Shared posts

01 Apr 13:00

Oxytocin: Still Not a Moral Molecule

by Ed Yong
Tertiarymatt

Oxytocin stokes the flames of in-group/out-group divisions. I once saw the spectacularly bad suggestion that cops should spray it on rioters.

Whenever the hormone oxytocin makes the news—and it does so regularly—the media can’t help but refer to it as the “love hormone”, “cuddle chemical” or “moral molecule”. Few substances enjoy such a positive public profile. Oxytocin, it is said, is at the core of all our virtues, from trust to empathy to cooperation.

This rose-tinted view is a sham.

As I’ve written before, oxytocin is more of a general social hormone—one that drives us to seek out social situations or that draws our attention to social cues. The results can be positive if we find ourselves in the right situation. Change the context, and oxytocin can reveal a dark side to its influence.

The latest example of this comes from Shaul Shalvi and Carsten de Dreu. They found that people who sniff oxytocin become more dishonest in a simple team game, but only if their lies benefit their group. If they play the game alone, oxytocin doesn’t change their behaviour for better or for worse. As de Dreu says, “This is the best evidence yet that oxytocin is not the ‘moral molecule,’. It doesn’t make people more moral or immoral. It shifts people’s focus from themselves to their group or tribe.”

I’ve written about the study in The Scientist, so head over there for the details. You might also enjoy my piece in Slate about the history of oxytocin hype and why it’s both dumb and dangerous.

29 Mar 16:00

I’ve Got Your Missing Links Right Here (29 March 2014)

by Ed Yong
Tertiarymatt

Lots of stuff, some of it funny, some of it depressing as hell.

Sign up for The Ed’s Up, a weekly newsletter of my writing. Here’s a recent example.

 

Top picks

Excellent piece by Erika Check Hayden on the problems with poorly conducted mouse studies: wasted money, wasted lives, harmed patients.

Great Barrier Reef: an obituary. An immensely sad, interactive tribute to a fallen ecosystem.

The humble heroes of weight-loss surgery are stomach acids and gut microbes. Great piece by Virginia Hughes

The rise of ancient DNA is one of the most spectacular recent developments in biology. Ewen Callaway gives us a tour

EPIC! All 339 books referenced In “Gilmore Girls”. Also, god I miss those people.

How will science confirm this week’s big discovery about cosmic signals from the infant universe? Nadia Drake on the week’s big discovery.

““I had never seen a brain inside out before,” Gazzaley told me. “After that I couldn’t get back to work.” Carl Zimmer on new ways of visualising the brain.

My short feature on camouflage in the natural (and human) world, for New Scientist. Paywall.

Scientists synthesise an entire yeast chromosome from scratch (and with surprisingly heavy edits). By me.

How psychedelics are helping cancer patients fend off despair. Nice to see a piece (and research) on palliative care in cancer.

A gif of the skull of a two-faced calf, getting cleaned by flesh-eating beetles. And the video that inspired it. By Emily Graslie. Not for the faint-hearted.

Robots, robots everywhere: here’s Oliver Morton’s guide to his wonderful Economist special on robots.

Don’t write a story that is wrong. This is harder than it sounds.” Ian Sample’s excellent tips on good science journalism.

The New Yorker on the quest to apply artificial intelligence to the Chinese board game Go

 

Science/news/writing

As climate change progresses, Bangladesh will face the consequences earlier than most.

FDA says almost all manufacturers agree to agricultural-antibiotic controls. End of the battle, or just more of the same?

Hypnotic Art Shows How Patterns Emerge From Randomness in Nature

Pterosaurs are amazing, but surprisingly rare. Why?

Cuvier’s Beaked Whale sets new deep diving mammal record at 9,816 ft, 2,500 ft deeper than sperm whale

Lion versus croc, in a fight over hippo

Deep brain stimulation–a tool for treating Parkinson’s, but also a new way of eavesdropping on the brain.

Google Flu has been a spectacular failure. When it comes to Big Data, you can’t polish a turd.

So, why do snakes have two penises? (Post features all the snake penis photos you could possibly want.)

Conchs foil human collectors by evolving to be smaller.

Boom! Kakapo baby boom.

260-million-year-old spider tracks

An homage to Jane Goodall, who turns 80 next week.

