One Year after Sandy, Uneven Recovery at New York University’s labs

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How were researchers faring one year after Hurricane Sandy? I wrote this article to answer that question. I got the cleaned-up version of reality from NYU Medical Center, and the unvarnished truth from some researchers. This article appeared on SFARI.org, and was also syndicated on Scientific American on 29 October 2013, Hurricane Sandy’s one-year anniversary.

Walking through Gordon Fishell’s lab now, you would never know that much of his research was swept away by last year’s superstorm. Other scientists at New York University’s medical center cannot say the same.

Walking through Gordon Fishell’s lab now, you would never know that much of his research was swept away by Hurricane Sandy, almost exactly a year ago.

The lab’s staff is back at work, studying — among other things — the role of certain neurons in disorders such as autism. With gleaming floors under glowing lights, the space resembles nothing of the dark, dank disaster zone it was back then.

“It’s really hard to remember how bad it was,” says Fishell, director of the Smilow Neuroscience Program at New York University (NYU). Until, that is, he begins to recall the damage.

On 29 October 2012, ‘superstorm’ Sandy surged through the east coast of the U.S., with water levels in New York Bay reaching 13.88 feet — 2.68 feet higher than the nearly 200-year-old previous record.

At NYU’s Langone Medical Center, which sits right next to the East River, the staff successfully evacuated 322 patients, including 20 babies from the neonatal intensive care unit. But mice and machines did not fare as well.

Read the rest of the article on Scientific American‘s website.

A new high-tech, grassroots effort to fight breast cancer

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I wrote this article for Slate’s Tech blog, Future Tense, after hearing about it from Joanna Rudnick, my close friend and one of the leaders of the project. You can see the article, which ran June 25, 2013 on Slate’s website here.

By now you’ve probably heard that, thanks to the Supreme Court, no one, and certainly not Myriad Genetics, can patent human genes. This decision was sensible and long overdue, but the celebrations have been short-lived. Because what you may not have heard is that Myriad still owns all of the information it has collected since the mid-1990s on the breast cancer genes—and it has no intention of releasing any of it.

Myriad’s interpretations of mutations are out there, but scattered in a million pieces—in the reports it has sent out to women, or, more often, to the clinical centers where they were tested. But a new volunteer grass-roots effort, led by a few women with a family history of breast cancer, is trying to Free the Data so that scientists everywhere can analyze it and help women make informed choices about their breast-cancer risk. In collaboration with the University of California-San Francisco, the nonprofit advocacy group Genetic Alliance, and a biotech company InVitae, these women are hoping to collect even a tiny fraction of the million or so reports Myriad has sent out over the past 17 years.

Read the full article on Slate.

Peer review: Trial by Twitter

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(I pitched this feature to Nature after hearing about Vinay Deolalikar, a well-known researcher who claimed he’d solved one of the biggest puzzles in computer science: the P/NP problem. Nature had covered it as news, but I thought there was more to the idea of science being reviewed on social media, particularly in biology–as opposed to math or computer science, where online review is an accepted tradition. You can also read the online version, or download a pdf of the article.)

Blogs and tweets are ripping papers apart within days of publication, leaving researchers unsure how to react.

“Scientists discover keys to long life,” proclaimed The Wall Street Journal headline on 1 July last year. “Who will live to be 100? Genetic test might tell,” said National Public Radio a day later.

These and hundreds of similarly enthusiastic headlines were touting a paper in Science¹ in which researchers claimed to have identified a set of genes that could predict human longevity with 77% accuracy — a finding with potentially huge implications for medicine, health policy and the economy.

But even as the popular media was trumpeting the finding, other researchers were taking to the web to criticize the paper’s methodology. “We expect that most of the results of this study will not have the same longevity as its participants,” sniped a blog posted by researchers at the personal genomics company 23andMe, based in Mountain View, California.

Critics were particularly perturbed by the genome-wide association study (GWAS) that the authors had used to identify their longevity genes: the centenarians and the controls in the study had been tested with different kinds of DNA chips, which potentially skewed the results.

“Basically anybody that does a lot of GWAS knows this [pitfall], which is why we all said it so fast,” says David Goldstein, director of Duke University’s Center for Human Genome Variation, who voiced his concerns to a Newsweek blogger the day the study appeared.

