Monthly Archives: April 2011

A $1000 Genome

Animation of an MRI brain scan, starting at th...Image via Wikipedia

It’s been the catch-phrase of science geeks hoping to drive DNA sequencing to the next level: The $1,000 genome. There is a National Institutes of Health project to get us there, an X Prize to reward whoever gets there first, and a book (a great read) named after the idea. The $1,000 genome – it promises a day when we all carry around our genetic code on thumb drives and use it to decide what medicines to take, what to eat, and what diseases to watch out for.

Great buzzword, but it may never happen, especially not any time soon and especially not at a cost of $1,000. Research costs for sequencing a human genome may drop that low very soon, but that doesn’t include paying the doctors or the cost of information technology to process the data. Research genomes are not accurate enough for medical use. Getting better accuracy requires sequencing the DNA more times, which drives the cost back up. I’d think if we’re talking about actual medical use, $10,000 is a more accurate number. Certainly, it is not going to drop below the $2,000 level for a magnetic resonance imaging scan. And once the technology is in use, I think it is possible that the costs will go back up.

Even in consumer electronics, costs don’t always go to zero. Buying a decent computer (not the chintzy netbook I use for everything) costs as much now as it did ten years ago – the power behind the device you get has simply increased. But medicine is not like consumer electronics. That’s why we often pay astronomical prices for drugs that have real benefits –$93,000 per patient for Dendreon’s prostate cancer drug Provenge, or $200,000 per patient per year for one of Genzyme’s rare disease drugs. Sequencing isn’t going to mirror the drug business. It might be more like the PET scan and MRI business, with select hospitals buying huge, expensive machines. Or it might be that people don’t get their whole genomes scanned except when they have a hard to diagnose disease – patients with cancer might have a few hundred or a thousand of their tumor genes sequenced in order to pick the right drugs, for instance. All of this comes with the hurdles that neither doctors nor regulators really understand sequencing yet, and that’s bound to come with all sorts of hiccups. On the other hand, the first cases of using sequencing in medicine are arriving now.

That said, one of the arguments that this could be quite big is that you can get to pretty gigantic market sizes whether the cost comes down a lot or not. To quote Jay Flatley, chief executive of DNA sequencing leader Illumina: “If you look at the potential it verges on being insatiable through the next ten years,” says Flatley. “If you look at sequencing entire countries the potential volumes are really staggering, even at $1,000 a genome.


Who owns our genes?

Women at risk for hereditary breast cancer—caused by two telltale genetic mutations—should be closely watching a gene-patent case under appeal in U.S. courts. At stake: who owns our genes.

Joy Y. Wang  | Newsweek

The case, commonly referred to as ACLU v. Myriad Genetics, is the first of its kind to address whether genes are patentable. Plaintiffs are arguing that genetic information should not be the sole possession of corporations, and people shouldn’t have to pay exorbitant fees to research their own DNA. The defendants say that without patent protection, private industry won’t invest in genetic testing and patients will suffer.

Earlier this year, a district court judge ruled that the breast-cancer genes—BRCA1 and BRCA2—are not patentworthy on the basis that they’re products of nature. Late last month, the Justice Department backed up this interpretation, breaking ranks with 30 years of precedents at the U.S. Patent Office. (The office has been issuing gene patents on the assumption that isolating genes requires human intervention, as well as substantial financial investment.) Myriad Genetics, the company with the patents, has had sole control over testing for BRCA1 and BRCA2. The tests can cost thousands of dollars, and patients have not had the option to get tested by a second source.

Myriad is appealing the ruling, but if it fails, patents on thousands of human genes—constituting about 20 percent of the human genome—may become invalid in the U.S. Some patent attorneys claim this will scare biotech firms away from ongoing research. “Without the incentive of patent protection, the investment by private industry would never occur,” says Sean Tu, a patent lawyer who specializes in biotech. Myriad estimates that so far, it has spent approximately $500 million on research and development of the gene (that figure also includes money spent commercializing and marketing the diagnostic testing). As of April, the company had not yet made a profit on the project.

But critics of gene patenting argue that companies could end up stymieing academic research on gene mutations. Even though Myriad maintains it has not stopped purely academic research, not all patent holders might be similarly inclined.

As for the profitability question, opponents also say that genetic research will continue out of curiosity alone, pointing to an international race to isolate the BRCA gene in the 1990s in which many of the research groups promised to not seek a patent.