Scientists convince people their hands are rocks

Nadia Drake asked a bunch of astronomers to name the Solar System’s biggest surprises

Mesmeric time-lapse scenes of swarming fireflies

A “fire tornado” whirls above a prairie

“Riding, poking, prodding or otherwise harassing a free-swimming large predatory animal for fun is a bad idea.”

18th century biologists made frogs wear tiny pants while having sex

New dwarf planet discovery hints at a hidden Super Earth in solar system

Neurosurgeons successfully implant 3D printed skull

Wagenmakers to priming psychologists: “nut up or shut up”.

Here’s Radiolab on what would happen if we annihilated all mosquitoes

Two halves of a fossil turtle bone are reunited after 163 years.

The de-extinction issue wastes considerable time “debating the consequences of a science that is yet to be realized.”

Squirrels Hibernate So Hard You Can Juggle Them

This post is a hilarious look at the sort of questions that people in medical charities get.

Heh. Classic children’s books that would be ruined by modern medicine

What happens when you put a fly in a particle accelerator? You get a really cool video

Nadia Drake has given the Milky Way 4 billion years to live, unless you concede to her demands.

Jimmy Wales has told a bunch of alternative medicine people moaning about Wikipedia where to stick it

Slo-mo vid of a goshawk flying through variously-shaped small holes

Gonorrhea bacteria hitchhike among people using ‘grappling hooks’ that grab onto semen proteins.

The cost of anti-vaccine fears in a gif. More from NPR

“What is it about meditation that opens the brain up to these kinds of hallucinations?”

When lab scientists used to pipette with their mouths

Homeopathic products recalled because they might contain actual medicine.

This computer can tell when humans are faking pain. More effective torture droids on the way.

Stick insects started mimicking plants 126 million years ago

Interactive images of how animals see the world

The evidence that phthalates damage male fertility is surprisingly strong. By Deborah Blum.

“The revived moss [has] been in a state of suspended animation since the age of King Arthur.”

Rootworm evolves resistance to GM corn, highlighting importance of crop rotation.

Why are there so many frickin’ huge ants?

“It might sound strange, but a shriveling Mercury is not unexpected.”

Add carbon nanotubes to plants to supercharge photosynthesis. Okay but how would you ever apply this in practice?

Weed: a gateway drug through the generations?

Refuting MMR/autism link decreased intent to vaccinate among parents w/ unfavorable vaccine attitudes

The NYT on the new generation of programmed ‘detect and respond’ brain implants for epilepsy

Two twins, separated by space. No, really, By Space.

“As consumers, when we own a black box, we’re letting other people design our world.” The wonderful Aatish Bhatia hacks Kinect to make a dance video

When Nature Looks Unnatural“—Sean Carroll on the recent discovery about inflation and the early universe.

10 persistent cancer myths and why there’s no evidence to back them up

What was the biggest animal gathering ever? Featuring herring, starlings, and Rod Stewart

 

Heh/wow/huh

“Mellow.” “Clucky.” “Stentorian grunting.” The mating calls of male tortoises

Dad turns kid vids into amazing superhero feats

Life before the internet

Bravo, Tom Whipple. You win the lede awards.

Huh. Cool things happen when you chuck sand in the air and photograph it with a high-speed camera

Onion: How a Predator drone works

A recent study has shown that if US parents read one more think piece about parenting they will go f**king apes**t”

Dr Manhattan performs Let It Go from Frozen.

Explaining phylogeny using candy bars

Teacher spoils a Game of Thrones death every time his class gets too noisy

Close-up shots of flames mid-burst look eerily like brains

Check out the winners of the Wellcome Image Awards, from a beautiful nit to a gorgeous kidney stone

The 20 best TED talks ever. This is absolute gold. Mine is basically #17

 

Internet/journalism/society

A journalist tells his mental illness story

Should you give journalists metrics about their stories?

“References enable TED to fulfil its goal of hosting ‘ideas worth spreading’ rather than mere ‘stories worth telling’.”

Utterly horrifying piece on what happens to ghost flights.

Q&A from Megan Garber, explaining Oculus Rift—Facebook’s recent mega-purchase. I especially like: “Sorry, but this whole thing sounds really nerdy.”

