Archive for June, 2012

I've got your missing links right here (30 June 2012)

By Ed Yong | June 30, 2012 12:00 pm

Top picks

“Despite appearances, this isn’t [a] cruelly bisected alien stone organism or a tomato thunderegg.” Amazing post from Bec Crew about a really unusual animal.

Incredible post from Craig McClain on how presidential elections are affected by a 100 million year old coastline

This scientist may be about to rewrite the mammal family tree, but doesn’t really care. Really good Nature feature from Elie Dolgin.

Science: it’s a people thing. Alice Bell is spot on about “Science: it’s a girl thing” fiasco. Plus: three actual ways of getting kids into science

A Tale of Two Robots – a very interesting piece by Andrew Wilson on what “embodied cognition” actually means.

Longread on EteRNA, a videogame that lets citizen scientists mess w/ RNA. By Brendan Koerner. The lede is wonderful, as is the rest.

Why isn’t there more coal? Because 300 million years ago, fungi evolved the ability to decompose trees. By David Biello.

Really nice advice for young writers: “Never describe yourself as an ‘aspiring’ anything.” And other tips.

A male chimp in an LA Zoo killed a baby chimp. That’s normal, and not something keepers can do much about. By Jason Goldman.

The lives of Africa’s mysterious fairy circles. Here’s the best writing but here’s a better discussion of potential causes

Great reporting from Deborah Blum on a new study on condors + lead ammo poisoning. Much better than my efforts.

How a Chinese man in space chatted to one in the deep ocean & what it means for science

Er, WOW? Oxygen microbubbles injected into bloodstream could sustain asphyxiated patients.

Lonesome George, last of his species of Galapagos giant tortoise, died. Henry Nicholls wrote a lovely obituary. And someone misquotes him really badly. The Guardian had a really sad gallery.

Student solves mystery after listening to Nature podcast! Ancient text may explain 8thC radiation spike.

A psychologist resigned over misconduct charges this week. As ever, Daniel Simons has some interesting thoughts about the implications for priming research and whether better disclosure of author contributions would help in fraud/misconduct cases. Ivan Oransky has more on anti-fraud data-sleuthing. And What happens to the co-authors when a scientist goes down for fraud? One of them will tell you himself

Massive congratulations to Aatish Bhatia for winning the Three Quarks Daily Science Prize. Go read his post on colour and the brain.

What the Supercool Arctic Ground Squirrel Teaches Us about the Brain’s Resilience. By Ferris Jabr.

How to solve impossible problems: Daniel Russell’s awesome Google search techniques. Try the building test!

My son has cancer. He can’t go into day care because of unvaccinated children.”

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Why supermarket tomatoes look great but taste bland

By Ed Yong | June 28, 2012 5:00 pm

If you’ve ever bitten into a wild tomato, you’ll have enjoyed a sweet, intense explosion of flavour. The tomatoes that line most supermarket shelves are a world apart. They look great – a wall of even, ripe red – but they taste like cardboard. These two facts are related.

Ann Powell from the University of California, Davis has found that farmers have inadvertently ruined the taste of tomatoes by selecting for ones that ripen together and look good. That aesthetic appeal has been driven by a single change in a single gene, which also affects how the fruits taste.

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New flu gene found hiding in plain sight, and affects severity of infections

By Ed Yong | June 28, 2012 2:00 pm

I could write the entire genome of a flu virus in around 100 tweets. It is just 14,000 letters long; for comparison, our genome has over 3 billion letters. This tiny collection of genetic material is enough to kill millions of people. Even though it has been sequenced time and time again, there is still a lot we don’t know about it.

A new study beautifully illustrates the depths of our ignorance. Brett Jagger and Paul Digard from the University of Edinburgh have discovered an entirely new flu gene, hiding in plain sight among the 12 we knew about. It’s like someone took the text of Macbeth, put the spaces in different places, and got Hamlet.

This new gene, known as PA-X, affects how the virus’s host responds to the virus. Oddly, it seems to reduce the severity of infections. “This is indeed an exciting finding in the flu field,” says virologist Ron Fouchier. “How can we have missed it?” asks Wendy Barclay, a flu researcher from Imperial College London who has worked with Digard before. “It just emphasizes how compact these genomes are.”

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CATEGORIZED UNDER: Genetics, Medicine & health, Viruses

Geckos evolved sticky feet many times

By Ed Yong | June 27, 2012 5:00 pm

Geckos are superb wall-crawlers. These lizards can scuttle up sheer surfaces and cling to ceilings with effortless grace, thanks to toes that are covered in microscopic hairs. Each of these hairs, known as setae, finishes in hundreds of even finer spatula-shaped split-ends. These ends make intimate contact with the microscopic bumps and troughs of a given surface, and stick using the same forces that bind individual molecules together. These forces are weak, but summed up over millions of hairs, they’re enough to latch a lizard to a wall.

