Begin at the beginning

Posted on by under GM Food

NOTE: This is the first in a series of blog posts investigating genetically modified foods and the controversy surrounding them.

Where do you begin the story of genetically modified food?

At a modern beginning, with Augustinian monk Gregor Mendel, arguably the father of genetics as we know it today? Perhaps it’s best to turn the clock forward 40 years or so to 1901. That’s the year an American businessman borrowed money to get into the artificial sugar business. He christened his start-up after his wife’s maiden name: Monsanto. A third option: Dive head-first into the “GM food must be bad” controversy replete with fear-mongering. (And fear assuaging as talented science writers debunk headline-grabbers.)

The beginning may come later. For now, I’d like to look at some main “arms” within the GM food controversy: definitions, logic, money. As I go forward on my journey to understand why the public struggles to accept GM food as safe, I will refer back to these main areas. (This tiny-sized and really incomparable quest is inspired by what Seth Mnookin set out to do with his book The Panic Virus — see sub-heading ‘Who Decides Which Facts Are True?’).

Definition of “genetically modified”

I have selected four definitions and classify them as “close-to-mutual” sources. All definitions were accessed from the included website links on March 20, 2013:

“Genetically engineered foods have had foreign genes (genes from other plants or animals) inserted into their genetic codes.” – University of Maryland Medical Center online encyclopedia

“Genetically modified foods (GM foods, or biotech foods) are foods derived from genetically modified organisms (GMOs), specifically, genetically modified crops. GMOs have had specific changes introduced into their DNA by genetic engineering techniques. These techniques are much more precise than mutagenesis (mutation breeding) where an organism is exposed to radiation or chemicals to create a non-specific but stable change. Other techniques by which humans modify food organisms include selective breeding and somaclonal variation.” - Wikipedia

“Genetically modified food: food from crops whose genes have been scientifically changed.” - Cambridge Dictionaries Online

“Genetically modified organism: An organism whose genetic characteristics have been altered by the insertion of a modified gene or a gene from another organism using the techniques of genetic engineering.” – The Free Medical Dictionary

PHOTO BY KATHLEEN RAVEN. This is a pretty shot of red clover as a cover-crop. It is not a GM crop in the sense of the definitions included here.

PHOTO BY KATHLEEN RAVEN. This is a shot of red clover as a cover-crop. It is not a GM crop in the sense of the definitions included here.

Logic arguments

Logical fallacies plague GM food arguments. For now, here’s a quick look at three popular ones:

The only certain thing about GM food is its uncertainty.

This is a contradiction in adjecto (self-contradiction) argument. Read more about this type of logically fallacy here.

GM foods are harmful until someone proves they are not harmful.

This is the burden of proof fallacy. Read more here.

If human genetic modifications are dangerous, then genetically modified plants are dangerous. Genetically modified plants are dangerous. Therefore, human genetic modifications are dangerous.  

This is a formal fallacy that can be expressed “If A then B. B. Therefore, A.” From this website.

Before moving on, I’d be remiss to leave out one of my favorite blog posts relating to this sub-topic. In 2012, Brian Dunning posted his own “argumentum ad monsantium” on Skeptic Blog.

Always about the money

One of the tenets of journalism is: Follow the money. Of course, this path is never paved with freshly minted dimes and nickels. In my cursory research, I could only find two figures. A New York Times article quotes the GM seed market at $6.9 billion in 2007, based on research from the consulting firm Cropnosis. According to Rob Carlson, author of the book Biology is Technology, the total worth of modified crops themselves – and this includes cotton – was about $65 billion in 2008. One of my research goals will be to independently verify these numbers and update them if possible.

TO BE CONTINUED . . .

My journalism mistakes: Please, read all about them

Posted on by under Science communication

Humans make mistakes every day. In some professions, errors can be shrugged off as costly mistakes. “Geez, it looks like we’ve installed the processor incorrectly on the last 50,000 widgets. Need a re-do.” Nurses, doctors and others in the healthcare know much higher stakes: the tiniest missteps can put a life on the line. Hence, the humble checklist, so beloved by aviators, helps prevent an untold number of  disasters. Journalists have an equivalent tool: it’s called fact-checking.

