knight science journalism Archives - Page 6 of 7 - Knight Science Journalism @MIT

by Maria Temming / May 2nd 2017 / KSJ News & Events

Carl Zimmer’s Cure for ‘Boring Genome Syndrome’

Carl Zimmer isn’t the only journalist for whom the gee-whiz veneer of genome sequencing has worn off. Photo: David Corcoran.

In October 2015, Carl Zimmer found himself in a peculiar predicament. He’d just gotten word from Illumina — the company he’d commissioned to sequence his genome — that his genetic readout didn’t raise any red flags. Although his clean bill of health was a personal relief, it also posed a professional problem: Zimmer had convinced the Boston-based health site STAT to cover the couple-thousand-dollar sequencing charge so he could write about it, and, well, it didn’t look as if he had much of a story, did it?

Fortunately, there was probably no one better suited than Carl Zimmer to spin his seemingly bland genetic data into narrative gold.

Zimmer is “a science journalist who really needs no introduction,” as Deborah Blum said in introducing him to the April 6 KSJ seminar on writing about genomes. Zimmer has authored several books, writes the New York Times “Matter” column, and frequently appears on shows like “Radiolab.” Since he has a new book about heredity in the works, Zimmer has been thinking a lot about genetics lately. But his reporting took a turn for the personal when he had his own genome sequenced.

By now, the genomes of tens of thousands of species have been sequenced, and transcribing the genetic instructions for a new organism is kind of like saying, “Oh, I discovered a new star,” Zimmer said. Still, as someone who was covering the biology beat when scientists first sequenced the genome of a cellular organism in 1995, Zimmer said it was kind of mind-blowing to think the procedure could be done on him. Unfortunately, the report Illumina delivered to Zimmer — which disclosed only whether it found any genetic variants with serious health effects — was pretty anticlimactic. He learned he was a carrier for two diseases that he hadn’t passed on to his children. “So that’s it. Done,” Zimmer said. “Now I’m wondering what the point of all this was.”

Genetic autobiographies, he said, have become something of a mini-genre in journalism: Writers get their genomes sequenced and then tell their (usually uneventful) tales. “What is it we’re looking for?” Zimmer said. “Really interesting, scary mutations? If you’re in good health, you probably won’t discover those.” As a result, journalism is suffering from what he calls “Boring Genome Syndrome,” and Zimmer was determined to find a cure. If humans have genomes that are four billion years in the making, “they can’t be boring,” he said. “They just can’t.”

Since Illumina’s report had barely scratched the surface of his genetic profile, Zimmer wanted some genome scientists to dig deeper and see what they could find. After securing his complete genome from Illumina, all 60 gigabytes’ worth on a hard drive, he let two dozen researchers have at it.

According to Zimmer, the scientists “had great fun” with this project, because they were so used to studying disembodied genomes, and his actually came with a name and a face. Their scrutiny yielded some new insights into Zimmer’s health, and his experience under the microscope yielded a three-part series on STAT titled “Game of Genomes.” “This is my stab at a treatment for Boring Genome Syndrome,” he said.

Zimmer hopes that people will eventually be able to look beyond the sheer novelty of genome sequencing, “because this is not just something that’s limited to things going on in laboratories,” he said. “This is more and more a part of our culture. This is a part of business. This is a part of the modern economy.”

Zimmer pointed to the movie “Assassin’s Creed” as a striking example of our culture’s fascination with genetic codes. He couldn’t contain an eye roll as he described the film’s plot, which involves the protagonist uncovering the memories of his 15^th-century assassin ancestor embedded in his DNA. Even worse, Zimmer continued, there’s an “Assassin’s Creed Testing Bundle” for sale that promises to reveal if users have the so-called warrior gene — which was once erroneously used to explain aggression among the Maori people of New Zealand.