Many geckos have these super-toes, but not all of them. There are around 1,450 species of geckos, and around 40 per cent have non-stick feet. A small number are legless, and have no feet at all. Initially, scientists assumed that the sticky toes evolved once in the common ancestor of all the wall-crawling species. That’s a reasonable assumption given that the toes look superficially similar. It’s also wrong.

Tony Gamble from the University of Minnesota has traced the evolutionary relationships of almost all gecko groups, and shown that these lizards have evolved their wall-crawling acumen many times over. In the gecko family tree, eleven branches evolved sticky toes independently of each other, while nine branches lost these innovations.

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Exposed: the severe ethical breaches of superhero journalists

By Ed Yong | June 27, 2012 11:35 am

Journalists have an almost superhuman ability to hold forth on the ethics of our own profession. And yet, despite endless talk about “self-plagiarism” or some such, we have been wilfully blind to the more grievous ethical breaches carried out by revered reporters who cover the so-called “superhero beat”. Perhaps we are unwilling to admit that those who write about truth and justice are the least likely to champion transparency and proper attribution. Here are some examples of the most severe offenders:

Clark Kent

When it comes to journalistic ethics, Mr Kent is not so super after all. He regularly reports about himself without disclosing as much. He deceives his employers by moonlighting during working hours as a doer of derring, leaping his contractual obligations in a single bound. Worst of all, he uses the privileged inside information that he gleans as a journalist for his own personal gain during his extracurricular activities. Here is a man who is faster than a speeding bullet, stronger than a locomotive, and about as transparent as either of those.

Lois Lane

Seemingly strong-willed and single-minded, Ms Lane superficially seems like a role model for aspiring journalists. But closer investigation reveals a troubling tendency to sit on stories that clearly belong in the public domain, especially when it benefits her friends. She has won a Pulitzer for reporting about a source who she has long been romantically involved with – a fact that remains undisclosed. Sympathetic readers will see a journalist torn between personal emotions and professional duty. Others will see a woman who is not just hiding the location of weapons of mass destruction from her readers, but is actually sleeping with one.

Jimmy Olsen

Or to give him his official epithet: “Superman’s pal: Jimmy Olsen.” His sin is in plain view: this hungry, young, and undoubtedly talented photographer has gone native. He has sacrificed his journalistic independence by revering one of his sources as some sort of lofty superhuman god, becoming little more than a snap-happy PR agent to the Man of Self-Promotion. Perhaps “Superman’s Pal” might better serve the public interest as “Superman’s Critical Friend”.

Peter Parker

Imbued with the proportional strength, speed and ethical judgment of a spider, Parker has made a career of taking photos of himself in a mask and selling them to his employers. Some might argue that Parker is merely a symptom of the poor wages awarded to photojournalists, and the intense pressures they face (“I want pictures! Pictures of Spider-Man,” his editor regularly exhorts). Amid such a cutthroat environment, this promising talent has clearly learned that with great power comes great ethical lapses.

Spider Jerusalem

Finally, a journalist whose ethics are beyond reproach. Hound of truth. Scourge of authority. Ignoring the guns and wanton drug use, here is a reporter we can all look up to.

(Inspired by this Daily Mash piece and the fact that discussions of journo ethics can get a touch po-faced. Contributions from Tim Carmody and Dean Burnett via Twitter.)

Mystery of the flatfish head solved *cough* four years ago *cough*

By Ed Yong | June 26, 2012 2:16 pm


Oh excuse me. I appear to have a cough.

There’s anew press release out about a fossil flatfish called Heteronectes, which is oddly half-committed. In modern flatfishes, like flounders or plaices, one eye moves across the other side of the body, allowing the animal to lie on its side. In this fossil species, the eye only made it halfway around. It’s a beautiful animal.

It was also discovered and described four years ago in a Nature paper, by the same authors. I wrote about it then. That fact is completely missing from the new release, which talks about “a new fossil discovery” described in a new study in the Journal of Vertebrate Palaeontology. Writer The person named on the press release (but apparently didn’t write it) Cody Mooneyhan ignored my email pointing this out.