Problem is, unlike with the Human Genome Project, gene patents often blur the line between public and private entities invested in a race for scientific discovery. For example, Myriad shares its patent on the BRCA genes with the publicly funded University of Utah. And while Myriad itself has not received government funding, one of the company’s founders, Mark Skolnick, initially worked with the National Institute of Health and the University of Utah on isolating the genes. “It does cost a fortune to find a gene, but much of the fortune was paid by the U.S. government,” says Michael Watson, the executive director of the American College of Medical Genetics, one of the plaintiffs.

The Conclusion: ACLU v. Myriad will be a milestone for U.S. biotech companies who seek to become profitable off genetic-patenting—and for those scientists and patients who think our genetic heritage should belong free of charge to anyone who cares to research it.

I will text and you will live with it?

David Carr
New York Times

YOU are at a party and the person in front of you is not really listening to you. Yes, she is murmuring occasional assent to your remarks, or nodding at appropriate junctures, but for the most part she is looking beyond you, scanning in search of something or someone more compelling.

Here’s the funny part: If she is looking over your shoulder at a room full of potentially more interesting people, she is ill-mannered. If, however, she is not looking over your shoulder, but into a smartphone in her hand, she is not only well within modern social norms, but is also a wired, well-put-together person. Add one more achievement to the digital revolution: It has made it fashionable to be rude. Continue reading

The Activist Artist of China

Ai Weiwei is famous for his criticism as for his provocative art. Now in detention, he’s becoming a symbol of a worrying crackdown. 

Austin Ramzy

When people write on Chinese websites that they “love the future,” it should be a sentiment the government can get behind. After all, the authorities in Beijing have pressed their subjects to embrace the country’s bright economic prospects. But of late, “love the future” has taken on a new meaning. Online, people have begun to use the phrase, which is ai wei lai in Mandarin, as a code for the artist and political activist Ai Weiwei, whose name became too sensitive to post or search for on many Chinese websites after his detention by police on April 3.

Ai is the country’s best-known modern artist, with a current exhibition of 100 million porcelain sunflower seeds at London’s Tate Modern museum. His collection of bronze animal heads — replicas of those looted from Beijing’s Summer Palace by French and British troops in 1860 — is set to go on display outside New York City’s Central Park next month. A son of Ai Qing, a beloved revolutionary poet whose words Premier Wen Jiabao can quote from memory, Ai Weiwei is a burly online oversharer with 78,000 followers on Twitter. And he has emerged as one of the most prominent critics of China’s ruling Communist Party, drawing public focus to some of China’s most tragic events.

After the 2008 earthquake in Sichuan, Ai began to ask how many children were killed in collapsed schools, eventually organizing volunteers who canvassed mountain towns and tallied nearly 6,000 dead children. Chastened, the government finally released its own total of student deaths. Ai also produced a documentary film about a man who killed six Shanghai police officers, apparently in revenge for abuse the man had suffered while in custody. More recently, Ai began to look into the case of Qian Yunhui, a village chief in Zhejiang province who some people in China suspect was murdered at the behest of corrupt officials. Now, after years of raising sensitive questions and tweeting his nearly every move and thought, Ai has gone uncharacteristically quiet. He has been held incommunicado at an undisclosed location as Beijing police investigate him for suspected economic crimes. His silence raises a sensitive question: How much — if any — dissent is the Chinese government willing to tolerate? Continue reading

Fueling efficiency, not finding new fuels.

Are we wasting our time and resources researching and developing unfeasible solutions? Will anything come out of our investments in biofuels and other alternatives? Would simply cutting down on our energy wastage and becoming more energy-efficient be a better solution?

Justin Gill
New York Times

One of the world’s great minds on issues of energy use, food production and the connection between them is a fellow named Vaclav Smil, of the University of Manitoba. Bill Gates reads him. He is No. 49 on Foreign Policy magazine’s list of the top 100 global thinkers.  Dr. Smil is just out with a fresh essay on energy, this time criticizing what he calls “the latest infatuations” in the field, like biofuels, hydrogen fuel cells, electric cars, and so on.

He is by no means a coal-and-oil-forever kind of guy; Dr. Smil believes the world must, and eventually will, convert to solar power, since it is the only renewable energy flux big enough to sustain human civilization. His main point in the new piece is not so much that researching energy alternatives is bad, but that rich countries, especially the United States and Canada, are guilty of focusing on these shiny, high-technology solutions, which he believes are not ready for prime time, while displaying an “astonishing unwillingness to adopt many readily available and highly effective existing fixes.”

He means greater efficiency in the use of the energy supplies we already have, of course. His argument to some degree echoes the work of other thinkers who have long argued that we waste enormous amounts of energy simply because we will not invest enough capital up front in more efficient ways of doing things, investments that would save us money in the long run by cutting energy bills.

