On “Leaving Science”

Posted on 2013.05.16 by Alan

I follow news about the science job market pretty closely, but perhaps the most reliable indicator I have of it isn’t in my RSS folder or Twitter feed. It’s my inbox. When graduate students and postdocs start to think their future is especially bleak, I start getting more notes from them asking about my choice of an “alternative” career. Many scientists have the naive impression that anyone with a PhD and a laptop can just take up science writing and make a decent living freelancing. I hope my previous two posts have disabused them of that notion.

Now I’d like to back up a bit and address a broader theme that comes up in these discussions: what’s it like to “leave science”? No matter how the question is phrased, the implicit assumption is that a career in basic research is the only valid purpose for earning a PhD in science. Choosing anything else carries a whiff of failure.

It’s not hard to see where this attitude comes from. In any worthwhile PhD program, students and postdocs are surrounded by principal investigators (PIs) who’ve made basic research their life’s work. Of course these people consider science the primary point of the training they provide their underlings – if they thought otherwise, they wouldn’t be where they are. Society has granted the PIs the extraordinary privilege of pursuing their own curiosity for a living. How could anyone want to do anything else?

What most PIs don’t see is that this privilege has costs, and those costs have skyrocketed in recent years. Jordan Weissmann recently provided an excellent and graphic summary of the situation, based on data from the National Science Foundation. According to those data, a biological science PhD graduating in 1973 had a better than 50% chance of becoming a tenure-track faculty member within five to six years. Those are today’s department chairs and deans. They grew up with that reality, and they have a hard time imagining that things have changed much. But things have changed, and radically; a PhD graduating today has less than a 15% chance of becoming a tenure-track faculty member over that time period, and that percentage is still declining. Basic research is now the “alternative” career. Most PhDs will do something else.

This isn’t a recent trend, and it’s not going to go away even if the idiots in Washington manage to fix the current budget clusterfuck. When I was nearing the end of my doctoral work at Columbia in the mid-1990s, the job market was already pretty tough. Many of my colleagues were brilliant and incredibly dedicated scientists, and some of these hard-core folks were heading for second postdocs, having spent more than a decade in “training” positions already. For those who couldn’t imagine themselves doing anything else, the prospect of becoming a PI was worth nearly any sacrifice. Like aspiring actors or artists, they were perfectly willing to forgo both free time and decent pay indefinitely, and dedicate their lives to pursuing their dream.

That wasn’t me.

I loved science and thoroughly enjoyed doing it. Had I graduated in 1973 I most likely would’ve pursued it as a career, but in a labor market that apparently had many more scientists than it needed, I could easily imagine doing something else. I rejected the outdated notion that a non-PI career track would constitute failure. The PhD was supposed to expand my options, not restrict them.

With longstanding interests in public policy and communication, I started looking around for jobs that would combine my scientific training with one of those fields. It didn’t take long to settle on science journalism. When I switched careers, though, I did not “leave science.”

I can’t leave science. It’s part of who I am. A scientist doesn’t punch the clock in the morning, think scientifically all day, then punch out and suddenly think some other way. It’s the same for writers; I didn’t suddenly become one the day I got my first byline. Writing, like science, is a way of thinking, and for most of us in this business it’s part of the way we’ve always thought. I’m a chimera, a scientist-writer currently employed as a science writer.

Of course one doesn’t need a doctoral degree to write science news, but I don’t think my half-decade in graduate school was wasted. Indeed, that training has helped me spot angles, carve out niches, and write stories that I doubt a nonscientist writer could’ve found. I frequently conduct 15-minute interviews that would take an English major an hour to get through, because the source and I share a common, high-throughput language. Even on stories I haven’t covered before, I can often cut a direct path to the background and sources I need to get up to speed. That’s not to say I’m better than non-PhD journalists, just on a different beat. I get jobs they probably couldn’t do and wouldn’t want, and vice-versa. There’s room for all of us.

If there ever stops being room for me, though, I won’t hesitate to change careers again. Doing research at the bench suited me when I was in graduate school, and reporting and writing stories as a freelancer suits me now. As I discussed in the previous post, business hasn’t been stellar lately, but that hasn’t been a major problem. If it becomes one I’ll move on. I won’t, however, stop being a scientist. Or a writer.

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How to Make $75,000/Year Writing (And Hate It)

Posted on 2013.05.10 by Alan

I’ve gotten some good feedback on the previous post, in which I disclosed my science writing income from the past decade and a half and explained where those numbers come from. Now it’s time to delve a little more deeply into it. Here’s the graph again , this time prettified with a line over the bars:

Profit from science writing, 1998-2012.