KSJ fellow Meera Subramanian asked Zimmer how science writers could help cultivate a media ecosystem in which accurate genetics news gets in front of the public, even if it’s less flashy than the Maori story. Zimmer suggested telling editors why they should be wary of pieces that definitively pin a genetic cause to a human condition. And when it comes to pitching stories that lack the “wow” factor of definitive answers, Zimmer recommended spinning scientific uncertainty as a positive: Thanks to complex genetic and environmental interactions, genetic risk for a condition does not equal fate. After all, Zimmer said, “everybody loves a happy story.”

by Kate Telma / March 22nd 2017 / KSJ News & Events

Building Tissue in a Cutting-Edge Lab

“Women’s health is a hugely underserved area”: Linda Griffith at the MIT Center for Gynepathology Research. Photo: David Corcoran.

“What should we be building? How do we influence cells?” asked Dr. Linda Griffith. “How do we get at their inner machinery and give them the cues they need to build a tissue?”

Griffith began the March 7 KSJ seminar and lab tour by squeezing the fellows into her office in the bioengineering department, where she gave a rapid overview of her work as the director of the MIT Center for Gynepathology Research and leading research to model human organ systems. Griffith manages interdisciplinary grants with multiple collaborators, teaching, advising students, and leading the Center, and keeps on schedule with a clock that rings six minutes ahead—with the sound of a revving Harley-Davidson bike.

Griffith started at MIT as a postdoc in regenerative medicine, engineering liver tissue and teaching at Harvard Medical School. She played a central role in the creation of the biological engineering department — leading the development of the first new undergraduate major at MIT in almost 40 years — and launched an initiative to study the systems and pathways that cause endometriosis, a disorder in which the uterine lining grows on other internal and reproductive organs, causing pain and often infertility in nearly one in 10 women.

“When we say engineers look at problems in society, I decided that women’s health is a hugely underserved area,” Griffith said, who has never missed a day of work for her nine endometriosis surgeries. Much is still unknown about endometriosis: There is still no method for correlating the size and characteristics of lesions with a patient’s symptoms, molecular profile, or prognosis in response to therapy, a routine step of many cancer diagnoses. “Part of my mission here is to educate by formulating problems in a way that my colleagues think they are tractable and interesting and exciting and useful to work on,” she said. “That’s why I have the center for women’s health.”

A barrier to creating new drugs, especially for women’s diseases, is the lack of efficacy models — either an animal or a lab-grown human tissue that will test how the new drug would work. Pharmaceutical companies “will do it for cancer but not for these diseases that are much more prevalent,” Griffith said. “I wanted to figure out how can we build efficacy models for these complex diseases.”

Griffith is program director and one of several principal investigators working with DARPA funding to create the Human Physiome on a Chip. The chip is a step toward better modeling for drug discovery — and a step away from using animal models. “We don’t want to kill them, but they also don’t represent the biology that we want,” Griffith said.

In the lab, grad student Luis Soenksen showed the fellows a plastic custom-machined chip. Wells in the chip hold several individual model organ tissues, often derived from a single patient’s induced pluripotent stem cells, and are connected via microfluidic channels attached to pumps. The heart cells beat like a heart. The neurons in the brain extend axonal projections to other neurons. The gut epithelium contains a sample gut microbiome, preventing bacteria from contaminating the rest of the system. Bloodlike media circulates between the organs, allowing them to interact as a system. One reason so many drugs fail late in development is unexpected effects on other organs.

At a neighboring bench, grad student Pierre Phabmixay passed around scaled-up 3D-printed models of the geometric scaffolds. He focuses on the brain and the liver, two organs that rely on dense networks of blood vessels. The larger models allow for easy visualization of each unique architecture, but Phabmixay ultimately prints microscopic scaffolds with biocompatible polymers that he seeds with human cells.

After dragging fellows away from Soenksen and Phabmixay, who were still eagerly focusing a microscope and explaining how microfluidic pumps could simulate blood distribution to organs throughout the body, Griffith herded the group back into her office to answer any final questions. She invited interested fellows to attend the lab meeting the next day, off the record.