For good reason, the ghosts of lying journalists past haunted my undergraduate journalism education. Their names were spoken in a hushed tone. Janet Cooke, Stephen Glass, Rick Bragg. The Jayson Blair scandal at The New York Times erupted at the end of my sophomore year. (Unfortunately, there’s a long list of offenders – updated through 2007 only – compiled by the Freedom Forum.)    I personally think Mike Daisey should bear a scarlet letter, thespian or not. A life-or-death threat rarely looms above a journalist as she tweaks here, borrows a bit from there, and slaps in some fiction for good measure. So another conscious-rattling consequence should be clear for journalists who plagiarize and fictionalize: a swift and total exile from non-fiction forever. No question. No meaningless mea culpas. Night has fallen for the moment on a particular journalism foundation in my eyes. I appreciate their response to the situation.

So I mean what I say in my tweet:

When all of the Jonah Lehrer (#infoneeds) controversy erupted on Twitter yesterday, I rolled my eyes and kept on with work. Why give even more attention to someone (and possibly an organization) that is clearly trying a shock technique to get attention? (I regret that the Knight Foundation didn’t think through the scenario of not only giving Lehrer a platform, but paying him $20,000 speak.) But as I read posts and heard thoughts from my fellow science writers today, I realized I needed to add my voice to the crowd.

Every single factual error I’ve made in my journalism career (I started as a Georgia Press Association intern at rural newspaper in 1999) has been seared into my memory. I carry them with me and I relive them as lessons in miniature. But I am proud of the small proportion of mistakes out of what has been hundreds of newspaper and magazine articles. I have written, with some breaks in between, for college newspapers, local newspapers, one local magazine, science publications and two dailies: The Statesville Record & Landmark and The Marietta Daily Journal for nearly 14 years.

As a journalist, I ask my sources tough questions. It is common sense to be completely transparent. A good journalist must be honest almost to a fault. That is very, very difficult to do. Smooth-talkers like Lehrer tear off another piece of the already much-battered public trust when they write fabricated stories, lie or simply don’t fact check. I refuse to be grouped into the “untrustworthy media.”

I’m sure I have made mistakes that no one ever alerted the publication to. Below are the ones I remember. I wish I could link to all of the articles, but some were published before online archiving began in earnest. Please, read all about them. I will do my best as a writer for “the public’s right to know” to avoid adding to the list.

1. Name misspellings (1999-2000)
2. A chart that incorrectly conveyed information (2001)
3. My story reported the opposite result of a vote at a city council meeting (2006)
4. When writing about high school test scores, I reported the inaccurate number of students who failed the test (2006)
5. Incorrect translation of percentages (2012)
6. The wrong amino acid sequence (2012)
7. Incorrect word use and wrong units of measurement (2012)

New genetic analysis narrows HIV vaccine targets

Posted on by under Archives

CROSS-POSTED from Nature Medicine’s Spoonful of Medicine

By Kathleen Raven

September 10, 2012

The road to a protective HIV vaccine has not been easy thus far. The failed STEP trial, halted in 2007, was just one major trip-up among several, and two years later the massive RV144 trial from Thailand spurred controversy about efficacy rates. Part of the problem is that researchers have long struggled over the best target for the HIV vaccine.

A study published online today in Nature from researchers in the US and Thailand should help scientists inch closer to settling that debate. Through genetic analysis, the study suggests that specific amino acid sequences found in the HIV V2 protein loop—there are five total loops on the outside of the viral envelope—could lead to improve vaccine effectiveness.

PHOTO BY tonrulkens Flickr, Creative Commons. Please click on the photo to see the original source.

The current RV144 vaccine contains three synthetic HIV genes.