Profit from science writing, 1998-2012.

The first thing a business-minded person will notice is that all of the numbers are positive. Unlike most ventures, my sole proprietorship has run in the black every year of its existence. That’s less a credit to my financial acumen than it is to the low entry barriers in this field; anyone with a computer and a phone can hang out a shingle as a science writer, and the checks from just a few articles will cover the office costs.

The second thing everyone will notice is the year 2005. Yes, I made about $75,000 from science writing that year. It was the last year my income exceeded my wife’s. That brings me to an important digression.

Laura and I started dating in 1995 and married in 2000, a few days after she’d graduated from the Columbia University College of Physicians and Surgeons. Contrary to popular belief, doctors do not step straight out of medical school and onto the gravy train. In fact, these days many of them never encounter anything remotely resembling a gravy train. We moved to Philadelphia that summer for her to start residency, which is to medicine what postdoctoral training is to science: an extended period of overwork and underpay, as part of a population of indentured servants without whom the rest of the enterprise could not function. We both made about the same amount for the next several years, but she worked much harder and had vastly more responsibility than I. My income stayed relatively consistent in those years, because I had a good assortment of regular clients providing regular work. Some years were a bit better, some a bit worse, but the average was adequate.

In 2003 Laura changed residency programs, so we moved back to New York. Two years later we started the lengthy, intrusive, and costly process of an international adoption. We were also paying off Laura’s student loans and of course living in one of the most expensive cities in the world. Our debts started piling up. Her income wasn’t negotiable, but it seemed that mine might be. I turned my job into a game, and decided to see how much I could make as a freelancer if I focused on nothing but money. The answer was $75,000.

In 2005, I was raking in more than I’d ever made before. And I was miserable. I pitched stories to any editor who would return my emails. I accepted assignments on any topic, no matter how dull or annoying I found it. I didn’t do anything outright unethical, but I came close. I spent most of my days hammering out text I didn’t care about. Even the fun, interesting stories for my regular clients started to annoy me. I became that guy – the one who hates his job but loves his paycheck. In the evenings, I drank.

After a year at that pace, I started to question my worth as a writer and even as a person. I had gone into this field because I thought the world needed better explanations of science. How does writing another stringer about intellectual property legislation for a throwaway trade rag feed that goal?

Midway through 2006, I was burned out. Fortunately, I also had an ideal excuse for turning away the editors who were now calling me every week: our adoption finally came through. In November Laura and I flew to China and brought home an amazing little girl. As children do, she dismantled our lives completely and reassembled them into something entirely different, and in most ways superior to anything that had come before. Those throwaway stringers may not have helped anyone understand science any better, but by making this possible they were worth every second I had spent on them.

The next couple of years were just about ideal. I still did a few of the crap jobs out of a sense of loyalty to the clients who’d been sending me that work, but by then Laura had finally finished her residency and fellowship and taken a position as an attending physician here in western Massachusetts. I didn’t have to do unpleasant gigs just to make ends meet anymore. My income shrank, but so did my liquor bill.

2008 brought the Great Recession and the simultaneous (though largely unrelated) death throes of much of the print media industry. Newspapers had been hemorrhaging money and staff for a few years already, but now the ax started to fall at magazines, even some of the niche publications I worked for. Meanwhile, nonprofits saw donations plummet, which put one of my biggest clients on the brink of bankruptcy. Freelance budgets are very easy to cut.

Those problems hurt my bottom line, but not my lifestyle. The cost of living here on the unfashionable side of Massachusetts is low, and with a wife who’s now well-employed and a daughter needing frequent attention, I’ve felt little urgency to return to the salt mine. These days, I focus on jobs that genuinely interest me. That leaves me enough free time to provide all of the services of a stay-home spouse, while still bringing home some of the bacon.

As I hope this story illustrates, “making a living as a freelance science writer” has as many definitions as there are freelancers. A handful of writers will hit the jackpot, perhaps in the lottery system we call book publishing, but most of us will bump along from article to article, making very modest profits while suffering the slings and arrows of an outrageous business model. With a lot of effort – and too much Scotch – you might be able to beat the average in this game. I don’t recommend trying.

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15 Years of Income as a Freelance Science Journalist

Posted on 2013.05.09 by Alan

I’ve been pondering – no – obsessing over this post for longer than I’d care to admit. On the one hand, I think it would be very useful for people considering a career in science journalism to get a direct view of the field’s financial realities. Income is the elephant in the room whenever I talk to aspiring writers. Of course anyone can simply Google “average income science writer,” and find a set of figures, but are those numbers really correct? Do they apply to freelancers as well as staff writers? How much does it vary from year to year? Has the death of newspapers and decline of magazines changed it? The simplest way to answer all of those questions and more would be to open my own books. I’m a sample of one, but I can provide very detailed data for that one, and I consider myself pretty average in most respects.