Dr. Smil brings the point home by noting that the United States and Canada use about twice as much energy, per person, as the citizens of European countries and Japan — “but, obviously, Pittsburghers or Angelenos are not twice as rich, twice as healthy, twice as educated, twice as secure or twice as happy as inhabitants of Bordeaux or Berlin.”

His main example of waste is the North American automotive fleet, which gets not much more than half the mileage per gallon as the European fleet.Indeed, Dr. Smil has been mocking the American penchant for sport-utility vehicles for years. One could make similar points about energy efficiency in buildings and factories, as the Obama administration has been trying to do with mixed success.

After making his case about waste, Dr. Smil then walks through the various ideas that have captured attention lately, and argues that most of them will make little contribution to our energy problems, at least in the next few decades. But he also finds some cause for hope: North American energy use per person is not rising. It has essentially been flat for decades, since the oil crises of the 1970s.

How hard could it be, Dr. Smil asks, to turn that flat line into a downward-sloping line, without anybody in the United States or Canada really feeling any pain?

In fact, with past support from Congress, the Bush and Obama administrations have already adopted efficiency standards for new cars, ending decades of inaction on that issue. With gasoline prices rising again, the market is pulling even as the government is pushing. If that automotive policy survives political attack in the new Congress, and if corporations continue to pursue their stated goals of reducing energy consumption, it is not out of the question that total North American energy use could start edging downward even as the population continues to grow.

The fuss over fracking

You read that right. Hydraulic fracturing (hydrofracking) is a method of drilling into reservoir rock formation and pumping water and chemicals (Benzene is used, which has been linked to cancer)  into the rock bed in order to increase the rate and ultimate recovery of natural gas.The controversy? Sputtering faucets (taps) containing combustible gases like methane, contamination of ground water with arsenic etc   Is the search for alternative energy sources, or the extraction of it all that safe?

Read up on the controversies behind the extraction of natural gas (called hydraulic fracking) from shale deposits (Pennsylvania in the USA is the 2nd largest Shale deposit in the world)

Watch trailer for Gasland:

A 2008 Time ‘Clean Energy Scam’ article is a good read on renewable/clean energy controversies. Click here

I would think clean energy and bio fuels would be a topic worth delving into in prep for 2011.

How far can we police the food we consume?

By Steven Gray

On Sept. 16, 2010, a team of U.S. Food and Drug Administration investigators arrived at a Shanghai purveyor of dough, macaroni and baby cereal. Federal authorities had long suspected that Shanghai Chuangi Food Co.’s plants were unsanitary. Many of its products, like soup base, had been shipped to the port of New York and ultimately placed in an unknown number of goods that ended up on kitchen tables in the U.S. That’s why federal authorities assigned to one of the FDA’s new Chinese offices warned that country’s government of their plans to pounce. FDA inspectors and a Chinese translator went to several Shanghai addresses listed for the company. Each time, representatives who answered the door refused to make executives available or allow inspectors inside. They even said the company didn’t ship to the U.S. — which, of course, was a lie. Within a month, the FDA issued an import alert, banning Shanghai Chuangi’s products from the U.S.

If you find that story reassuring, don’t. The U.S. receives scores of tips about unsafe imported food each year, but the FDA inspects only about 1% of the roughly 10 million products shipped into the country annually. Blame it partly on a lack of funding and, until recently, authority. (See a quick guide to the FDA.)

In January, however, things changed. President Obama signed the Food Safety Modernization Act, potentially the most sweeping overhaul of the nation’s food-safety system in nearly three-quarters of a century. The law directs the FDA, regulator of about 80% of food consumed in the U.S., to prevent outbreaks of food-borne illnesses like salmonella. That’s no small matter: nearly 1 in 6 Americans — 48 million people — contracts a food-borne illness each year; 3,000 die as a result. Much of the new law will deal with domestically grown food, which accounts for about 85% of what Americans eat. But one of the most intriguing effects of the law will be the launch of a massive effort to inspect the increasing amount of imported goods: in the coming years, the FDA is expected to spend nearly $1.4 billion to hire hundreds of staffers and private contractors to inspect the expanding number of foreign food suppliers.

The question is, Can the FDA police the world? It was only a century ago that Upton Sinclair wrote The Jungle, a groundbreaking book that described, in horrific detail, how spoiled meat was doused with soda to remove the scent of rot before it was hauled off to free-lunch counters. The book led to the enactment of the Pure Food and Drug Act and the formation of the FDA. (See the top 10 medical breakthroughs of 2010.)