This critical onslaught was striking — but not exceptional. Papers are increasingly being taken apart in blogs, on Twitter and on other social media within hours rather than years, and in public, rather than at small conferences or in private conversation.

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Spain gives great apes legal rights

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(This article was #64 in Discover Magazine’s top 100 stories of 2008.)

On June 25 the Spanish Parliament’s environmental committee approved a resolution to grant legal rights to great apes, covering chimpanzees, bonobos, gorillas, and orangutans. The resolution, expected to be enacted into law by June 2009, gives great apes the right to life and protects them from harmful research practices and exploitation for profit, such as use in films, commercials, and circuses.

“This is an important historical step,” says Peter Singer, a professor of bioethics at Princeton University and cofounder of the Great Ape Project. Since 1993, when Singer and Italian philosopher Paola Cavalieri established the group, its members have advocated for a United Nations declaration that great apes, like humans, are entitled to life, liberty, and protection from torture.

The great apes’ ability to use language and tools, to feel pain, and to form lasting relationships with others is evidence, the Great Ape Project maintains, that apes are part of a “community of equals” with humans. “This decision is the first step to recognizing that the gulf between human and nonhuman animals is not absolute but a matter of degree,” Singer says. “I do hope it helps people look differently at their relationship with nonhuman animals.”

The resolution also calls for the Spanish government to promote a similar declaration throughout the European Union. Singer notes that the Netherlands, Britain, and countries in Scandinavia have already taken steps to phase out research harmful to great apes.

The FDA tackles tainted drugs from China

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(This story was #3 in Discover Magazine’s top 100 stories of 2008.)

Following a series of high-profile scandals concerning tainted food and drugs imported from China, the U.S. Food and Drug Administration (FDA) announced in March that it would establish a drug-monitoring office in that country.

The most alarming report involved contaminated batches of the blood thinner heparin, which caused at least three deaths and is under suspicion in dozens of others. In February FDA officials admitted that they had never inspected Changzhou SPL, the manufacturing plant in Changzhou, China, to which they traced the contaminated heparin. When the FDA eventually inspected the Changzhou SPL plant (in February), it found a host of quality-control and hygiene problems.

Many drugs sold in the American marketplace are now imported, transforming what was once largely a domestic agency to one that must police products from more than 200 countries, notes Murray M. Lumpkin, FDA deputy commissioner for international and special programs. “The reality of globalization has hit the products for which we’re responsible very, very significantly,” he says. The pharmaceutical production process is also vastly more complex than it used to be. Individual ingredients are made in one place, put together in another, and bottled and labeled in still other sites.

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Cloned hamburger, anyone?

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(This article was #64 in Discover Magazine’s top 100 stories of 2007.)

Meat and milk from cloned cattle, pigs, and goats are safe to eat, the Food and Drug Administration has declared, setting the United States on course to become the first country to approve such products. The agency’s draft risk assessment says food from clones can safely be marketed without any labels to distinguish it.

In an article in the journal Theriogenology last January, agency scientists analyzed dozens of studies—many of them from cloning companies Viagen and Cyagra—and concluded that meat and milk from clones showed no “nutritionally or toxicologically important differences” from products now consumed.

But some advocacy groups aren’t buying it. “We’re very concerned,” says Charles Margulis, spokesman for the Washington-based Center for Food Safety. “We don’t think there’s really enough science to show that clones are safe.”

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Controversy over cervical cancer vaccine

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(This article was #26 in Discover Magazine’s top 100 stories of 2007.)

This past year, several countries and at least 24 states in the United States introduced laws to mandate vaccination against cervical cancer for preteen girls. Although the vaccine was initially hailed as a breakthrough, urgent proposals to make it mandatory quickly triggered a backlash. “In the long term,” says Susan Wood, a former director of the FDA Office of Women’s Health, “the rush to get this mandated immediately has done more harm to the issue.”

The FDA approved Merck’s Gardasil vaccine in 2006, after clinical trials showed that it protects against four strains of human papillomavirus (HPV), which together cause about 70 percent of cervical cancers and 90 percent of genital warts. HPV is the most common sexually transmitted virus among Americans (and cervical cancer is the second most common cancer in women worldwide). Because the vaccine doesn’t reverse existing exposure, the CDC recommends it be administered before the age of sexual activity—specifically to girls ages 11 to 12. As for women who already have HPV, two separate studies published in May in the New England Journal of Medicine reported that the vaccine’s effectiveness in preventing cervical lesions dropped to 20 percent or less.