One, called the ENV gene, produces the ‘envelope’ (Env) protein loops. To understand how the vaccine exerted influence on the virus, the researchers sequenced more than 1,000 HIV virus genomes from 110 ‘breakthrough’ viruses isolated from 44 vaccinated participants and regular viruses found in 66 placebo recipients.

The analysis centered on the idea that viruses that ‘break through’ vaccine protection contain a genetic signature, visible by changes in the amino acids chains they encode, compared with viruses the vaccine fends off. “Viruses that escape [the vaccine] carry the scars of the immune response,” explains Jerome Kim, a virologist at the US Military HIV Research Program (MHRP) in Silver Spring, Maryland and senior author on the paper. Based on the frequency of virus sequences in the two groups, he and his colleagues calculated that when the HIV virus and the vaccine code for the same 169 amino acid position, the vaccine is 48% effective. However, the vaccine is estimated to be 80% effective when the virus and vaccine sequences match at position 169 and—unexpectedly—do not match at position 181.* The overall efficacy rate in the original RV144 trial hovered at just 31%.

The finding raises the possibility that a future, retooled vaccine (especially one to fight the HIV virus subtype E found in Thailand) could contain an HIV envelope gene engineered to present the V2 protein loop in a way that would prompt a more effective antibody and overall immune response.

The new study also provides an independent confirmation of a correlative study published in April in the New England Journal of Medicine, which suggested that when the body produced antibodies geared toward the V2 protein loop, the result was lower rates of HIV infection. “We know that the vaccine induces antibodies, those antibodies exert some immune pressure, and so we expected to see the consequences of that pressure on the [HIV] viruses,” says Morgane Rolland, a virologist at MHRP and study co-author.

“I am cautiously optimistic [about the results],” says Andrew McMichael, an immunologist at the Weatherall Institute of Molecular Medicine in Oxford, UK, who was unaffiliated with the study. He says he is optimistic that this study confirms that V2 antibodies may play an important role in preventing HIV infection. However, McMichael points out that the mutation of the amino acid position 181 was mostly found in viruses of the placebo participants and therefore may be difficult to link to a V2 antibody response since those patients did not receive the vaccine.

But Barton Haynes, an immunologist at Duke University School of Medicine in Durham, North Carolina, and senior author of the NEJM study earlier this year, thinks research on a vaccine from the RV144 trial is moving ahead like clockwork. “It adds support to the hypothesis that these V2 antibodies may in some manner be involved in protection,” he says. The next step, which should happen soon, he says, would be to try out a retooled vaccine with this added antibody protection in macaque monkeys.

*CORRECTION: An earlier version of this post incorrectly stated the vaccine is 80% effective when the virus and vaccine sequences match at amino acid position 181. Researchers are still studying to understand how a mismatch at this site might be beneficial.

Generalists and specialists can coexist

Posted on by under #sci4hels, Science communication

The University of Toronto began an interesting journalism school experiment this year: They recruited students already specialized in a field, and then began teaching them a few journalism skills. This and ascendance of New York Times statistician Nate Silver has caused renewed anguish for aspiring reporters who still attend J-school: to specialize or not?

Seven years ago when I graduated from college with a degree in “Newspapers,” — a specialized degree if there ever was one — the expected path for journalists went something like this: Get an entry-level, general-assignment reporting job at a good daily newspaper. Work hard. Climb the ranks, reach for the bigger stories and move on to jobs at bigger dailies. Soon, your blood, sweat and tears will be rewarded by an editor’s decision to give you ownership of a beat. Editors will assign fewer daily stories. Your sole existence as a newspaper reporter will be  to cover your beat. Establish deep connections in the community. And finally: Break stories related to your beat first. So while many journalists began as generalists, they had a good chance of becoming specialists.

The many reasons the above model is antiquated is beyond the scope of this post. But I relate that story to remind readers how quickly the generalist-to-specialist route in journalism has been upended. Nate Silver of the 2012 U.S. election fame has taken the upended model and thrown it clear out the window. And I’m glad he did, for some reasons. He pushed past the “he-said-she-said” reporting model and gave us nearly un-subjective information.