“She seems like the ultimate interdisciplinary scientist and collaborator, bringing together systems biology, engineering and medicine,” said KSJ fellow Lauren M. Whaley, “as a journalist interested in biotechnology and women’s health, I was thrilled to meet Linda Griffith and visit her lab. I want to spend a lot more time there if she’ll let me!”

by KSJ@MIT / March 17th 2017 / KSJ News & Events

Undark and KSJ Head South for a Weekend

David Corcoran, center, with the New York Times science writers John Noble Wilford and Natalie Angier.

Hey, health care journalists! It’s time to prep your story pitches for Undark magazine.

David Corcoran, Undark’s senior editor, will be one of about two dozen editors participating in the Freelance PitchFest at the annual Association of Health Care Journalists conference in Orlando, Florida, on Friday, April 21, from 1:40 to 3:50 p.m. Eastern time. On March 31, at 1 p.m. Eastern, he’ll also take part in a pre-conference live webcast for AHCJ members, “Mastering the Art of the Pitch.”

While you’re at the conference, stay through Saturday, April 22, to hear Lauren M. Whaley (Knight Science Journalism Fellow 2016-17) speak on a panel about how to “stay the course in a sea of patient activism” (#ahcjpatientactivism).

Corcoran is a veteran of the pitchfest, a kind of journalistic speed date in which freelancers are given seven minutes to present one or more story ideas to an editor, who then gives them feedback in real time. He participated in at least half a dozen such sessions at AHCJ and other conferences during his tenure as editor of Science Times, The New York Times’s weekly science section.

He has this advice for prospective pitchers:

Don’t expect a definitive yes or no during your seven-minute session. Pitch your story or stories in person, then follow up by email. And you can leave the résumés at home; briefly tell the editor about your qualifications, but attach the CV to your email pitch — along with at least two references.

Even if he likes the idea, “I’m not going to green-light anything without getting references,” said Corcoran, who is also associate director of the the Knight Science Journalism Program at MIT.

A few other suggestions:

Read Undark. This may be obvious, but Corcoran has been at pitchfests where the journalist clearly had no idea what his publication was about. “Undark is an online magazine devoted to the intersection of science and society, so we like pitches about public health, about climate change, about things that affect people in the public realm,” he said. “We’re not so interested in scientific breakthroughs.”
Think 1,000 to 2,000 words. Undark runs a monthly long-form feature of 5,000 words or more, but its “bread and butter” is the shorter feature.
Get right to it. Seven minutes isn’t that long.
And whether you’re at the conference or not, the way to pitch Undark is to go to undark.org, scroll to the bottom of the homepage, and click the “Submissions” button in the lower left.

To participate in the March 31 webcast, you must be an AHCJ member. For the pitchfest, you must be registered for the conference. Online sign-ups end at 1 p.m. EDT on March 28. You can also sign up in person from 3 p.m. on April 19 through 3 p.m. on April 20.

In her panel discussion, from 4:40 to 6 p.m. on April 22, Whaley will address how to cover forces behind non-evidence-based ideas without resorting to false equivalence. Whaley is a California-based multimedia journalist covering mental illness, perinatal care, health disparities, and public health issues.

by Raleigh McElvery / December 15th 2016 / KSJ News & Events

Climate Change: The View From 35,000 Feet

Steven Barrett, right, with Lauren Whaley and Iván Carrillo, 2016-17 KSJ fellows. (Photo: Raleigh McElvery.)

On November 29, Dr. Steven Barrett blew through the doors to KSJ — his flight home from London to Boston had been delayed, and he was in a rush. Scheduling snafus aside, Barrett is no stranger to aviation; he’s an aeronautics and astronautics professor here at MIT. An expert on the relationship between aviation and the environment, Barrett spoke to the KSJ fellows about the ways in which high-altitude transportation accelerates climate change.

