [27:18-19]
Do you know the IRON found on earth does not belong to earth ???...Ofcourse you dont know because you dont read quran....If you read surah 57 verse 25 allah[swt] says :
We verily sent Our messengers with clear proofs, and revealed with them the Scripture and the Balance, that mankind may observe right measure; and He revealed iron, wherein is mighty power and (many) uses for mankind, and that Allah may know him who helpeth Him and His messengers, though unseen. Lo! Allah is Strong, Almighty.
Iron was sent down from the sky by allah[swt]....In the late 20th century it was revealed by the researchers that iron found on earth has come from the giant stars in outerspace
There are many examples in holy quran that talks about technology and development, its just that you have to open you eyes and READ
If you read quran H.Solomen [as] communicated with ants...We humans can only hear upto certain frequency....Please refer to holy quran verse [27:18-19]
Do you know the IRON found on earth does not belong to earth ???...Ofcourse you dont know because you dont read quran....If you read surah 57 verse 25 allah[swt] says :
We verily sent Our messengers with clear proofs, and revealed with them the Scripture and the Balance, that mankind may observe right measure; and He revealed iron, wherein is mighty power and (many) uses for mankind, and that Allah may know him who helpeth Him and His messengers, though unseen. Lo! Allah is Strong, Almighty.
Iron was sent down from the sky by allah[swt]....In the late 20th century it was revealed by the researchers that iron found on earth has come from the giant stars in outerspace
There are many examples in holy quran that talks about technology and development, its just that you have to open you eyes and READ
shiraz.virani wrote: Do you know the IRON found on earth does not belong to earth ???...O fcourse you dont know because you dont read quran....If you read surah 57 verse 25 allah[swt] says :
We verily sent Our messengers with clear proofs, and revealed with them the Scripture and the Balance, that mankind may observe right measure; and He revealed iron, wherein is mighty power and (many) uses for mankind, and that Allah may know him who helpeth Him and His messengers, though unseen. Lo! Allah is Strong, Almighty.
Iron was sent down from the sky by allah[swt]....In the late 20th century it was revealed by the researchers that iron found on earth has come from the giant stars in outerspace
There are many examples in holy quran that talks about technology and development, its just that you have to open you eyes and READ
I have read Quran many times, since childhood, I am unable to see in this verse what you are saying. Where does it say that Allah sent iron from the sky to earth and in today's understanding of the universe, may I remind you we are not the center of the universe?
And if Allah revealed Iron, did he not revealed the remaining of the creation? Why bring hocus pocus in religion?
Any person can then say from any verse any meaning he wants. That called day-dreaming.
I am sure there are more appropriate verses that you could have come forth with. You could have copy pasted for instance a couple of example from the book "La Bible, le Coran et la science" by Maurice Bucaille - there is science in all religious books, Ginans are also an unlimited source of knowledge and of science for those who are blessed by Allah with understanding them.
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shiraz.virani
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Its always easy to read holy quran admin....the problem is with the understanding of the holy quran...Now if you could please allow me to explain to you that IRON found on earth comes from the giant stars ....And mind you my friend...Not just the iron on earth but also the entire solar system comes from outer space.I have read Quran many times, since childhood, I am unable to see in this verse what you are saying. Where does it say that Allah sent iron from the sky to earth and in today's understanding of the universe, may I remind you we are not the center of the universe?
The temperature of the surface of our sun is 6000 degree Celsius which is not enough for the formation of iron...Iron can only be produced in much larger stars [larger than the sun] whose temp reaches a few hundred million degrees...With that kinds of temperature the star my dear friend IF it exceeds the limit of the amount of iron over a certain level the star can no longer withstand that and EXPLODES and that is called SUPERNOVA...The iron particles then scatters all around the space.
