As science writers, we make a lot of fuss over the importance of peer review as one indicator of the legitimacy and importance of science But what happens when peer reviewed conclusions clash with our politics?

I have no way of knowing whether reporters’ political views shaped the coverage of the PLOS Medicine study alleging that doctors at Guantanamo ignored evidence of torture. But the study did not receive the coverage I thought it might, and I think it’s reasonable to raise the question. With the national focus on jobs and the economy (and, in some quarters, Obama’s birth certificate), we–and I include in that all of us who are science writers–might be skipping too lightly over an issue that is of great potential importance but out of sync with the national mood.

The press release from PLOS Medicine was direct:

Inspection of medical records, case files, and legal affidavits provides compelling evidence that medical personnel who treated detainees at Guantánamo Bay (GTMO) failed to inquire and/or document causes of physical injuries and psychological symptoms they observed in the detainees…In each of the nine cases, GTMO detainees reported abusive interrogation methods that are consistent with torture as defined by the UN Convention Against Torture, as well as the more restrictive US definition of torture (known as “enhanced interrogation techniques”) that was operational at the time. Examples of torture the detainees endured included severe beatings resulting in bone fractures, sexual assault and/or the threat of rape, mock execution, mock disappearance, and near asphyxiation from water. Detainees were also subject to enhanced interrogation techniques including sleep deprivation, exposure to temperature extremes, serious threats, forced positions, beatings, and forced nudity.

Strong stuff, if true.

Peter Aldhous of New Scientist apparently didn’t think it was true. Rather than reporting the conclusion, he ledes with a question: “Were the doctors who were looking after Guantánamo Bay detainees complicit in torture by neglecting, or failing to report, evidence of abuse? He describes the study’s conclusion as a “contention,” again impugning its reliability.

After summarizing the paper in a brief graf or two, he then further questions it, writing, without attribution, that the charge of ignoring torture “may be hard to substantiate. One problem is that the detainees often refused to cooperate with medical evaluations, which may have made accurate diagnosis difficult. More generally, it is notoriously difficult to assess the adequacy of a diagnosis from a later analysis of someone’s medical records.” He might be right, but he seems to be making this critique on his own authority, not on the authority of someone who has, for example, examined people who’ve been tortured or who is otherwise knowledgeable on the issue. A subsequent quote from a psychologist does not support these criticisms from Aldhous.

Stephanie Pappas at Live Science played it straight in a longer story, reporting the study’s conclusions, interviewing one of the authors, and adding a quote from an outside source. She might have done more reporting, but the story is serviceable. Spencer Ackerman at Wired‘s Danger Room discussed the findings intelligently, and also went to the Pentagon for a response. Aside from that, however, he didn’t interview anyone else, although he did provide some helpful background on the issue. Peter S. Green at Bloomberg wrote a strong, straightforward lede, but did little reporting. He, too, called the Pentagon, but when he didn’t get an immediate answer, he left it at that.

The San Francisco Chronicle ran a dense blog post by Winston Chung, identified as a child psychiatrist, whose lede was: “Salus aegroti suprema lex is Latin for the ‘wellbeing of the patient is the most important law’.”

It might sound as though I’m taking a point of view on the Guantamo torture. By arguing that this study wasn’t covered adequately, I could be saying that I think the study’s conclusions were correct and that this story should have been front-page news everywhere.

I’m not. I have no way of knowing whether the study is sound. My complaint is that I’m getting very little help from the coverage. Many news outlets ignored the story. Because they think it’s old? Because they think readers don’t want to hear about torture? Because the government believes this kind of information should be kept secret? Who knows?

Whether this study’s conclusions are sound or not, the importance of the issue should have prompted science writers to take a deeper look. I think it was a mistake that they didn’t.

- Paul Raeburn

Brian Switek

The old media are still apparently gasping their last gasps, and gasping and gasping. As Brian Switek eloquently points out on Laelaps, it’s past time for all of us to ignore assertions about who is a real science journalist, and to just get on with our writing.

Switek, nervously on the eve of quitting his day job, wandered into a session on maintaining “high journalism standards” on the web at the recent professional development sessions organized by the D.C. Science Writers’ Association. There he found–no surprise to some of us, but apparently it was to Switek–that the audience included some curmudgeonly characters who thought blogging was not worth the paper it isn’t written on:

Traditionally-trained journalists seemed to want a way to cordon off science blogging from journalism. Among the proposed metrics was the idea that science blogs are not edited. When I pointed out that my Smithsonian blog – Dinosaur Tracking – is edited, and that my editor was actually sitting in the front row, another attendee suggested that I was not actually blogging, or that my edited efforts were being mislabeled.