My hunch is that after all of this specialization talk has settled down, there will again be a demand for generalist writers–either at a paper publication or at an online site. Specialists will stay around, too.

What is sterling example of how professionals with broad knowledge in many areas and acute knowledge in one or two fields coexist? Doctors. Freshly minted medical students who pursue primary care medicine are brave, in extreme demand and draw lower salaries, on average, than their specialized counterparts. We of course appreciate the anesthesiologist who visits us before surgery. But in our day-to-day affairs, we are comforted by a family doctor who knows a little about a lot and can help steer us in the right direction.

Likewise, I admired Nate Silver’s brilliant way of using data to move past the surface talk. But I’ve frankly found little use for his further blog posts. They come across as a list of facts of information. Now I want to read political stories from a writer who casts a wide net to interview multiple sources, does rigorous research into not only statistics, but also history, previous news coverage and social sciences.

The writer who, specialized or not, tells me a story — as some online writers like Nate, in my opinion, do not — is the one who I will follow regularly, online or on paper. I will check in on Nate and others when I need specific information. But to keep the news media ecosystem thriving, we need generalists and specialists. Just like Nature.

Finally, to be clear, a journalist doesn’t need J-school to become a good storyteller. However, whether someone aspires to be an online writer on one subjects or many, it is still good to know a few simple rules about journalism.

ScienceOnline 2012 – Behind the #scio12 hashtag

Posted on by under Archives

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In 2005, two bright-eyed friends, sipping coffee in North Carolina’s Research Triangle, hatched a plan. Why not gather professionals and amateurs of all stripes, under the heading “science online,” in a cozy space with free-flowing caffeine and see what happens? Bora Zivkovic and Anton Zuiker (later joined by Karyn Traphagen) could not have known that the wire they tapped would explode to life. Seven years later—a short time period in the life of any conference—ScienceOnline has morphed from an obscure meeting to an event worthy of a mention in The New York Times and a post on BoingBoing. With the latter being, perhaps, a bigger deal.

 

The reason the ScienceOnline conference—or “unconference,” the category its organizers prefer (it is better nomenclature, you’ll see)—rocketed to recognition might have something to do with the possibilities on hand each year. The party thrown last month at North Carolina State University’s McKimmon Conference Center was no exception. For example, conference-goers could strap their mobile devices and laptops onto one of the fastest broadband Internet connections in America. Ready, set, tweet! If you were torn between which concurrent session to attend, your heart leapt at the realization that your colleagues, equipped with otherworldly tweeting abilities, actually live-tweeted every single session, dutifully including the appropriate hashtag—#scio12—on each tweet. With such insightful tweeting, a person really could be in two places at once. Other possibilities included: feeling surprisingly intimate with the 449 other conference attendees; delightfully drowning yourself in more information than you ever thought possible; marveling at the on-the-fly art produced by talented artists; and, certainly not least, taking home important lessons about communicating medicine and science to the public.

 

Wait, we’re talking about a conference/unconference, right? Doesn’t this seem a bit… hyperbolic? You should ask Paul Raeburn of Knight Science Journalism Tracker that question. (Hint: He would probably agree the hype is fair and warranted.) And if so many people are pumped about the conference, then why only 450 total attendees? And now we arrive at one of the most rare and gifted qualities of this particular conference: you don’t have to physically be there to share and participate in the excitement and learning. Ideally you are there, sharing a pint with a fellow blogger or discussing the merits of citizen science over a muffin at breakfast. But anyone who’s interested in science online can get involved. Now. The ScienceOnline 2013 planning wiki is already posted!