On the other hand, I’m an American man. My culture has programmed me since birth to believe that my net worth is the primary, if not the only, determinant of my value as a human being. That message was filtered through the upbringing of a Southern gentleman, through which I also learned that it is impolite to discuss one’s income, or for that matter anything to do with money, in public. If you’re rich you’ll make people feel uncomfortable, and if you’re poor it’ll sound like you’re begging. Where I come from a man disclosing his income is in the same position as a woman posing nude; it’s only appropriate in very private settings. Yes, of course I know that’s all wrong. Valuing men for their money and women for their bodies are constructs of an oppressive patriarchy, and as an enlightened 21st century feminist moderate Democrat I should reject that paradigm … yadda yadda yadda.

But it still gives me the creeps, okay?

As a result, I usually answer questions about my income with vague comparisons or outright evasions: “Last year I made about as much as a public school teacher,” or “You can make a living at it, but don’t go into it for the money.”

Lately, though, I’ve decided that disclosing this information would probably benefit others more than it would harm me. So here are the data.

Inflation-adjusted profit from freelance science writing, 1998-2012.

Inflation-adjusted profit from freelance science writing, 1998-2012.

You’ll notice that I labeled the graph “adjusted profit,” not “income.” That’s because I run a business, and the appropriate way to think about business income is in terms of profit and loss. The “adjusted” part is adjusting for inflation. These figures are in 2013 dollars. I used the handy online calculator from the Bureau of Labor Statistics because I’m in the US, but analogous tools are available for other currencies.

Side note to all journalists: always adjust for inflation when comparing money figures over time. Otherwise you may crank out idiotic stories saying “Prices for X are at all time highs!” when in fact the price of everything is almost always at an all-time high.

Even after adjusting for inflation, the profit figures aren’t exactly comparable to income you might get from a regular paycheck. Every expense that’s directly related to my work is a business cost. If you’re on a salary and you buy a new home computer, your income doesn’t change. When I buy a new computer, it’s a business expense that reduces my total profit for the year by that amount. My Internet bill, a portion of my mortgage and home expenses (because my office is in my house), and other items also count against profit. That said, profit from my sole proprietorship is the closest analogue to income in the regular paycheck-based world.

I also rounded the figures to the nearest $10 to make it impossible to back-calculate my exact income to the dollar from this graph. If you’re planning to post similar data I suggest you do the same, as one’s income for prior years sometimes pops up as a “security question” for tax and banking purposes.

Having established where the numbers come from, what do they mean? What the hell happened in 2005, for example, and what about 2010? How does one adapt to an income that can swing up and down so wildly? What about health insurance and retirement savings? I’ll delve into those questions in a later post. Right now, I need to go put on some more clothes.

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The DSM-5: What’s Your Alternative?

Posted on 2013.05.08 by Alan

Last week, Thomas Insel, Director of the National Institute of Mental Health (NIMH) made an announcement that set science bloggers and medicine-watchers atwitter:

In a few weeks, the American Psychiatric Association will release its new edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5). This volume will tweak several current diagnostic categories, from autism spectrum disorders to mood disorders. While many of these changes have been contentious, the final product involves mostly modest alterations of the previous edition, based on new insights emerging from research since 1990 when DSM-IV was published. Sometimes this research recommended new categories (e.g., mood dysregulation disorder) or that previous categories could be dropped (e.g., Asperger’s syndrome).

The goal of this new manual, as with all previous editions, is to provide a common language for describing psychopathology. While DSM has been described as a “Bible” for the field, it is, at best, a dictionary, creating a set of labels and defining each. The strength of each of the editions of DSM has been “reliability” – each edition has ensured that clinicians use the same terms in the same ways. The weakness is its lack of validity. Unlike our definitions of ischemic heart disease, lymphoma, or AIDS, the DSM diagnoses are based on a consensus about clusters of clinical symptoms, not any objective laboratory measure. In the rest of medicine, this would be equivalent to creating diagnostic systems based on the nature of chest pain or the quality of fever. Indeed, symptom-based diagnosis, once common in other areas of medicine, has been largely replaced in the past half century as we have understood that symptoms alone rarely indicate the best choice of treatment.

As a result of the DSM’s shortcomings, Insel says that NIMH will be abandoning this classic manual of psychiatry, in favor of something he calls “Research Domain Criteria.” Under this plan, future psychiatric research will focus on characterizing and treating diseases on the basis of their underlying biology, rather than the DSM’s symptomology.