Barrett explained that as countries become wealthier, modes of high-speed transport, like trains and planes, become more popular. This trend is especially pronounced in Asia, where aviation is growing at an extremely fast pace. During his talk, Barrett forecast that carbon dioxide emissions from global aviation could double or even triple by midcentury. And even though air travel accounts for just 4 percent of the CO₂ produced today, that kind of increase could undermine hopes of reducing emissions 80 percent by 2050.

The most obvious remedy, he said, is to build more efficient planes. But they would have to be much more efficient — burning 90 percent less fuel to meet the 2050 emission goals — and the technology to do that is still a long way off. So experts like Barrett are looking at alternatives.

For instance, “biofuels” are made from natural plants, which already contain CO₂ taken from the air during photosynthesis. This plant-based carbon can be converted into fuel, burned, and then returned to the atmosphere whence it came.

“In theory it’s a closed loop,” said Barrett. “However, in practice it’s not quite that simple; there a few problems.”

Planting biofuel crops in previously open swaths of land decreases the Earth’s available surface area to reflect sunlight. As a result, the planet retains more heat than it expels — a phenomenon known as the albedo effect. Clearing forests to make room for biofuels could “unlock” the CO₂ stored within the decimated trees, adding more carbon to the atmosphere.

To make matters even more complicated, Barrett emphasized that CO₂ is just one of many factors that contribute to aviation-induced climate change. “On the ground, one ton of fuel gives you about three tons of CO₂,” he said. “Up at high altitudes, you still get the same three tons of CO₂, but you also get a bunch of other chemical effects too, like contrails.”

These white, puffy streaks form in the wake of aircraft if the atmosphere is cold and wet enough. As the airplane burns fuel, it emits water vapor that condenses onto the carbon soot in the exhaust. This creates billows of ice crystals suspended in the sky — the contrails we see from down below.

Just like greenhouse gases, contrails are worrisome because they trap the heat given off by the surface of the Earth. But not all contrails are created equal. Those generated during the day aren’t as concerning; they trap radiation from the planet but simultaneously block incoming heat from the sun. While these two temperature effects nearly balance each other out during the day, at night there is no solar radiation to reflect. As a result, nighttime contrails serve to hold in the Earth’s warmth like a blanket of insulation. To make matters worse, contrails are most likely to form at 35,000 feet — the optimal altitude for air travel.

Contrails last for only about three hours before dissipating, which means their warming effects fade shortly thereafter as well. By comparison, CO₂ persists in the atmosphere for thousands of years. While contrails don’t sound so bad in this context, Barrett expressed that “the last three hours of flights actually produce as much warming through contrails as CO₂ emissions have over the last 60 years.”

By altering the combustion process, Barrett thinks daytime contrails could be brightened so they reflect more sunlight and nighttime contrails could be thinned out to permit heat from the Earth to escape. “Over all, that strategy could reduce contrail warming by 50 percent,” he said.

KSJ fellow Iván Carrillo called Barrett’s talk “quite depressing, but realistic at the same time.” “I hope we’ll be tough enough to face the challenge, and change our air transportation system in the future,” he said. “It’s a big issue for humanity.”

Asked if there was reason for hope in the face of such daunting challenges, Barrett told the fellows, “Lots of us do still have hope,” and added, “At the same time, this isn’t the sort of trivial challenge that can be solved instantly when a politician signs an agreement.” It’s much bigger than that.

by Greta Friar / December 6th 2016 / KSJ News & Events

Author, Author, Author: Three Books From KSJ

From left, Meera Subramanian, Maura O’Connor, and Mark Wolverton spoke to KSJ classmates about the joys and perils of writing and publishing. (Photos: Fabio Turone, left; Meera Subramanian, center and right.)

“I never thought that I would be in competition with Bill Clinton,” said Mark Wolverton, a current Knight Science Journalism Fellow. He was referring to how his second book, The Depths of Space: The Pioneer Planetary Probes, was published in the same month as the former president’s autobiography, My Life, in 2004. It was one of the many unexpected challenges confronted by the book authors in this year’s class.