 

Another attribute of the annual event that contributes to its “unconference” nature is the lack of a common, overarching theme. This translates to wide and varying session topics—from science tattoos (yep, Carl Zimmer wrote the book on ‘em) to preserving digital science online. The professionals and amateurs that Anton and Bora originally targeted can still choose from the dim-sum of science-related topics available. The variety also makes summarizing the contents of ScienceOnline quite difficult. Instead of more description, I’d like to make a prediction: Science journalists will be seeing (and doing) more reporting based on data journalism and the semantic web. Two recent graduates from New York University’s science writing program showcased the possibilities of how to turn data into art during one session. In another discussion, two researchers described a Matrix-like world behind the world wide web: the Semantic Web. Here’s an example of Semantic Web in action. If you’re curious to learn more about ScienceOnline, be sure to check out a complete listing of the conference experience here.

 

This was my second consecutive year attending the three-day mad dash. And there’s something extremely reassuring about the classic, core values that continue to be the force behind excellent science communication online: writing/video/audio should be clear, factual and compelling. 

Mourning loss of water (good-tasting)

Posted on by under Archives

I’ll be the first to tell you: I’m a water snob.

You would be, too, if you grew up drinking pure groundwater preserved in sediment rock. This isn’t Evian, which, frankly has a stale finish. I’m not talking about Fiji and that bottled brand’s clean but flat taste. The water that nourished me for 18 years tasted like underground, undiscovered Eden. You couldn’t bottle that sweet, dewy, unmistakably fresh water. I knew what pristine tasted like and as long as I could get it, I would have it.

When I moved back to live in Athens, Georgia, about a 20-minute drive from the homestead, I insisted on getting that water again.

Beginning in earnest last year, I made weekly trips to my parents’ home under the auspices of a visit. But with 20 empty glass bottles clinking together in bags on my shoulders, I couldn’t hide the fact that my appearance was partially prompted by a low water supply.

So my parents smiled at my hardheadedness and we joked about my “water problem” and I happily quenched my thirst during the week with the water I’d grown up with. Given the extra effort to get this water, I didn’t necessarily take it for granted. I also didn’t think the water could possibly change. I was pessimistic enough to think that what is happening in Australia would probably happen in due time to the southeastern United States. But even that bad-case scenario was years off.

Or so I thought.

A little over one week before Christmas Day, the well pump at my parents’ home clogged up with years of soil minerals and sputtered to a stop. The next day two well repairmen maneuvered heavy equipment over to the simple well pump structure. They tore up the old pipe, replaced the filter, and then dumped Clorox into the water supply to (ironically) prevent contamination.

As Clorox settled around unseen, unproven germs in the well, the purebred water taste dissipated. On my last visit to my parents’ home, I used, with some hesitation, a faucet filter, as I filled up a glass. The water tasted okay. Still disbelieving that our well water was changed, I dumped out the glass, switched off the filter, and filled up another glass. I held the water up to my nose. I could smell the bleach.

The well repair workers assured my mother and father that the chemical taste would go away in two weeks. Almost four weeks have passed since the repair.

The whole experience was a reminder: Do not take for granted the access to clean water.

Must start somewhere, starting here

Posted on by under Archives

Last month a bunch of scientists, the best and the brightest, flew, drove, or took the train to Yale University for ScienceWriters2010 sponsored by the National Association of Science Writers (NASW). For any writer with an insatiable interest in the sciences, this is a spiffy event. A person practically trips over the news story possibilities. This meeting in New Haven marked my second journey, a pilgrimage, really, to be with writers and storytellers of all backgrounds bound by a common interest: science is fun.

I wanted to rush home and write, write, write! I sorely missed the thrill of writing for daily newspapers, where I’d earned a living before returning to the University of Georgia for graduate degrees in conservation ecology and health & medical journalism.  Sure, the writing would be fun. But who would read what I wrote? How?

Start a blog, everyone said. Such advice fell on skeptic ears. Sure, I knew about blogs and I had even started one a while back for a class project. But for a blog to be successful, I thought the blogger needed to be mostly famous or part of a larger publishing group. Then I began to have conversations with other bloggers, in particular the writers of A Blog Around the Clock (thanks for the encouragement, Bora!), Superbug on Wired and Speakeasy Science, all of whom had humble beginnings, but who now reach thousands and more readers each day.

So here’s my voice. Here’s my humble blog beginning. Thank you for reading.