This drew loud cheers from longtime critics of psychiatry, who are legion. Here at last was a high-profile statement affirming their belief that the field’s “Bible” – and by inference the entire field – is bogus. Many news articles picked up the same angle, but that view vastly overstates what’s actually going on here. In fact, what we’re seeing is just the normal progression of medical science, in a way that should surprise exactly nobody.

Almost every field of medicine has had transitions like this. Two hundred years ago, the germ theory of infectious disease was widely considered absurd. Now we know it is fact, and infectious disease is the most definitive of medical specialties. That doesn’t mean the old knowledge was entirely useless, though; Edward Jenner developed a highly effective vaccine against smallpox without ever understanding its underlying mechanisms.

The DSM catalogues mental disorders the way an early 19th century doctor would’ve catalogued rashes. It’s probably right, and in some cases very right, about a few of them. It’s probably wrong about many more. Psychiatrists I’ve met (and the one I married) generally regard the DSM categories as a necessary evil, not a definitive reference. The “Bible” moniker is a straw man. Nobody likes the DSM, but it serves a purpose and has no obvious alternatives.

And that’s the rub. The NIMH’s brief is research, so they can reject or adopt whatever categories they like for their studies. Nobody shows up there for routine treatment of schizophrenia, or major depression, or bipolar disorder. NIMH should be using the latest neuroscience. The latest neuroscience, though, can’t tell us much about the vast majority of mental disorders, and some of the things it can tell us may turn out to be wrong. We might someday have a blood test for depression, or we might not. We can say with certainty that we don’t have one right now.

Insel’s alternative framework is nowhere near ready for prime time. Until it is, what should we do about the guy who’s running out into traffic to tell people he’s the Messiah, or the woman who is in perfect physical health, but catatonic, or the elementary-age child who can only communicate in screams?

It’s telling that some of the people calling for the death of the DSM-5 are remarkably reticent when it comes to offering alternatives. Perhaps that’s because the more you ponder the problem the trickier it gets. Tell patients with no medical training that the field’s diagnoses are largely theoretical and expect them to appreciate the nuances? Let all of the world’s con-men sell them snake oil? Tell them to come back in a few decades? Or use a deeply flawed framework that at least has a chance of being partly correct?

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Poo and Shit, Revisited

Posted on 2013.04.12 by Alan

Correspondent Bob has provided an interesting update on some research I did on relative publication rates back in 2010:

Just as a follow up to your Poo vs Shit analysis, a PubMed search today (11 April 2013) reveals that Shit is on the rise with 23 articles now with A. having first authorship on 7 and second on 4. That’s a 3.3-fold increase overall compared to Poo’s modest 16.9% increase from 359 to 420. As an additional modicum of irony, A. [Shit]’s articles are mostly related to BROWNian particle motions.

Shit’s fans will no doubt be pleased with these new hits.

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NEC-4 and Software Security Revisited

Posted on 2013.03.28 by Alan

Almost a year ago, I tore the folks at Lawrence Livermore National Lab a new one over their security policies for a computer algorithm called NEC-4. The short version is that this is a very useful antenna modeling algorithm developed with government funds, but LLNL keeps it locked behind a seemingly absurd paywall. Students, amateur scientists, and would-be entrepreneurs interested in wireless technology have to pay a steep entry fee if they want access to this highly useful tool, even though it was developed entirely with taxpayers’ money.

Recently, though, I received a note from someone at another research center who explained the situation much better than the LLNL folks do. His name is Jim. Here are some excerpts from our exchange:

I work at JPL, and it costs us substantially more than $300 to distribute export controlled software, just to handle the paperwork. There’s at least 3 people involved: the “software release authority” who deals with all software distribution; the export control record keeping person; and me. One of the first two runs the name/business name through some search databases. Pretty fast, but by the time you’re done, you’ve probably consumed a couple or 3 work hours.

Part of the problem is that even for non-export controlled software, there’s a record keeping requirement imposed by Congress. They want to know how many people are benefiting from using the government developed software so we have to keep records so we can report to some nameless entity who can summarize it in a report that probably never gets read except when someone complains to the IG or when some Congressperson gets interested.

Apparently I was mistaken about the actual costs of distributing this software. I stand corrected: it probably does really cost LLNL a few hundred dollars to provide a copy, solely because the algorithm is covered by US export control laws. More on that in a moment.