The radiovota: a 1930s “Like” button for the radio… that took 7 hours to register

Retraction Watch is a bastion of solid, important science journalism. Help Ivan Oransky and Adam Marcus with a small donation

Solid advice on story structure in book writing, and drawing inspiration from screenwriting.

Reason #7394 to kick the Daily Mail in its pathetic bigoted crotch

 

 

02 Apr 04:00

27p33

by Christopher Hastings
Tertiarymatt

At least the Doc knows he's fucking up?

27p33

27p33 is a post from: The Adventures of Dr. McNinja Ads by Project Wonderful! Your ad could be here, right now.

27p33 is a post from: The Adventures of Dr. McNinja

Ads by Project Wonderful! Your ad could be here, right now.
16 Mar 19:49

The Birds And the Bees and the Pollinator Syndrome [Science Ink Sunday]

by Carl Zimmer
Tattoo by Dave Kotinsley, Gainesville, FL

Tattoo by Dave Kotinsley, Gainesville, FL

Jacob Landis writes, “I’m a graduate student at the University of Florida studying flower evolutionary development with a focus on plant/pollinator interactions. My ink represents the concept that I have been working on for almost 6 years now. This piece shows three species in the Phlox family. The red and white flowers are both part of the genus Ipomopsis and the blue/purple flower is in the closely related Polemonium. The pollinator of each flower is shown interacting with the flower. These interactions represent the concept of pollinator syndromes: certain features of the flower will attract certain pollinators. The long red tubular flowers attract hummingbirds, the white tubular flowers attract hawk moths, and the more open blue/purple flowers often attract bees.”

You can see the rest of the Science Tattoo Emporium here or in my book, Science Ink: Tattoos of the Science Obsessed(The paperback edition comes out in May; you can pre-order here.)

02 Apr 04:52

How To Draw A Kitty

Tertiarymatt

Feed is wonky, but click through for gud comic.




Ads by Project Wonderful! Your ad could be here, right now.

I am back from Seattle and completely wiped out! So here is a comic thing I did for my tumblr a while back. Regular strips resume tomorrow!

01 Apr 05:01

on Fairness

by Ian

on Fairness

31 Mar 08:00

Prisoners of the Horde-Orcs.

Tertiarymatt

Ba-dum-tish.

Comic #2626

Comic Rank
27 Mar 15:30

These Are Some of the Solar System’s Biggest Surprises

by Nadia Drake
Tertiarymatt

So. many. links.

The universe is full of surprises, but two discoveries in the outer solar system are dominating astronomy news this week.

First, astronomers reported yesterday that they have found a distant, tiny world – a small, icy body that lives in the darkness far beyond the orbit of Neptune. Called 2012 VP113, the world’s existence challenges theories describing the infant solar system, and flames speculation that a large planet hides on the fringes of detection. 2012 VP113 and its sibling Sedna are now the two farthest-flung, roundish objects we’ve spied whose gravitational allegiance lies with the sun.

Next, we learned of an asteroid-like body with rings. Called Chariklo, the ringed world is a Centaur – an icy, rocky object that lives between the orbits of Jupiter and Neptune. Chariklo is the first not-planet in the solar system known to have a ring system. And it isn’t just any old ring system – there are two bright, glimmering icy rings encircling the enigmatic, 248-kilometer-wide world. For decades, scientists had thought a small body’s gravity would be too weak to cling to rings like Saturn’s. “When it appeared, it was a complete surprise,” said Felipe Braga-Ribas, a planetary scientist at the National Observatory in Brazil, who discovered Chariklo’s rings hiding in a few seconds of observational data. “We started trying to understand it.”

While discussing the discovery with various planetary scientists, it became apparent that such surprises are the norm in planetary science. It seems the solar system has no shortage of unexpected offerings. “It’s one of these discoveries that you just don’t expect to have happen. But that’s the story of planetary science,” said Joseph Burns, a planetary scientist at Cornell University, while talking about Chariklo. “We go out and see what nature says.”

In honor of this week’s outer solar system double feature, I thought it would be fun to ask some scientists which discoveries they consider the most surprising. Whether recent or decades-old, nearby or faraway, groundbreaking or just “wow,” the discoveries described below invoke a delightful tour through the solar system’s many eclectic treasures.