In his book Nature’s Destiny, the well-known microbiologist Michael Denton emphasizes the importance of iron:
“Of all the metals there is none more essential to life than iron. It is the accumulation of iron in the center of a star which triggers a supernova explosion and the subsequent scattering of the vital atoms of life throughout the cosmos. It was the drawing by gravity of iron atoms to the center of the primeval earth that generated the heat which caused the initial chemical differentiation of the earth, the outgassing of the early atmosphere, and ultimately the formation of the hydrosphere. It is molten iron in the center of the earth which, acting like a gigantic dynamo, generates the earth’s magnetic field, which in turn creates the Van Allen radiation belts that shield the earth’s surface from destructive high-energy-penetrating cosmic radiation and preserve the crucial ozone layer from cosmic ray destruction…
“Without the iron atom, there would be no carbon-based life in the cosmos; no supernovae, no heating of the primitive earth, no atmosphere or hydrosphere. There would be no protective magnetic field, no Van Allen radiation belts, no ozone layer, no metal to make hemoglobin [in human blood], no metal to tame the reactivity of oxygen, and no oxidative metabolism.
“The intriguing and intimate relationship between life and iron, between the red color of blood and the dying of some distant star, not only indicates the relevance of metals to biology but also the biocentricity of the cosmos…”
Admin bhai these days the so called Iron oxide particles are used to kill cancer cells
Having said this admin, all this shows that iron did not form on the Earth, but was carried from Supernovas, and was "sent down," as stated in the verse
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shiraz.virani
- Posts: 1256
- Joined: Thu May 28, 2009 2:52 pm
YUSUFALII have read Quran many times, since childhood, I am unable to see in this verse what you are saying. Where does it say that Allah sent iron from the sky to earth and in today's understanding of the universe, may I remind you we are not the center of the universe?
57:25
We sent aforetime our messengers with Clear Signs and sent down with them the Book and the Balance (of Right and Wrong), that men may stand forth in justice;andWe sent down Iron, in which is (material for) mighty war, as well as many benefits for mankind, that Allah may test who it is that will help unseen, Him and His messengers; for Allah is Full of Strength exalted in Might (And able to enforce His will).
PICKTHAL
57:25
We verily sent Our messengers with clear proofs, and revealed with them the Scripture and the Balance, that mankind may observe right measure; and He revealed iron, wherein is mighty power and (many) uses for mankind, and that Allah may know him who helpeth Him and His messengers, though unseen. Lo! Allah is Strong, Almighty
ABDUL DARYABADI
57:25
Assuredly We sent Our apostles with evidences, and We sent down With them the book and the balance, that people might observe equity. And We sent down iron wherein is great violence and also advantages Unto mankind, and that Allah may know him who succoureth Him, unseen, and His apostles. Verily Allah is Strong, Mighty.
TAQI USMAN
57:25
We have indeed sent Our messengers with clear proofs, and sent down with them the Book and the Balance, so that people may uphold equity. And We sent down iron in which there is strong power, and benefits for the people; 10 and (We did it) so that Allah knows the one who helps Him and His messengers without seeing (Him). Surely Allah is Strong, Mighty.
Now please go and translate the word "ANZALNA" mentioned in that verse and see for yourself and not just that the name of the surah itself is AL HADEED, please find the translation of that as well
Are Humans Necessary?
Margaret Atwood on Our Robotic Future
http://www.nytimes.com/2014/12/04/opini ... 05309&_r=0
Many of our proposed futures contain robots. The present also contains robots, but The Future is said to contain a lot more of them. Is that good or bad? We haven’t made up our minds. And while we’re at it, how about a robotic mind that can be made up more easily than a human one?
Margaret Atwood on Our Robotic Future
http://www.nytimes.com/2014/12/04/opini ... 05309&_r=0
Many of our proposed futures contain robots. The present also contains robots, but The Future is said to contain a lot more of them. Is that good or bad? We haven’t made up our minds. And while we’re at it, how about a robotic mind that can be made up more easily than a human one?
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The Soular Backpack
DO WATCH…
SHARE/PASS ON TO FRIENDS & FAMILY
https://www.indiegogo.com/projects/the-soular-backpack