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.
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?"
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.
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.
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.
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.
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.
******
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.
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.
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.”
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.
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
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.
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.
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