The three authors — Wolverton, Meera Subramanian, and Maura O’Connor — shared their experiences of writing and selling their books with the rest of the fellows in the comfort of the conference room on the dark, rainy afternoon of November 15.

The authors gave practical advice about writing a book proposal, finding the right agent, and paying for travel and research, among other topics. Subramanian showed a step-by-step slide presentation called “Anatomy of a first book deal (and how to survive while actually writing the book).”

But along with giving specific tips, such as looking at the acknowledgments pages of books you admire to find agents and editors who might be a good fit, the authors tackled the issue of — as Wolverton put it, adding a choice expletive — “Why do you write a book in the first place?”

All three KSJ authors emphasized that writing a book could be a painful process — as could trying to sell it — and that there were no guarantees of fame and fortune. Most authors will never earn out their advances, let alone get large royalty checks or hit the top of the best-sellers list.

So why bother?

Subramanian knew she was ready to write a book when, after struggling for years with a difficult book proposal that she could not quite make work, she was inspired by a new idea and came up with a complete proposal in three weeks. She said the idea that became a published book felt different. The narrative arc came easily and the idea was something that wouldn’t let go of her. To get through the slog of finishing a book, the writer needed to be captivated by the topic, to feel “even straight-up obsession,” she said. The result was A River Runs Again: India’s Natural World in Crisis, From the Barren Cliffs of Rajasthan to the Farmlands of Karnataka (2015), which features five stories of sustainability efforts in India.

As a career journalist, O’Connor knew that not every assignment she got was going to excite her. “The best reason to write a book is that it is intellectually satisfying,” she said, adding that the size of the advance and the size of the audience aren’t important. “Does this make me happy?” she asked. “If yes, do it.” O’Connor’s first book, Resurrection Science: Conservation, De-extinction, and the Precarious Future of Wild Things (2015), discusses the complexities and contradictions of wildlife conservation, as well as the possibility of reviving extinct species.

Wolverton described a different type of satisfaction. “I’m sure all of us remember the first time we published something, but that’s not the same as having something you can hold,” he said. A book felt more permanent than an article, more lasting. “There will be times when you hate the stupid thing,” he said, but “after all the agony, you get to walk into a bookstore and see this.” And he showed a picture of a tall stack of copies of his third book, A Life in Twilight: The Final Years of J. Robert Oppenheimer, in a bookstore, waiting to be sold. His expression as he looked at the photo was clear: All of the bad writing days, the arduous negotiations, and the unexpected challenges had been worth the joy of picking up his work from a bookstore table and holding it in his hand.

by Raleigh McElvery & Greta Friar / October 13th 2016 / Fellowship Life

Of fire and flat tires: The lives of KSJ fellows

The road to the small fishing village near Lake Turkana, Kenya, was so rough that Rosalia Omungo’s car broke down — air hissing from the punctured tire. On the day of the incident, Omungo, a producer for the Kenyan broadcaster KBC TV, was on her way to investigate plans to build a dam on the Omo River, which would decrease the flow of water to Lake Turkana and jeopardize the local fishing industry. Just a typical day on the job for a reporter and current Knight Science Journalism fellow.

Rosalia Omungo looks on as her car tire is fixed. Photo: Chris Lomusia.

Each year, the KSJ program at MIT provides 10 established science journalists with the opportunity to take classes and participate in a broad array of activities, trips, and workshops over the course of nine months. On Sept. 8, a few weeks after the fellows arrived on campus, the program held its annual “Soundings” meeting, in which they gathered to share career highlights and their expectations for the year ahead.

Robert McClure, an environmental journalist and executive director of InvestigateWest, shared excerpts from his piece “Lost in the Deep Dark Swamp,” describing his expedition through the alligator-infested Everglades, published in the Sun Sentinel during the mid-90s. Since that time, McClure has been honored as a Pulitzer Prize finalist and named one of Seattle Magazine’s “most influential” people.