If I were there, I would have asked to see a copy of Switek’s birth certificate–which he has never produced.

Switek is one of a growing corps of smart, young writers who cover science far more thoroughly, and better, than any newspaper could hope to do. Newspapers aren’t quite dead yet, and as even a quick glance at the Tracker could tell you, they are doing some wonderful stories–and I trust they will continue to do so.

But so are the blogs. Switek’s rumination on journalism and blogging is worth reading, as are his science stories. And any discussion about maintaining “high journalism standards” on the web ought to look off the web to see what it is that we want to maintain. The Tracker daily uncovers examples of old-media journalism to which no standards seem to have been applied at all. Maintaining online standards that equal those of old media is not a very challenging goal. A better one would be for bloggers to hold themselves to higher standards than those of the old media.

And note that I said it’s up to bloggers to hold themselves to the standards. The late Jerry Bishop of the Wall Street Journal, whose journalism would exceed anybody’s standards, used to remind us that we have a free press, and the last thing we want is to have anyone tell us what to write–even if they’re trying to tell us to write better.

The reason we want to write well, and hold ourselves to high standards, is because that, ultimately, that’s what attracts readers. It’s a selfish goal. We write and report well because it matters to us, and it matters to our readers. And if that somehow makes us rich and famous–well, we won’t send back the checks.

- Paul Raeburn

If there is intelligent life elsewhere in the universe, Earthlings won’t learn of it any time in the near future. Northern California’s SETI Institute, devoted to searching the skies for radio signals broadcast by an alien civilization, has run out of operating funds–much of which had come from federal and California governments–and is shutting down operations until new money can be found. In the photo are some of the antennas of the institute’s new array, funded by a gift from Microsoft’s Paul Allen.

Lisa M. Krieger, of the San Jose Mercury News, for whom the story is local, notes that the shut-down comes just as hundreds of potential Earthlike planets have been found by instruments such as the Kepler space telescope. She offers this quote: “There is a huge irony,” said SETI Director Jill Tarter, “that a time when we discover so many planets to look at, we don’t have the operating funds to listen.” Let’s not quibble about whether they are looking or listening.

Also local is the San Francisco Chronicle‘s David Perlman. He quotes Tartar saying, “The Kepler mission for the first time has made people really understand that planets far away really might be very much like Earth and hold life – perhaps even civilizations – and that’s what the SETI search is all about.”

The Guardian‘s Alok Jha ledes by recalling Carl Sagan’s novel and movie, Contact.

–Boyce Rensberger

We know about extremophiles, those microbes that live in environments once thought inhospitable to life–very high temperatures, very high or very low pH, surrounded by solid rock, and so on. To the list of extreme environments we may add very strong gravity, like, say, 400,000 Gs.

When researchers spun E. coli (micrograph) and other bacteria in a centrifuge and revved it up to its fastest speed, the bacteria not only lived through the experience, they reproduced. Anything above 40 or 50 Gs can injure or kill human beings.

So, writes Space.com‘s Mike Wall, alien life could exist in places, such as very big planets or even failed protostars such as brown dwarfs.

Ker Than wrote it for National Geographic News, leading with the notion that “… you don’t have to be big to be tough.” In fact, of course, it’s being very small that makes these critters tough.

The Tracker missed this story when it broke on Monday, but that’s not too bad when you consider that the first scientific report of bacteria thriving in hypergravity was published in 1963. Not even scientists paid much attention back then.

–Boyce Rensberger

It was a preposterous idea in 1991. Build a giant terrarium and connected Habitrail of other enclosures, seal the whole thing up airtight and ask some people to live in it for years, growing their own food and more. The hubris was evident in the name the amateur ecologists chose for the whole thing: Biosphere 2 (photo). As if it were a successor to the original biosphere.

It looks cool, but the experiments never worked. For one thing, it leaked and, worse, the people really couldn’t survive long on what they grew.

The AP‘s Allen G. Breed has a good, long story (picked up by several outlets) on the place as it exists today: “The only creatures inhabiting Biosphere 2 are cockroaches, nematodes, snails, crazy ants and assorted fish.” But next month, Breed reports, researchers will begin a new, $5 million, 10-year project in which water will be made to flow down soil slopes to see how vegetation, topography and other factors affect what the simulated rain eventually carries into the water table. It’s something ecological scientists already do in the real world, but hey. Breed recounts some of B2′s checkered history and efforts by its various owners and operators to make the thing sound like a good idea.