Jim also commented on my contention that the “security check” required to obtain the algorithm is meaningless. It seems that I was more or less correct about that:

As for “paying a U.S. person to get the CDROM and forward it,” that’s a pretty clear violation of the export control laws. The person doing this is setting themselves up for pretty severe penalties if the govt got its dander up. Oddly, not much is required in terms of authenticating or verifying that the person you give it to is actually a U.S. Person under the law. Their statement that they are is sufficient. They can lie, and that puts the violation on the recipient, not the sender.

Last I checked, the countries and organizations we need to worry about are universally willing to lie and break our laws, so “put[ting] the violation on the recipient” accomplishes nothing.

In other words, export control laws mean that LLNL has to keep this useful algorithm locked behind a paywall, and has to cite “security” as a justification for that, but it would be much easier for everyone – and no less secure – to make the thing freely available.

There may be a way out of this silliness, though:

In reality, what someone should do is see if they can reclassify it as not export controlled. If you were to seek a determination for NEC-4 today, I doubt it would wind up controlled. It’s unclear to me what parts of it triggered the controls in the first place, but probably it’s the parts with improved models for insulated antennas submerged in lossy dielectric mediums (like seawater) and that probably triggered the export control rating. However, I would think that stuff has been published in the open literature by now.

It sounds like a properly motivated member of Congress could accomplish a lot of good here. Removing NEC-4 from export control and making it freely available would allow amateur experimenters, students, and other interested folks to learn more about antenna modeling and maybe come up with some new ideas. It would also enable the Open Source community to work on the underlying algorithm, possibly improving it. With breakthroughs in wireless communication now producing massive economic benefits, these are topics that could clearly use more brains. I certainly plan to make that argument in a letter to my representatives. If you agree, here’s where you can find your Congressional representative, and here’s the contact information for your Senator.

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Threading the NEIDL

Posted on 2013.03.07 by Alan

After two long days of shooting and hundreds of hours of editing, the American Society for Microbiology and This Week in Virology are proud to release the documentary “Threading the NEIDL.” This video provides an unprecedented (and probably never-to-be-duplicated) look inside a state-of-the-art Biosafety Level 4 laboratory. BSL-4 labs are the ones that work on the most dangerous human pathogens, and the National Emerging Infectious Diseases Laboratories (NEIDL) at Boston University is the newest facility with labs built to the incredibly strict standards this type of science requires.

As you’ll see, we were able to get a detailed view of the inner workings of the NEIDL because it’s not operating yet. It seems that opening a high-level containment lab in the middle of a densely populated city didn’t sit well with the neighbors, and lawyers and government officials are still haggling over its fate. Meanwhile, this brand-new $200 million building is mostly empty. The silver lining is that the TWiV team was able to get inside and see spaces that would normally be inaccessible to outsiders. We also tried on some BSL-4 suits to see what it’s like to work in that environment, and chatted at length with the scientists who hope to do research in the NEIDL’s containment labs if and when they open.

The video ends on a positive note about the need to study dangerous pathogens, but it’s not a promotional piece. Community objections and BU’s handling of them get some coverage, and we went into more detail about those controversies in the associated podcast episode we released back in September. I’m still not convinced downtown Boston was the best place to stick the NEIDL. However, it does seem to have been built well, and I’d really hate to see a nine-figure sum of NIH funding flushed down the toilet now that the deed is done. Check out the video and make up your own mind:

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Betrayals of Trust

Posted on 2013.02.08 by Alan

I wish I’d been wrong about polio eradication. Really, I do. Against the ever-extending deadlines, outbreaks of vaccine-associated poliomyelitis, and deadly violence, there’s no comfort in having anticipated failure.

Way back in 1997, when Vincent Racaniello and I penned the first major scientific criticism of the World Health Organization’s polio eradication campaign, we were actually naïve enough to think that our objections might make a difference. Instead, we were waved aside and assured that everything would work out fine.

But the goalposts had already started moving. The original plan was to eradicate polio by the year 2000. When Vincent and I wrote our critique of the campaign’s reliance on oral polio vaccine (OPV), the WHO had already adjusted the deadline to 2005. As that year approached, the date slid further. Bill Gates now thinks that his foundation can help the WHO finish the job by 2018, continuing a longstanding tradition of keeping the goal at least five years in the future.

Don’t get me wrong, there is a chance we might eventually eliminate this virus. There’s even a tiny chance we might get it done with just OPV, but I wouldn’t bet a dollar on it, let alone the billions of dollars the WHO’s funders have pumped into that dream.