Today, of course, the FDA is a massive agency: it regulates more than $466 billion worth of food and about 25¢ of every consumer dollar spent. Yet its imported-food mandate will be difficult to execute, mainly because globalization has sharply broadened the American palate. At ordinary supermarkets in Chicago, Charlotte, N.C., or Boise, Idaho, ingredients like chipotle sauce, couscous and coconut milk are no longer marginalized to the imported-food aisle — if such a section exists. About 60% of the U.S.’s fresh fruits and vegetables are imported, as is about 80% of seafood, much of it from countries with questionable food-safety regulations. “Globalization has presented its own food-safety challenges, which must be addressed,” the FDA’s deputy commissioner for foods, Michael Taylor, told a Shanghai audience recently.

The truth is, the FDA has struggled to keep up with the globalized food business. The evidence regularly appears on the evening television news: In 2008, the FDA warned that melamine, a compound frequently used to make plastics, had been found in Chinese infant formula, leading the agency to ban such products. In another case that year, clusters of illnesses in the U.S. prompted the FDA to investigate how jalapeño and serrano peppers imported from Mexico had become infected with salmonella. Ultimately, the agency warned consumers to avoid the peppers. Partly in response to such cases, the FDA has opened offices in far-flung cities like Guangzhou, Mumbai and Mexico City and has even dispatched a team of seafood experts to train Bangladeshi officials about U.S. food-safety standards. (See the top 10 scientific discoveries of 2010.)

The new law will take those efforts to a higher level. For starters, the FDA will hire hundreds of staffers to inspect thousands of overseas food facilities in the coming years. In Shanghai recently, Taylor said, “It is clear that the FDA can’t be everywhere all the time, especially when it comes to the oversight of imported foods.” So the agency will hire third-party certifiers. The handful of firms that inspect and certify food are preparing for an uptick in business. One of those firms is Bureau Veritas, a French concern. The company is already familiar with the U.S. regulatory process. Its office across from Walmart’s Bentonville, Ark., headquarters advises the retail giant on how its products can meet U.S. safety standards. The company has conducted certification tests with the FDA on Vietnamese shrimp. Patrick Bele, Veritas’ food-business-development manager, says of the new safety law: “It’s going to be an opportunity to hire more people, invest in more labs. It will give us an extra push in growth.”

Two potential barriers to the law’s implementation are politics and money. Congressional Republicans have suggested that the FDA’s budget be trimmed by $220 million. “Certainly, food safety is a high priority,” says Congressman Jack Kingston, Republican of Georgia, who argues that the relative rarity of food-borne illness means the current system is effective. “But money is scarce,” he says. (See the top 10 quotes of 2010.)

It may seem easy to dismiss such rhetoric since the Senate, which remains dominated by Democrats, is unlikely to erode a signature legislative victory backed by the Obama Administration and Big Food. But the law’s advocates fear that the drive to cut the FDA’s budget could gain traction in the next two to four years if Republicans take control of both chambers of Congress. “It’s good to say the food supply is safe, but it has to turn out that way,” warns Caroline Smith DeWaal, food-safety director at the Center for Science in the Public Interest, a Washington advocacy group. She adds, “There are risks to their own constituents if they’re exposed to contaminated foods … The Republicans will be left holding the bag.”

Meanwhile, back in China, Shanghai Chuangi hasn’t taken key steps toward redemption, like testing questionable plants. FDA inspectors have yet to return to the company’s facilities either. Without adequate funding, it’s worth wondering if they ever will.

The biggest health threat is (drumroll)

no surprises here – Global warming.

Hot button issue of 2009: the  much talked about Copenhagen Summit (more talk than action – and widely decried as a failure)

Huffington Post, 8 Apr 2011

Recently a commission run by The Lancet namedwhat they called the biggest global health threat of the 21st century. HIV/AIDS? Nope. Heart disease? Not at all. Cancer? Keep trying. To get your head around the biggest health threat of all, you might have to change how you think about health entirely. That’s because the biggest threat of all, in the view of this blue-ribbon panel, was climate change.

In the last few years, leading medical professionals have begun to speak out about the extraordinary threats climate change poses to human well-being. The American Academy of Pediatrics stated inPediatrics, its professional journal that “children are likely to suffer disproportionately from both direct and indirect adverse health effects of climate change.” The American Nurses Association described the challenges of global climate change as “unprecedented in human history” and called for nurses to “speak out and advocate for change.” Cecil Wilson, MD, the president of the American Medical Association, stated at a congressional briefing that climate change could cause “devastating events with serious human health implications.”

How can our warming climate affect our health? In some surprising ways, as we describe in our new book, Changing Planet, Changing Health. Continue reading