–Boyce Rensberger

Ivan Oransky broke the story at Retraction Watch, and now National Geographic confirms it.

National Geographic “has assumed management of day-to-day operations for Scienceblogs.com, expanding a relationship with Seed Media Group that started when National Geographic took on ad sales responsibility for Scienceblogs.com in 2009.”

ScienceBlogs came under fire last July when Seed media group, which ran it until today, allowed Pepsi to publish a blog that looked like all the other blogs, but which was a piece of corporate promotion. Some of the site’s bloggers left in protest, but the ScienceBlogs overcame that debacle and it remains a popular destination for readers of science blogs.

We’ll be watching to see what National Geographic does with ScienceBlogs. This could be interesting.

- Paul Raeburn

Beware posts done in haste: I initially wrote that USA Today illustrated its story with a picture of an iPhone, but as a reader points out, it did not; the photo was of an Android phone. Apologies to Williamson, who will probably not let me forget this.-PR

Jeff Williamson of USA Today reports a survey sure to spark conversation (and texts and tweets) among geeks and Google and Apple fans:

“Nielsen: Android edges Apple in mobile survey.”

How the mighty iPhone has fallen, we’re ready to exclaim!

But wait. According to Williamson, a Nielsen survey of “mobile consumers” (stationary consumers were excluded?) found that Android beat Apple 31 percent to 30 percent–31 percent of consumers plan to buy an Android phone, compared to 30 percent who “wanted Apple’s iOS.”

I don’t now what the margin of error was in this survey–and Williamson doesn’t say, an important error–but we can be nearly certain that the margin of error was more than 1 percent. The margin of error on this thing is very likely be the usual 3 or 4 percent.

But that didn’t stop Williamson, who writes, in his lede, ”Google’s Android operating system is now the most desired smartphone OS.”

Nope. They’re tied. But I bet Google loved that lede!

I linked to Nielsen to try to find out the margin of error. And, at least in this release, I couldn’t find it. Even Nielsen doesn’t think it’s important to report the margin of error? Woe is us!

Nielsen’s writer never says what Williamson said–that Android wins. But he or she cleverly implied the same thing. The headline asks, “Who’s the Most Wanted?” And the 31-30 percentages are in the second graf. That comes as close as possible to saying Android is the most wanted, without actually saying so. Nielsen escapes condemnation on a technicality.

And a question for both Nielsen and Williamson: Did the survey really ask people what OS they wanted? Quick: Which OS are you buying when you need a new phone, Android or iOS? If so, I can imagine a lot of people saying Android, because they’ve heard of it. How many people know what iOS is?

Or did the survey ask folks which phone they were going to buy next? And if so, why did Williamson report it as a contest between OS’s? (I don’t believe in using apostrophes for plurals, but OSs looks ridiculous.)

I believe I’ve now made my point and should quietly sign off.

One last question: What OS do your want for your next computer?

- Paul Raeburn

Update, April 27th: Carolyn Johnson of The Boston Globe alerted me to a story that ran after the story I linked to below. This later story adds a little more information to the mix, including an emailed response from Hauser.

On August 10th and 11th, 2010, The Boston Globe and then The New York Times reported that the well known Harvard psychologist Marc Hauser was going on leave pending an investigation of allegations of scientific misconduct. Both papers wrote lengthy stories, although the Times won hands down with its pointed headline: “Expert on Morality Is on Leave After Research Inquiry.” (Compare that to the Globe’s drab “Author on Leave After Harvard Inquiry.” And note that these were the headlines on the web; I do not know what appeared in print.)

On August 20th, the Times reported that Harvard had found Hauser “’solely responsible’ for eight instances of scientific misconduct.” On August 28th, the Globe reported that a journal editor said the only plausible conclusion he could draw from Harvard’s internal investigation of the matter was that “some of the data had been fabricated.”

Yesterday, the journal Science reported that Hauser had redone the experiment and replicated the findings. That gets Hauser partially off the hook (a separate study that was challenged is still awaiting explanation.)

Our question here is: Did the papers do a fair job of reporting this partially exculpatory evidence, as we might call it?

Both papers did indeed report this latest development (Nicholas Wade was the reporter at the Times, and Carolyn Y. Johnson at the Globe). Both noted that this was far from a complete exoneration of Hauser, although the Times did a better job of explaining the remaining outstanding issues.

Neither paper devoted as much ink to the controversy as they did last August, which might pass muster, considering that last August’s developments were more newsworthy, and more dramatic, than this partial explanation of the problem.