The problem is that OPV, originally developed by Albert Sabin, contains live attenuated viruses that routinely revert to wild-type, paralytic strains in vaccinated people. It’s the only vaccine in general use that can cause exactly the disease it’s meant to prevent, and it does so in one of every few million vaccinees. For the eradication effort, a bigger problem is that many, if not all vaccinees secrete the reverted virus for some time. Kids take the vaccine, and a few days later they’re pooping out live, potentially paralytic virus. That’s not a big deal if everyone around them is vaccinated, but in areas where vaccine coverage is spotty it can – and does – lead to outbreaks of polio caused by vaccine-derived strains.

There’s no obvious way to end an OPV-only campaign. People with immune disorders can excrete vaccine-derived poliovirus indefinitely. Eradication mandates eliminating OPV because it’s a source of new infections, but if we stop vaccinating then the existing reservoirs of infection will start new outbreaks. That’s why even the eradication campaigners now admit, more than a decade after we told them so, that switching to the inactivated vaccine may be an essential step.

Unfortunately, inactivated polio vaccine (IPV) is much more expensive to make, transport, and administer than OPV. The price differences aren’t noticeable in developed countries with plenty of pediatricians, but they become prohibitive if your goal is to vaccinate the whole world right now. Getting IPV to every child would require building a functional public health infrastructure everywhere, but we can get OPV to them without having to make that commitment.

In other words, the WHO and its supporters have made a deliberate choice to value the quick elimination of a single disease over establishing lasting improvements in public health.

Back in 1995, when I first heard a presentation about the eradication campaign from a WHO/CDC representative at a conference, the rationale was that eradication is much easier to “sell” to developing countries than the hard, unglamorous work of building public health infrastructure. Eliminate polio in five years and you can claim a distinct, easily defined victory. Spend the same time and money building rural clinics and covering urban sewers, and nobody will notice. I was told that polio eradication was an achievable goal that politicians could understand. I also inferred the subtext: that it was the kind of career-defining accomplishment that WHO and CDC officials would love to put on their resumés. I had a problem with that rationale then, and I still do.

I’m certainly in favor of people advancing their careers, and I’d love to see infantile paralysis eliminated from the world. Public health is chronically strapped for cash and people, though, and pouring huge sums and millions of person-hours into a quixotic charge against one disease inevitably entails shortchanging other, more pressing needs.

There’s also another price that’s only become clear recently. In order to make the eradication campaign work, the WHO has enlisted thousands of volunteers all over the world. The Rotarians committed themselves to the effort early, and have provided an astonishing amount of logistical support. But in the last polio-endemic countries, the real ground troops are local volunteers, mostly women, who’ve had a short course in vaccine delivery. These dedicated individuals are motivated by nothing but a desire to help their neighbors. Their reward is a mother’s thanks, a child’s smile … or a bullet:

Nine female polio vaccinators have been killed in two shootings at health centres in northern Nigeria, police have told the BBC. In the first attack in Kano the polio vaccinators were shot dead by gunmen who drove up on a motor tricycle. Thirty minutes later gunmen targeted a clinic outside Kano city as the vaccinators prepared to start work.

Some Nigerian Muslim leaders have previously opposed polio vaccinations, claiming they could cause infertility. On Thursday, a controversial Islamic cleric spoke out against the polio vaccination campaign, telling people that new cases of polio were caused by contaminated medicine.

This is the latest in a string of such killings, but it’s the first I’ve heard of in Nigeria. It’s become fashionable to blame the CIA for causing this spate of anti-vaccinator violence, but as I’ve pointed out before that’s an oversimplification. The latest incident underscores that point.

If any agency is to blame for these deaths, it’s the WHO. They’ve recruited women to do a job that makes them stand out, in places where armed religious fundamentalists fly into a rage whenever women stand out. Then the WHO has trained these women to administer a vaccine that can cause the very disease it’s meant to prevent. When a local cleric claims that new cases of polio were caused by “contaminated medicine,” what are these volunteers supposed to say? He’s sort of right. Finally, all of this is being done in the service of a public health campaign that’s probably doomed. Meanwhile, malaria, tuberculosis, and HIV remain rampant and vaccines for other preventable diseases can’t be distributed because of a lack of infrastructure.

Perhaps it is much easier to convince politicians to back an eradication campaign than to build real public health systems. But it’s not cheaper.

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Who’s Afraid of the Big, Bad ORF?

Posted on 2013.01.22 by Alan

A recent paper in the journal GM Crops and Food has generated an outsized splash in the press, particularly in biotechnology-averse Europe. I won’t reward a muckraking tabloid with a link, but here’s a screenshot that shows the basic theme:

Daily Mail hype.

Oh No, Toxic Genes!

