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In the caves of Slovenia and Croatia lives an animal that’s a cross between Peter Pan and Gollum. It’s the olm, a blind, cave-dwelling salamander, also called the proteus and the “human fish”, for its pale, pinkish skin. It has spent so long adapting to life in caves that it’s mostly blind, hunting instead with various supersenses including the ability to sense electricity. It never grows up, retaining the red, feathery gills of its larval form even when it becomes sexually mature at sweet sixteen. It stays this way for the rest of its remarkably long life, and it can live past 100.

The olm was once described as a baby dragon on account of its small, snake-like body. It’s fully aquatic, swimming with a serpentine wriggle, while foraging for insects, snails and crabs. It can’t see its prey for as it grows up, its eyes stop developing and are eventually covered by layers of skin. It’s essentially blind although its hidden eyes and even parts of its skin can still detect the presence of light. It also has an array of supersenses, including heightened smell and hearing and possibly even the ability to sense electric and magnetic fields.

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Imagine trying to rewind the clock and start your life anew, perhaps by moving to a new country or starting a new career. You would still be constrained by your past experiences and your existing biases, skills and knowledge. History is difficult to shake off, and lost potential is not easily regained. This is a lesson that applies not just to our life choices, but to stem cell research too.

Over the last four years, scientists have made great advances in reprogramming specialised adult cells into stem-like ones, giving them the potential to produce any of the various cells in the human body. It’s the equivalent of erasing a person’s past and having them start life again.

But a large group of American scientists led by Kitai Kim have found a big catch. Working in mice, they showed that these reprogrammed cells, formally known as “induced pluripotent stem cells” or iPSCs, still retain a memory of their past specialities. A blood cell, for example, can be reverted back into a stem cell, but it carries a record of its history that constrains its future. It would be easier to turn this converted stem cell back into a blood cell than, say, a brain cell.

The history of iPSCs is written in molecular marks that annotate its DNA. These ‘epigenetic’ changes can alter the way a gene behaves even though its DNA sequence is still the same. It’s the equivalent of sticking Post-It notes in a book to tell a reader which parts to read or ignore, without actually editing the underlying text. Epigenetic marks separate different types of cells from one another, influencing which genes are switched on and which are inactivated. And according to Kim, they’re not easy to remove, even when the cell has apparently been reprogrammed into a stem-like state.

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Antics

I spoke at a Science Blogging Talkfest earlier this week – I had a great time and was honoured to feature on a lot of the attendees’ picks for favourite blog. There’s a transcript of the entire event here as told through Twitter, a nice write-up from Noodlemaz, and an audio recording at some point. In advance of the event, Alice Bell did a set of four great interviews with British bloggers Daniel Macarthur, Imran Khan, Mun-Keat Looi and Jenny Rohn.

I did a photoshoot with some other science journalists for Geekcalendar, a (non-nude) initiative looking to raise money for Libel Reform. Have a look at some outtake photos here.

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The Benguela region, off the coast of Namibia, is a shadow of its former self. In the first half of the 20^th century, it was one of the world’s most productive ocean areas and supported a thriving fishing community. Today, the plentiful stocks of sardines and anchovies, and the industries that overexploited them, are gone. The water is choked of oxygen and swarming with jellyfish. Plumes of toxic gas frequently erupt from the ocean floor. But one fish, the bearded goby, is positively thriving in this inhospitable ecosystem. It’s a critical link in a food web that’s on the verge of collapse.

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In October 2007, the British band Radiohead released their seventh album – In Rainbows – as a digital download that customers could pay whatever they liked for. The results of this risky venture are a guarded secret, but the album’s popularity was clear. It topped the charts and allegedly sold 1.2 million copies in the first day alone. Even though many fans paid nothing (the average contribution ranged from $2.26 to around $8 depending on the survey), the band still earned more money from In Rainbows than their previous album, Hail to the Thief. But according to a new study, Radiohead could have earned even more money by adding a slight twist to their plan – telling people that half their voluntary payments would go to charity.

Many businesses are trying out new strategies that appeal to the better nature of their customers. Some promote the fact that they donate a proportion of their profits to charity. Others, from Radiohead to restaurants, invite people to pay what they like for their products. People often get away without paying anything but in practice, they frequently cough up something. But according to Ayelet Gneezy from the University of California, San Diego, the best strategy is to fuse the two approaches.