It’s worth noting, as I’ve observed before, that neither the Times nor the Globe linked to the Science article, something that all newspapers should by now be doing. It should be as easy for them as it is for me. Nature News published a very short item on Hauser  yesterday. It should have done more, but even this short item supplies far more information than the Times or the Globe by virtue of the 9 links in the three-paragraph item.

The Hauser story is complicated by Harvard’s refusal to release any information from its ongoing investigation, which may well be doing Hauser an injustice, allowing speculation and innuendo to substitute for fact. Harvard is not administering swift justice, and you might argue that, by waiting so long, it is not administering justice at all. The longer Hauser remains in limbo, the harder it will be for him to resume his career–if it turns out that he was guilty of mistakes, not fraud.

- Paul Raeburn

Above the fold in this week’s New York Times section about all you can see is a photo (at right) of people looking up at great green gobs of. . . .  Of what? It’s an eye-catching photo, which is good. In a science section you like it when readers say, “Wow. That’s cool. What is it?” Curiosity is good in science and journalism. But, as is becoming more common these days in many publications, photos have captions that say nothing about the image or no caption at all. Nowhere are readers told what those green blobs are.

Below the fold is a smaller photo of a guy looking at a computer screen and it bears this caption: “DUET “Life: A Cosmic Journey,” at the Morrison Planetarium in San Francisco, relies on reams of digitized data as well as on animation.” That could be a budget line for the story accompanying the photos, a fine piece by John Markoff, the Times’s worthy correspondent from the frontiers of computing, which starts in the aforementioned planetarium.  (Aside: when will we drop that antique name for these theaters that have less and less to do with planets?)

Markoff proceeds from the planetarium show to a range of other ways high-powered computers are mashing up real data to create visualizations at every scale of size from the subatomic to the extragalactic. So, are those green blobs vesicles in a cell or rubble in an asteroid belt?

Nicholas Wade‘s “Scientist at Work” feature is about a vice president of the Sloan Foundation who has steered scores of millions of dollars into “environmental reconnaissance” projects to census Earth’s living species and monitor environmental changes.  Jesse H. Ausubel is the scientist/V.P. but the work described here is that of organizing, motivating and funding others.

The third story fronted in the section is John Tierney‘s often (though not today) contrarian column, “Findings.” Tierney looks at the increasingly vain and angry lyrics of much of today’s pop music. The most startling example he cites is a song set to the lovely melody of the Shaker hymn, “‘Tis the Gift to Be Simple.” Today’s lyrics: “I’m the meanest in the place, step up, and I’ll mess with your face.”

But wait, there’s more. And you can find it here.

–Boyce Rensberger

Well, we've either found the Higgs boson or Fred's put the kettle on.

Scientific leaders at the Large Hadron Collider in Geneva are taking pains to confirm that the leaked memo is real– evidence that could mean the fabled Higgs boson has been seen is not a hoax. But they are also emphasizing that it is very far from being confirmed, a  long way from a genuine discovery.

Of the evidence seen to date, the collider’s official spokesman said lots of findings start out looking this good but, “The majority of these things turn out to be nothing at all.”

Most of the stories this morning couldn’t resist calling the Higgs the “God particle.” Sarah Anne Hughes has a compact account of how the particle got its popular moniker on a Washington Post blog. She notes that Peter Higgs, credited with first hypothesizing the particle, “hates” the term.

The stories that came up in the Tracker’s net this morning were short, derivative or behind the news. The major league news outlets didn’t make much of the recent rumors, so didn’t bother to follow up. No need to click further, but if you want, check it out on Google News.

–Boyce Rensberger

Ah, the amazing-animal story, that standard of gee-whiz journalism that few of us can resist. Nor should we.

Comes now a report in PNAS by mechanical engineers at Georgia Tech, which is situated in fire ant country. When the insects’ burrows are flooded, the ants don’t drown or float off in all directions. They glom together by the thousands, forming a raft that can float for days or weeks until it finds dry land, whereupon the colony is still together and ready to dig in again. (In the photo, a small raft is pushed down by a twig but remains afloat. Photo by researchers Nathan Mlot and Tim Nowack.)

But how do they float, the engineers wondered.  When individual fire ants are dropped in water, they float, buoyed by tiny bubbles of air trapped among hairs over the body. Drop a whole colony in water, and the insects grab onto one another,  jaws and legs intertwined and clamped, effectively merging their individual air pockets to form one huge bubble weaving through the entire raft.

The Washington Post‘s Brian Vastag knew full well what his editors really cared about. His lede: “Congress-and perhaps the rest of us–could learn a thing or two about teamwork from Solenopsis invicta, the dreaded fire ant.”