Apparently the genetically modified food crops that hundreds of millions of people around the world have been eating without incident for more than a decade are in fact horribly toxic. But it turns out that the research that triggered this alarm proves no such thing. How did an arcane scientific finding get turned into a completely incorrect, apocalyptic headline? Let’s dig into it like scientifically educated journalists.

If we start by going to the source, we immediately hit an obstacle: there’s the abstract, but if we want to read the paper itself we’re expected to pony up $29. It would probably help a lot if journals made papers about important public policy issues freely accessible by default, but we don’t live in that world yet. Fortunately, journalists have an easy way to get around this: contact the authors directly. The Daily Mail appears to have failed at this, as all of the quotes in their article are from other sources. Other articles on the new work similarly lack any representation by the folks who actually did it.

It’s rare for scientists to blow off reporters completely, but sometimes they can be hard to reach, out of the office until after the deadline, or just uninterested in helping. Perhaps that was the case here. Let’s see. The first author is Nancy Podevin of the European Food Safety Authority in Parma, Italy. When I sent a note to her identifying myself as a journalist and asking for a reprint, she replied minutes later: “Please find the article attached. Please be aware that the content of the article has been incorrectly reflected in recent press articles.”

Not exactly hard to reach. Or reticent.

Alright, let’s dig into the work. Here’s the basic plan from the introduction:

Bioinformatic tools are increasingly being used in the evaluation of transgenic crops. Guidelines, proposed by WHO/FAO19 and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity and toxicity. With this aim, the EFSA GMO Panel has updated its guidance for the risk assessment of GM plants and proposed to identify all new ORFs due to the transformation event. New ORFs are defined as strings of codons uninterrupted by the presence of a stop codon at the insert genomic DNA junction and within the insert. The putative translation products of these ORFs are then screened for similarities with known toxins and allergens.

This is a study done entirely on computer databases, in which the scientists looked for novel open reading frames (ORFs) in the transgenes of modified crops, then checked to see if any of those ORFs match any known allergens or toxins. The existence of an ORF doesn’t prove that it gets transcribed and translated into a stable protein, so we’re still several steps short of reality here, but it’s a useful exercise to define what might be possible. In this case, the investigators are looking specifically at a sequence called P35S, a gene promoter borrowed from cauliflower mosaic virus (CaMV). P35S promotes constitutive (constant) expression of the gene in front of it, so it’s been a popular choice for driving introduced transgenes in genetically modified crops. 54 of the transgenic crop strains currently approved in the US use this promoter.

In its original context, the P35S sequence overlaps with a CaMV sequence called gene VI. That means that the P35S sequence could potentially encode a piece of gene VI. Podevin and her colleague Patrick du Jardin searched the various P35S sequences used in transgenic crops, and identified a couple of ORFs. Remember, this is all on a computer. The paper contains no wet lab experiments showing that these ORFs are actually producing stable proteins in any cell. But let’s assume they do for now.

Translating those ORFs on the computer and searching against databases of known allergens and toxins, the researchers found … wait for it …

Nothing.

That’s right, these hypothetical proteins that might not even exist don’t match any known allergens or toxins anyway. They did an additional test that sets the bar lower, and found that by this standard, one of the putative proteins might be allergenic. But it’s a stretch:

The vector support machines (SVM) in AlgPred indicated on the basis of the dipeptide composition that the ORF that encoded part of P6 might have some allergenic properties. The sensitivity and specificity of this method is 88.87% and 81.86% respectively and should therefore always be used in combination with other tools.

All the other tools, though, found no allergenicity. Having established that there’s essentially no human risk, the authors speculated that there could still be effects on the plants themselves, such as plant stunting and late flowering. Considering that the entire point of most crop biotechnology is to increase yields, it seems unlikely that this applies to any of the current commercial strains, but product developers should probably keep an eye out for it in future strains. Either that, or they could simply follow the authors’ final advice:

The -343 variant [of P35S], identified by Odell and colleagues, contains all of the necessary elements for full promoter activity and does not appear to result in the presence of an ORF with functional domains, rendering it and its related variants the most appropriate promoter variants for avoiding unintended effects.

To put this all in context, plant viruses commonly infect all sorts of crops. One survey (PDF here) found CaMV and its colleagues widespread in numerous types of produce. We’re already eating huge quantities of plant viral proteins – not hypothetical ones, real ones – all the time. If there is an ORF from CaMV gene VI being expressed as a protein in transgenic crops, it’s likely one you’ve digested before, even if you eat exclusively organic food.