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Walk among the Arctic ice and you’ll sometimes encounter distinctive patches of red snow. They’re caused by a species of bacteria called Colwellia psycherythraea. It’s a cold specialist – a cryophile – that can swim and grow in extreme subzero temperatures where most other bacteria would struggle to survive. Colwellia’s cold-tolerating genes allow it to thrive in the Arctic, but Barry Duplantis from the University of Victoria wants to use them in human medicine, as the basis of the next generation of anti-bacterial vaccines.

Colwellia’s fondness for cold comes at a price – it dies at temperatures that most other bacteria cope with easily. By shoving Colwellia genes into bacteria that cause human diseases, Duplantis managed to transfer this temperature sensitivity, creating strains that died at human body temperature. When he injected these heat-sensitive bacteria into mice, they perished, but not before alerting the immune system and triggering a defensive response that protected the mice against later assaults. The Colwellia genes transformed another species of bacteria from a cause of disease into a vaccine against it.

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In humans, two chromosomes – X and Y – determine whether we are male or female. Of the two, Y tends to get more attention because of its small, degenerate size. Both X and Y probably evolved from a pair of ordinary chromosomes that have nothing to do with sex (also known as autosomes). The story goes that one of these autosomes developed a gene that immediately caused its bearer to become male, and eventually became the Y chromosome of today. The other one became X.

Throughout its history, Y has been a hotbed of genetic change, gaining, losing and remodelling its genes at breakneck pace, and shrinking by 97%. Its partner – X – has allegedly had a less eventful past, and should faithfully represent the ancestral autosome. This history of X and Y was first proposed in 1914 by Herman Muller, and ever since, his assumptions about X’s stability have gone untested. Now, it seems that Muller was wrong. Daniel Bellott from the Howard Hughes Medical Institute had uncovered the secret history of X, which turns out to be no less storied than Y’s tale.

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Pepsipocalypse

­­­The big news this week was the mass exodus of bloggers from ScienceBlogs following the unveiling of a new PR blog by PepsiCo. Everyone and their monkey has blogged about this. Here are the best takes on the fracas, from my perspective:

• Why it matters: Martin Robbins very neatly sums up the major issues. PalMD was the first to speak out and subsequently clarified what the issues are; Brian Switek did the same.  Journalists like Maryn McKenna and John Rennie talk about the conflict of interest issue from the perspective of people in the know. And Jennifer Ouellette discusses the wider implications of Pepsigate, and why it shows that blogging has come of age.
• What the press said: Mainstream journalistic outlets like the Knight Science Journalism Tracker, the Guardian and the Columbia Journalism Review, were clear in their criticism.
• What could have happened: Abel Pharmboy talks about how it could have gone down
• Why it still matters: David Dobbs was one of the first to leave and explains why he’s sticking with that move. At the Guardian, Gaia Vince spills the beans on how a column she wrote about the Bhopal disaster was axed by a SEED editor because Dow Chemicals (the company behind the disaster) was a potential advertiser. And Abel, myself and others clarify why deciding to stay at ScienceBlogs doesn’t say anything about the principles of individual bloggers.

It genuinely saddens me to see these events unfold, especially because I have many friends and colleagues who are being directly affected. From my experience, ScienceBlogs has always succeeded because of the passion of its bloggers and the community managers that assisted them. It has succeeded  in spite of, rather than because of, the actions of upper management.

I urge you to please go and visit the various blogs, both those that left and those that stayed. There’s some truly fine stuff there and it deserves your support. Carl Zimmer is tracking the migrating bloggers and cites the problems involved in taking a stand and moving elsewhere. And Chris Clarke set up an RSS feed so you can follow all the dispersed bloggers.

News

Oh dear. That study I wrote about last week on longevity genes may not be all it’s cracked up to be. The paper seems to have severe problems with the methods – see Newsweek and Genetic Future for more. I’m a little chagrined that I covered this so positively – chalk it up to a failure of journalism and not contacting the right people…

When asked to show that they’re not telling lies about their products, an entire industry has a massive hissy fit. Apparently, gathering evidence is very difficult and if you make a claim with poor evidence, people reject it. The meanies.