And please, whether scientist or not, feel free to comment on this post and share your most surprising solar system moment – what has our planetary neighborhood surprised you with?

Now.

Q: Which discovery (or discoveries) in the solar system has most surprised you, and why? (responses have been lightly edited for length and clarity)

Ryan Anderson, astrogeologist, U.S. Geological Survey

For me, the biggest recent surprise was the discovery of plumes at Europa. A lot of times the big “surprises” make perfect sense in retrospect. We think Europa has liquid water under the ice and that the ice is shot through with fractures, so it makes sense that it might have plumes much like Enceladus at Saturn. But still, making sense of the discovery in retrospect doesn’t change the fact that it’s surprising and exciting when you first hear about it.

Erik Asphaug, planetary scientist, Arizona State University

My biggest surprise was seeing a comet split up into a dozen pieces in 1993, with the discovery of Shoemaker-Levy 9 when I was graduating from Arizona. Wow! I remember thinking, “How many comets get made in this way?” Twenty years later we’ve all been blown away by the sequential space missions to Wild 2, Tempel 1, and Hartley 2. They are all so different. After all this time we still know basically nothing about comets as geologic bodies, which makes them the most fun and rewarding objects of investigation.

Fran Bagenal, planetary scientist, University of Colorado

Volcanoes on Io, which revealed the most geologically active object in the solar system, and moons around asteroids (how did they get there?).

Michele Bannister, postdoctoral fellow, University of Victoria

How active so many of the icy worlds (moons, dwarf planets) of the Solar System are. Not only active in the great, slow past of geological time, but active now: We can see their surfaces change in our lifetime. Geysers on Enceladus, possible plumes on Ceres and Europa, suggestive geyser-features on Triton, storms and rivers on Titan…we’re living in a Solar System that is changing and dynamic.

Bill Bottke, planetary scientist, Southwest Research Institute

The Nice model, where the giant planets possibly started in a very different configuration than they have today; the ~200 km diameter naked iron core represented by the asteroid Psyche; the discovery of the Kuiper belt and more recently, Sedna and its brethren; not quite a discovery, but the paucity or absence (depending on who you believe) of ancient rocks on Earth that are older than 4 billion years; ice within the permanently shadowed craters on the Moon and Mercury; the prediction that many icy moons have deep oceans; the equatorial ridge around Iapetus, and the absolute weirdness of Miranda; how much our view of the solar system has fundamentally changed since the advent of fast computers and efficient numerical integration codes.  (Exoplanets!)

Mike Brown, astronomer, Caltech

Since the story on the second Sedna body is coming out, I am reminded just how incredibly surprised we were when we discovered Sedna. So surprised that we didn’t believe it for about a month until we got multiple confirmations and ruled out every other possibility. It was the only thing ever found so far away and it lived in an area of space where nothing should have been. I always said, at the time, that this is the best part of doing science, because when you find something that is not supposed to be there, you have learned something new about how the solar system works.

Joseph Burns, astronomer, Cornell University

If you go back long enough, a big [surprise] is just the nature of natural satellites. When I was growing up as an academic, satellites were supposed to be just bombarded, barren, cratered objects. Uninteresting. Why would you want to look at them? And then we got in orbit around Mars and saw Phobos and Deimos, and they were pretty bizarre-looking. And then Voyager went out – and suddenly you see Io. And it’s got volcanoes and sulfur, it looks like a pizza and has some sort of bizarre surface. And it turns out, when you go to every system, every one of the satellites is unique – and now, three of the possible abodes for life in the solar system are on moons.

Athena Coustenis, planetary scientist, Observatoire de Paris-Meudon, CNRS

For me, the most surprising discovery were the jets at Enceladus, because it demonstrated that we could find liquid water under the surface of the icy moons at 10 astronomical units, and challenges all the conventional habitable zone models…

Luke Dones, planetary scientist, Southwest Research Institute

We went in a decade from, “only Saturn has rings” to ring systems around all four giant planets. The ring arcs of Neptune were particularly surprising. Also, the very complicated orbital structure of the Kuiper Belt/trans-Neptunian region/inner Oort Cloud/whatever you want to call it. Most of the populations beyond Neptune could have formed closer to the Sun and moved out to their current locations, but there’s a “cold classical” population that seems like it’s always been where it is now.