So there you have it. This was a research paper that used bioinformatic methods to ask yet again if GM crops are any more dangerous than non-GM crops. It ended up adding to the large pile of established data showing that they are not. Through what can only be described as laziness and ideologically blinded reporting, it served as a handy news hook for stories claiming exactly the opposite.

Update 2013.1.22 12:49: After writing this post, I saw this discussion thread, in which several smart folks make essentially the same points.

Update 2013.1.23 7:07: After Dr. Podevin graciously sent the paper, I pinged her with a few additional questions about the work because, well, that’s what I do. I received her reply this morning:

I have been overloaded with requests for the paper and as I am no longer working at EFSA it is difficult for me to react.

To answer you[r] questions I am not planning to work on this topic further. It is difficult how headlines on toxic genes in GMOs can be seen to be linked to our paper as we concluded that there are no indications for toxicity of the encoded protein. This virus has been infecting Cauliflower and related plants with no recorded health effect.

It should also be noted that this promoter [has] an ORF overlaps with Gene VI but that no functional gene is present. So in most cases this gene fragment will not lead to the production of a protein.

Update 2013.1.24 15:06: I’ve now received a note from the journal publisher as well:

I am the publishing director at Landes Bioscience – and for GM Crops & Food. Thanks for your excellent piece which was just brought to my attention. Would also quickly like to note that we have now made this paper OA, ie, freely available to anyone who wants to download and read. [link]

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Sentient Spambots vs. Journalism

Posted on 2013.01.11 by Alan

As a blog owner, I get a lot of spam. Of course my automatic filters weed out the usual ads for anatomical enlargement, financial offers from alleged Nigerian clergy, and suggestions to earn advanced degrees from diploma mills, but in recent years a new category has cropped up, and it’s getting harder and harder to classify it.

Consider the infographic link spammers. These folks use standard online tools to create some marginally interesting illustration, then promote it to any blogger who covers even tangentially related topics. The infographic includes code that helps direct traffic to another site, helping them increase their search engine rankings. I haven’t posted any of these, partly because I’m not into running other people’s ads for free, and partly because the graphics tend to be gimmicky, often misleading representations of questionable data. All the ones I’ve received have included links to “get your degree online” types of sites, which are themselves just extended advertisements for diploma mills. So as an evolutionary byproduct of their efforts to circumvent ever-more-sophisticated filters, the University of Phoenix’s spambots have finally achieved sentience.

Recently, though, I got a note that’s pushed this trend even further, to the point that it’s right next door to legitimate journalism:

Hello,

I help maintain the site [name similar to Diploma-Mills-R-Us.com], and I am writing to let you know about an article we have created that shares essential information on the 2012-2013 Flu Vaccine. You can view part 1 here: [link, to which I've added a nofollow tag].

As you may already know, it is flu season and as the seasons change, the weather gets colder and many people start feeling under the weather. The article offers guidance and information on how and why you should get the vaccine and the effects it may have on your health.

We’re trying to spread the word about this article, and hopefully spread awareness on this subject as many people today are still not getting their flu vaccine and having to pay the consequence. So, if you find it to be useful and interesting, and think others would too, I’d be thrilled if you would share it with your readers, or anyone else you think could benefit from it.

The linked post rehashes information that’s easy enough to find elsewhere, but it isn’t a simple copy-paste job. The author actually created original content, summarizing an important issue and promoting public health. My only real objection to it is that the sponsoring site exists solely to sell dubious training programs for healthcare practitioners.

I can’t get on too high a horse about that, though. Most of the publications my colleagues and I write for make a significant amount of their money from advertising, and for many of them (“controlled circulation” trade magazines, virtually all news web sites) it’s the only revenue source. All of my clients are diligent about maintaining a firewall between the advertising and editorial departments, so the former never directly influences the latter. Reduced to its essence, journalism’s business model is to draw readers to original, independent, useful content, and pay for it by showing them some ads at the same time. The main distinction I see is that at “legitimate” news outlets the content is viewed as the primary product, and the ads as a sort of necessary evil. For sites like the one above, the ads are the main point, and the original content is just eyeball bait. It’s largely a question of intent.

In practical terms, the problem with the latter model is that there are certain types of stories that, while highly relevant to the target audience, could never be permitted to appear there. For example, I wouldn’t expect an unbiased investigative report on the business practices of online degree programs from a site whose existence depends on them. Similar conflicts can arise at traditional news publishers of course, but keeping a diverse stable of advertisers mitigates them, and a business philosophy that values content for its own sake tends to discourage serious abuses.

While I don’t expect the spammers to make the final step in this journey and turn themselves into legitimate journalists, I can’t help wondering whether we’re living in a version of this xkcd comic.

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