Maura O’Connor, a Brooklyn-based freelancer, has explored popular false statistics and the biases that inform them. She said she’d learned to “question what we accept as fact.” For a forthcoming article on Haiti’s forests, for example, she discussed how outsiders’ views of Haitian culture distorted perceptions of the country’s environment. She’s at work on a book about human and animal navigation.

“My story is about stories leading to other stories,” said Meera Subramanian during her presentation. A print journalist specializing in environmental issues, she began her journey on a 40-acre land trust in the Oregon wilderness. Despite her passion for nonprofit work, Subramanian eventually ventured to New York City for graduate school. Here, her impulse to locate the wild among the urban led from falcons in the financial district to declining vulture populations in India, and finally to her first book, “A River Runs Again.”

Meera Subramanian releasing a wild peregrine falcon on South Padre Island in Texas after biologists collected health data and affixed an identification band to its leg. Photo: Gregg Doney.

The path of Italian science writer and editor Fabio Turone had “less space for dreams,” at least early on. “Those came later in my career,” he said. Still, as he realized his writing held promise for social change, he became committed to supporting international science journalists, as well as improving rapport between writers and researchers. He is now director of the Erice International School of Science Journalism and leads the professional organization Science Writers in Italy.

Chloé Hecketsweiler writes about the business side of health care for the French newspaper Le Monde. She investigates pharmaceutical companies, writing about marketing strategies, lobbying, and conflicts of interest. She has traveled to Africa to investigate why medical drugs aren’t getting to the populations that need them. Lately she has become “obsessed” with genetic engineering and its potential to redefine the human identity.

Iván Carrillo, a Mexico City-based science journalist with a background both in print and television, boasts the earliest foray into the field, having started a school newspaper at age 8 — and later contributing to National Geographic Magazine LA, Newsweek Magazine en Español, CNN en Español, and SPR News. At “Soundings,” he displayed images from his time as editor of the magazine Quo, as well as video clips from the science-based TV program Los Observadores de TV Azteca, which he currently hosts.

Journalist in training: Iván Carrillo in 1979.

Bianca Vázquez Toness, a Massachusetts-based journalist, spoke about how her experiences reporting on technology and development in India gave her a new appreciation for the importance of the internet for quality of life and economic development.

Lauren M. Whaley, a California-based multiplatform journalist focusing on health care policy, likes “putting a human face on health issues.” She has photographed people with mental illness, produced a video profile of a young child with lead poisoning from paint, and even reported on her own medical issues to “make it easier for others to talk about theirs.” One of her radio and video pieces led to “a side gig in birth photography.” Whaley also likes “finding stories that are hidden in plain sight.” When other reporters were writing about the anti-vaccine movement during the 2015 measles outbreak in California, she sifted through kindergarten entrance records and discovered that many under-vaccinated children came from families that didn’t necessarily oppose vaccination. Schools granted conditional entrance based on “plans to vaccinate,” and families either forgot to get their children the rest of their required shots or had trouble doing so. Talking about what she wants to accomplish at MIT, Whaley expressed a dilemma common to many fellows: “I want to do that and that and … and …”

Mark Wolverton, a Philadelphia-based freelancer and author, began his “Soundings” presentation with a look at the bigger picture. When asked what it takes to become a science writer, Wolverton says he often replies that it’s nothing short of an Olympic feat — and not in the sense of the Games. He quoted one of the first full-time science writers, William Laurence, who once proclaimed: “True descendants of Prometheus, science writers take the fire from the scientific Olympus, the laboratories and the universities, and bring it down to the people.”

While these journalists may not make the trek to and from the scientific Olympus, the KSJ Fellows seemed to agree that their job is to bring both the knowledge of fire and the fire of knowledge to the masses — which may entail a few flat tires along the way.

From left, Maura O’Connor, Robert McClure, Iván Carrillo, and Sally Deneen listening to a Soundings presentation. Photo: Raleigh McElvery.