It’s a shame. All it would take to cross the line from misleading to accurate would be a brief acknowledgement of the initial description and then some detail about what the new paper actually entails. As far as I’m aware, it’s a more detailed description of the same specimen, and some discussion about its relationship to other fish. Or maybe what’s new is that they’re writing about it for the second time, which they clearly couldn’t do the first time round :-/

You may not care. After all, a very beautiful fossil gets another shot at the limelight and we can all agree that this is a good thing. The science itself is accurate, even if the timeline is fudged. But I’m a stickler about this. I really don’t think that science is in such a desperate state that we need to wilfully hide information in order to make things more appealing. It’s just cheap, and frankly, I think it takes us journalists for fools. Andy Farke also pointed out on Twitter that the Journal of Vertebrate Palaeontology selects just one paper per issue to be laid before the Gods of Media. Some other paper could have used the slot more effectively.


Why a new case of misconduct in psychology heralds interesting times for the field

By Ed Yong | June 26, 2012 6:04 am

[Update: The mysterious avenger has been revealed as Uri Simonsohn. He is one fo the co-authors on the Simmons paper that I wrote about below.]

Social psychology is not having the best time of it. After last year’s scandal in which rising star Diederik Stapel was found guilty of scientific fraud, Dirk Smeesters from Erasmus University is also facing charges of misconduct. Here’s Ivan Oransky, writing in Retraction Watch:

“According to an Erasmus press release, a scientific integrity committee found that the results in two of Smeesters’ papers were statistically highly unlikely. Smeesters could not produce the raw data behind the findings, and told the committee that he cherry-picked the data to produce a statistically significant result. Those two papers are being retracted, and the university accepted Smeesters’ resignation on June 21.”

The notable thing about this particular instance of misconduct is that it wasn’t uncovered by internal whistleblowers, as were psychology’s three big fraud cases – Diederik Stapel (exposed in 2011), Marc Hauser (2010) and Karen Ruggiero (2001). Instead, Smeesters was found out because someone external did some data-sleuthing and deemed one of his papers “too good to be true”. Reporting for ScienceInsider, Martin Enserink has more details

“The whistleblower contacted Smeesters himself last year, the report says; Smeesters sent him a data file, which didn’t convince his accuser…. In its report sent to ScienceInsider, the whistleblower’s name is redacted, as are most details about his method and names of Smeesters’s collaborators and others who were involved. (Even the panel members’ names are blacked out, but a university spokesperson says that was a mistake.) The whistleblower, a U.S. scientist, used a new and unpublished statistical method to search for suspicious patterns in the data, the spokesperson says, and agreed to share details about it provided that the method and his identity remain under wraps.”

This might seem like a trivial difference, but I don’t think it could be more important. If you can root out misconduct in this way, through the simple application of a statistical method, we’re likely to see many more such cases.

Greg Francis from Purdue University has already published three analyses of previous papers (with more to follow), in which he used statistical techniques to show that published results were too good to be true. His test looks for an overabundance of positive results given the nature of the experiments – a sign that researchers have deliberately omitted negative results that didn’t support their conclusion, or massaged their data in a way that produces positive results. When I spoke to Francis about an earlier story, he told me: “For the field in general, if somebody just gives me a study and says here’s a result, I’m inclined to believe that it might be contaminated by publication bias.”

Francis has reason to be suspicious, because behaviour is surprisingly common. This is another notable point about the Smeesters case. He didn’t fabricate data entirely in the way that Stapel did. As one of his co-authors writes,“Unlike Stapel, Dirk actually ran studies.” Instead, he was busted for behaviour that many of his peers wouldn’t consider to be that unusual. He even says as much. Again, from Enserink’s report:

“According to the report, Smeesters said this type of massaging was nothing out of the ordinary. He “repeatedly indicates that the culture in his field and his department is such that he does not feel personally responsible, and is convinced that in the area of marketing and (to a lesser extent) social psychology, many consciously leave out data to reach significance without saying so.”

He’s not wrong. Here’s what I wrote about this in my feature on psychology’s bias and replication problems for Nature:

“[Joseph Simmons] recently published a tongue-in-cheek paper in Psychological Science ‘showing’ that listening to the song When I’m Sixty-four by the Beatles can actually reduce a listener’s age by 1.5 years7. Simmons designed the experiments to show how “unacceptably easy” it can be to find statistically significant results to support a hypothesis. Many psychologists make on-the-fly decisions about key aspects of their studies, including how many volunteers to recruit, which variables to measure and how to analyse the results. These choices could be innocently made, but they give researchers the freedom to torture experiments and data until they produce positive results. [Note: one of the co-authors behind this study, Uri Simonsohn, has now been revealed as the whistleblower in the Smeesters case- Ed, 28/07/12, 1400 GMT]

In a survey of more than 2,000 psychologists, Leslie John, a consumer psychologist from Harvard Business School in Boston, Massachusetts, showed that more than 50% had waited to decide whether to collect more data until they had checked the significance of their results, thereby allowing them to hold out until positive results materialize. More than 40% had selectively reported studies that “worked”8. On average, most respondents felt that these practices were defensible. “Many people continue to use these approaches because that is how they were taught,” says Brent Roberts, a psychologist at the University of Illinois at Urbana–Champaign.”