Katharine Gammon, of Inside Science News Service, run by the American Institute of Physics, was clearly writing for a science savvy readership, wrote that the ants “can form a raft that stretches the boundaries of the laws of physics.”

Other takes: Wynne Parry of LiveScience and picked up by MSNBC.com. The National Geographic‘s Web site has a brief story by Rachel Kaufman plus a link to a video of fire ants swarming but not forming rafts. Scientific American‘s Cynthia Graber has another brief account plus a podcast and writes that “This discovery could help roboticists interested in building self-assembling flotation devices.” Maybe so, but do we really need to reach that way when we’re just doing a nice, easy gee-whiz story?

Grist: The PNAS article.

–Boyce Rensberger

As anyone who writes for a living knows, one of the most important decisions a writer makes is one a reader never sees: the decision to do one story rather than another–or to do no story at all. Critics who like to deconstruct articles to show a writer’s bias might not realize that such biases are often more clearly revealed in story choices than in anything a writer writes. A decision, for example, to do a perfectly balanced, objective story on the hazards of nuclear power in the wake of Fukushima, will send a message that nuclear power is dangerous. Or a writer could decide not to do a story–a writer who, perhaps, thinks a detailed examination of Fukushima would unfairly tar nuclear energy, no matter how the writer tried to balance the story.

In the same way, we could imagine the decision a writer might make about a doctor who has been accused of medical ethics violations and scientific impropriety, who has lost his job and his medical license, who has fled his country and been accused of setting medical research back 10 years–and of endangering children. One might decide not to write a story about such a person, especially if that person is widely known and the story has been told dozens or hundreds of times before.

Or one might decide to write the story. Such a story–if done fairly–would balance some of the horrors, such as the time “he lined up kids to give blood samples at the birthday party of one of his children” because “he needed a control group of children…” It might also, for balance, paint a sympathetic portrait of a man who, despite adversity, clings to his beliefs, who has “a mild professorial air,” and who, “broad-shouldered and fair at 54, he still has the presence of the person he once was: a conventional winner, the captain of his medical school’s rugby team, the head boy at the private school he attended in England.” A man who “has become one of the most reviled doctors of his generation” but–but!–whose followers “applauded wildly” when he took the stage recently, and who say, “We stand by you!” and “Thank you for the many sacrifices you have made for the cause!” A man who “has depended on his followers for financing and for the emotional scaffolding that allows him to believe himself a truth-teller when the majority of his peers consider him a menace to medicine.”

This is the story Susan Dominus wrote in The New York Times Magazine yesterday. The story is about Andrew Wakefield, the British doctor whose report in The Lancet in 1998 was largely responsible for fueling the anti-vaccine furor that has led countless parents around the world to refuse to vaccinate their children, out of concern that vaccines might cause autism. The quotes are from her story, which, in my view, goes a long way toward restoring Wakefield’s image as a kindly, misunderstood doctor who simply wants to protect children. Despite the balance, despite the recitation of Wakefield’s sins, Dominus has written a story that will persuade many readers that maybe Wakefield is not such a bad guy at all, even if, as she writes, among many other things, that he failed “to disclose financing from lawyers who were mounting a case against vaccine manufacturers.”

As any reporter should know, a “study” of a few children proves nothing, and a study of a handful of children that has found no confirmation and has indeed been roundly and extensively rebutted might not deserve yet another hearing for its author in the press.

Dominus needs no instruction from me about fairness and objectivity, but she must know that her story is far from objective. We’re too sophisticated here to blame Dominus for the headline, but the editors call Wakefield “an autism guru.” That’s where a writer might stand up and protest, and maybe Dominus did so, and lost.

Every strand of evidence concerning Wakefield and his “study” suggests that it proved nothing and succeeded only as a touchstone for agonized parents of children with autism, desperate for anything that might help their children, or, at the very least, make of their suffering something that would help other children.

That is not the message that Dominus conveys. The Wakefield story has been told over and over again. The critics and Wakefield’s supporters have debated the issue for more than a decade–every side of this story has been minutely examined. Most recently the British medical journal BMJ did an investigation and concluded, as it said in a headline, that “Wakefield’s article linking MMR vaccine and autism was fraudulent.”

So why would the Times do this story now?

Here’s why not to do it: I believe that this story will prompt more parents to refuse to vaccinate their children. Some of those children will suffer or die from illnesses that the vaccines would have prevented.

Stories have consequences, and it’s often difficult to predict what those might be. I could be wrong about this. But I would have stayed far, far away from this story.

- Paul Raeburn