“For more than 30 years, people of all ages have been dropping dead from sudden cardiac arrest in northern Yunnan.” The killer? A mushroom… Richard Stone reports in ScienceNews. You need a subscription but trust me, this is worth it.

For Nature News, Elie Dolgin braves Andrew Wakefield’s book launch and makes it out alive.

“At a speech at the Royal Institution today, science minister David Willetts revealed how the government plans to win over children and save British science,” says the Guardian. It involves launching dinosaurs into space. Or something.

Mojoceratops. Heh.

This from New Scientist is a nice addition on the non-debate about whether tyrannosaurs were scavengers.

Ivan Oransky’s some kind of policy-changing superhero. Watch Embargo Watch strike a blow for sense

A great post by Christine Ottery on whether climate journalists should try to motivate people to act on climate change.

Nature News: Astronomers and conservationists team up to fight for the right to not have bright night lights.

This is how a village dies: Gaia Vince has some amazing frontline reporting on how climate change is affecting a Bolivian village, augmented by great photos.

Parasitic worms cause ant bellies to swell up, mimicking fruit so that they get eaten by birds. Wow. Just… wow. From Brian Switek.

“Mouse sleeps with scientist. Scientist thrilled,” says NPR.

A great post from Vaughan Bell about why neuroplasticity is a dirty, undefined word. I can feel my brain rewiring as I read it…

Your inner fish explains why you sometimes get haemorrhoids, according to Neil Shubin interviewed at NPR. Damn you, Tiktaalik!

Heh/wow

The evolution of life in stop-motion graffiti. Even more amazing than it sounds.

No please tell me that you didn’t discover a gene that controls the sexual inclination of female mice and name it FucM… Oh wait, you did.

“The squid’s sexual agitation caught the researchers by surprise.” Yeah they all say that. Learn about the incredible sex organ of the deep-sea squid. And speaking of squid, some can use their jet propulsion to glide for several metres.

Monkeys use trees to catapault themselves out of Japanese laboratory. Fly my pretties, fly!

This is the “bionic handling assistant”. One step closer to Doctor Octopus…

The best science teacher ever tricks students into joining a NASA mission, covered at 80Beats.

An incredible shot of a launching space shuttle, as seen by skydivers.

You should know what this is. If you don’t, Google “Stanley Milgram”

Junk Charts – a blog where bad infographics go to die

Journalism/writing/internet

The ABSW Science Writer awards are back after a two-year hiatus. I won the Best Newcomer award last year when a smaller version was run, but I had the honour of being on the judging panel this year. Here are the nominees

Frank Swain has released a small excerpt from his upcoming book Zombology, about zombies.

Jo Marchant discusses how journalists ran with a conspiracy story about King Tut’s replaced penis, which she debunked in her New Scientist blog.

A couple of nice pieces on the role of opinion in news. Michael Arrington at Techcrunch bemoans the tactics used to provide opinion without making it look like you’re doing so. “An added adjective here, an added paragraph there, just the right quote from a source and voilà, you’ve got yourself an opinion piece masked as a straight up unbiased piece of reporting.” Jay Rosen agrees: “The wise newsroom will trade polarity for plurality. Lose the binary, news people! Instead of two rigid poles—neutrality or ideology, news or opinion, reporter or blogger, adults or kids—I recommend a range of approaches that permit journalists to report what they know, say what they think, develop a point of view in interaction with events, and bid for the trust of users who have many more sources available to them. A plurality of permissible styles recognizes that trust is a puzzle unsolvable by a single system of signs.”

Animals must wage a never-ending war against parasites, constantly evolving new ways of resisting these threats. Resistance comes in many forms, including genes that allow their owners to shrug off infections. But one species of fly has developed a far more radical solution – it has formed a partnership with a bacterium that lives in its body and defends it against a parasitic worm. So successful is this microscopic bodyguard that it’s spreading like wildfire across America’s besieged flies.

The fly Drosophila neotestacea is plagued by a nematode worm called Howardula. Around a quarter of adults are infected and they don’t fare well. The worm produces thousands of young in the body of its hapless host, and the little worms make their way into the outside world via the fly’s ovaries. Not only does this severely slash the fly’s lifespan, it also always sterilises her. But according to John Jaenike from the University of Rochester, the fly is fighting back.

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