I look at the Smeesters case and wonder if it’s just the first flake of the avalanche. If psychologists are developing the methodological tools to root out poor practices that are reportedly commonplace, and if it is clear that such behaviour is worthy of retraction and resignation, there may be very interesting times ahead.

Image by Chagai

CATEGORIZED UNDER: Neuroscience and psychology

I won an award (and a very touching one)

By Ed Yong | June 25, 2012 7:07 pm

At tonight’s Association of British Science Writers Awards, I got a runner-up prize in the Feature category for my profile of illusion master Henrik Ehrsson, and I won in the Science Communication in a Non-Science Context category for this podcast I did about the trillions of microbes that share our bodies and lives.

I’m delighted. The award is new, and it’s for a piece of science communication that exists outside science magazines, science sections of newspapers, or something similar. It’s for talking to people about science in places where they wouldn’t normally hear about it.

There’s a nice twist. The award is in memory of Stephen White, a science writer who passed away 2 years ago. Stephen taught the 2-day course that I attended at Cancer Research UK which first clued me into the possibility of being a science writer, and spent a very gracious evening in the pub fielding my naive dumbass questions. Tonight, I got to thank his wife Liz, who presented me with the award. It meant a lot.

Also, I’m thrilled about the runner-up prize in Features too, which was won by Helen Pearson for her story of the study of a lifetime. Frankly, any other result would have been an utter travesty. Helen’s one of our finest feature writers (disclosure: she regularly edits me) and her piece is amazing. Go read it.

CATEGORIZED UNDER: Journalism, Links

Californian condor not extinct yet, but still regularly poisoned by lead

By Ed Yong | June 25, 2012 3:00 pm

The image above, which may be the worst photo of a Californian condor ever taken, was the best shot I snapped during a four-hour condor-watching trip in 2010. But even this grainy image is important, for it captures one of the 405 last Californian condors in the world.

Myra Finkelstein from the University of California, Santa Cruz writes that the condor is “a symbol of environmental tragedy and triumph”. The huge bird, with its three-metre wingspan and eerily smooth flight, was once widespread across North America. Between power lines, guns, and pesticides, their population plummeted. The birds were frequently poisoned by lead after scavenging off shot-filled carcasses, and that’s if poachers weren’t filling them with lead shot in a more direct way.

By 1982, there were just 22 Californian condors left in the world, and all of them were in captivity. An intense captive breeding programme began, and it has been an apparent success. There are currently around 400 birds, more than half of which fly free and wild.

But this might be a pyrrhic victory. Finkelstein has now shown that the condor’s fate is far from certain. Even though we have brought it back from the cusp of extinction, its old enemy – lead – is still a major threat. If conservation efforts are scaled back, the condor will disappear once more unless the use of lead-based ammo is severely or completely curtailed. Read More

CATEGORIZED UNDER: Animals, Birds, Conservation, Environment

I've got your missing links right here (23 June 2012)

By Ed Yong | June 23, 2012 12:00 pm

Top picks

The EU released a teaser video of its campaign to get young girls into science. It did not go down well. The Knight Tracker has a copy of the video (now taken down) and collated all the reactions.

Really fascinating piece about how complicated “informed consent” is becoming in the era of big data. By Erika Check Hayden.

Vivid, well-told feature on the climate wars, by Tom Clynes.

How flight beat float: Megan Garber on the death of the dirigible.

The only good abortion is my abortion. This piece by Maggie Koerth-Baker is amazing not just because it’s brave but that it allows others to be brave. Salute

In 1935, a radio program sponsored by the FDA wrote a ditty praising arsenic. Great post by Deborah Blum.

Most people who bang on about science literacy are talking crap. This brilliant piece shows why.

I was sad as a kid when I learned that tractor beams weren’t real. But they might be!

Astonishing. Your brain looks different depending on whether the data analysis is done on a Mac or PC

These are wonderful: famous landmarks, seen through the eyes of hundreds at once

Women with super-vision live among us, and one scientist is trying to track them down. Cool piece by Veronique Greenwood.

XKCD: All 786 known planets drawn to scale

“If you were a mantis shrimp, your rainbow would be unimaginably rich” – two great posts on the nature of colour

“Caution about over-interpretation. Over-interpretation.” – Vaughan Bell’s template for all neuroscience stories

Typically excellent piece by Carl Zimmer on how the microbes within us are turning doctors into wildlife managers.

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