Some conservative groups oppose targeting preteens, arguing that because the virus is sexually transmitted, the vaccine will encourage promiscuity. Meanwhile, bioethicists who are skeptical about compulsory vaccination laws note that all other mandated vaccines protect against diseases easily transmitted in schools. “In my opinion, there’s not a compelling ethical reason [to mandate],” says Richard Zimmerman, professor of family medicine at the University of Pittsburgh. “The ethics is the opposite: to strongly recommend, but not to mandate.”

FDA says cold medicine is not for children under 6

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(This article was #18 in Discover Magazine’s top 100 stories of 2007.)

In October, Food and Drug Administration (FDA) advisers recommended against the use of most nonprescription cold and cough medicines for children under age 6, citing the lack of evidence of safety or efficacy in this age group. Prior to the announcement, most manufacturers had already voluntarily restricted sales of medicines formulated for children less than 2 years old.

The FDA review of the medications began after a report by the Centers for Disease Control in January found that, between 2004 and 2005, more than 1,500 children under the age of 2 had wound up in emergency rooms after taking over-the-counter cough and cold medicines. In another development that prompted the review, Baltimore city officials filed a citizen petition with the FDA in March, noting that the remedies do not help children under 6 years of age and may in fact harm them.

There are roughly 800 products on the market containing antihistamines, decongestants, anticough agents, and other chemicals intended to treat colds and coughs in children. Like many pediatric medicines, they have been tested only in adults and are simply packaged to deliver smaller doses to children.

In September, the FDA also required that, by November 2007, drug companies stop making unapproved prescription drugs containing the narcotic cough suppressant hydrocodone for use by children younger than 6. Manufacture of all other unapproved hydrocodone products must halt by December 31.

Rx for the FDA

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(This article was #5 in Discover Magazine’s top 100 stories of 2007.)

For the Food and Drug Administration, the agency charged with ensuring drug safety, 2007 brought a slew of charges undermining its credibility. The most widely reported involved a study by Cleveland Clinic cardiologist Steven Nissen showing that the diabetes drug Avandia, FDA-approved in 1999, raised the risk of heart attack by 30 to 40 percent. The agency was also called to testify before Congress about its inaction regarding side effects of the antibiotic Ketek and a widely used class of anemia drugs. In addition, a study published in the Archives of Internal Medicine in September found that reports of serious side effects and deaths caused by FDA-approved medicines nearly tripled between 1998 and 2005, to about 90,000.

The accumulation of evidence apparently forced a reckoning in Congress and the White House. On September 27, President Bush signed into law an amendment giving the agency unprecedented new powers to conduct and demand safety studies on approved drugs, police drug advertisements, and require companies to register data from their clinical trials in a publicly available database. The new law also boosts the agency’s budget, an increase approved in time to avert the layoffs of some 2,000 FDA employees, including many researchers.

“This has been a tough year,” acknowledges Janet Woodcock, deputy commissioner of the FDA and acting director of the agency’s Center for Drug Evaluation and Research. “[But] I do think this is an inflection point about the communication on drug safety. We have the opportunity to set up new systems.”

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Don’t rush your vaccines

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(This Opinion column ran in Nature’s news site on May 17, 2007. You can read the original post here.)

The ethical debate about a vaccine for a sexually transmitted disease has been premature, says Apoorva Mandavilli; we don’t even know how well it works.

Here’s a good lesson: before you start pushing for a controversial vaccine to be made compulsory, best wait for the research — and I mean all the research — to come up with results.

For more than a year, we’ve been hearing that there is a vaccine that is 100% safe and effective in protecting young girls and women from the deadly viruses that cause cervical cancer.

Merck’s Gardasil, a vaccine against human papilloma virus (HPV), has been hailed as perhaps the biggest boon for women since the contraceptive pill. Across the world, including many American states, politicians and activists have proposed laws to make Gardasil mandatory for girls in their early teens or younger. Australia has already started a national programme of free vaccines for young girls.

All that sounds a bit premature — and rightly so. As we find out more about this vaccine, including new studies in last week’s New England Journal of Medicine¹^,², it’s clear we simply don’t know enough about it to be giving it to young girls en masse.

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