And, the first extrasolar planets were found around a pulsar, of all places.

Lindy Elkins-Tanton, director of the Department of Terrestrial Magnetism, Carnegie Institution for Science

I was really surprised when Mercury’s magnetic field was found to be offset to the north; we’re used to a magnetic field whose pole can wander relative to the spin pole of the planet, but what about one whose magnetic equator is north of the planet’s equator? This surprise gives me the exciting idea that we may not understand magnetic dynamos very well after all!

Jay Farihi, astronomers, University College London

Comets in the main asteroid belt – they’re like comet-spies in the inner system where they don’t belong. Some main belt asteroids sometimes exhibit characteristics of comets – tails, outflows, etc. They are still poorly understood; it’s not clear if ice and volatiles are evaporating or being released from collisions or rotational break up.

David Grinspoon, astrobiologist, U.S. Library of Congress

I have been repeatedly surprised by the level of activity in small worlds that we “knew” should be old and dead, before we started exploring the outer solar system. Volcanoes on Io, geysers on Enceladus and now evidence of surface water on Asteroid Vesta?  The apparent prevalence of liquid water environments far beyond the sunny inner solar system is a delightful, ongoing set of surprises.

Avi Loeb, astrophysicist, Harvard University

The discovery of ice on Jupiter’s moon Europa – with potentially liquid water under it – was most surprising to me because this environment might host life (in other words, there might be fish in that water). Another surprising discovery was of Sedna, which is a Pluto-size object on an eccentric orbit extending thirty times farther than Neptune’s distance from the Sun. 

Ralph Lorenz, planetary scientist, Johns Hopkins University Applied Physics Laboratory

I wrote a paper in 1995 anticipating that we would not find sand dunes on Titan, which may be one of the most outstandingly bad predictions in planetary science (for interesting reasons) since some 15 percent of Titan turned out to be covered in giant dunes. Bigger picture, Titan turned out to be much more diverse than anyone remotely expected.  Pre-Cassini, everyone thought in one-dimensional terms – Titan is the same everywhere. We thought it would be wet (no dunes), and yet it has vast deserts.  It turns out climate (latitude) controls a lot – it’s wet too, just around the north polar regions. And nobody, not even us, expected us to be able to see the bottom of Ligeia Mare, all the way down to 170 meters. Titan’s seas must be amazingly clear.

Franck Marchis, planetary astronomer, Carl Sagan Center, SETI Institute

Asteroids are mini geological worlds with complex surface activity, differentiated interiors, complex evolution histories, and moons. Also, the satellites of Saturn – their shape, structure and evolution (captured or formed from the ring?) – and the complex interactions between Saturn, its ring system and its satellites. Io (with its outburst eruptions) and Europa and Jupiter’s magnetic field. There is still a lot to learn about the interaction of satellites and the giant planet’s magnetosphere — maybe a future promising way to detect moons around exoplanets?

Sarah Milkovich, planetary geologist, NASA’s Jet Propulsion Laboratory

I’d say three things: The plume at Enceladus, because this tiny moon is spitting out enough water to form the E-ring around Saturn! The plumes at Europa, because we didn’t see them from the Jovian system with the Galileo spacecraft, but from Earth with Hubble. The recurring slope linea (RSL) at Mars, because the idea of any kind of liquid water-related activity on Mars today is rather mind-boggling.

Catherine Neish, planetary scientist, Florida Institute of Technology

I think my top three are: 1. Ice on Mercury’s poles. Although I was only 11 when this was discovered using ground-based radar, I still think this stands out as one of the neatest discoveries in planetary science. The fact that there is water ice on the closest planet to the Sun just seems so incongruous (even though in retrospect it makes perfect sense). 2. Plumes on Enceladus. Water jetting directly into space! How neat is that? 3. Titan: The desert planet. Prior to the Cassini mission, a lot of people thought that Titan would be covered by a sea of liquid hydrocarbons. The Cassini-Huygens mission revealed it to be much more of a desert planet, with vast sand dunes near the equator, and only smaller lakes and seas near the poles.

Alex Parker, planetary astronomer, University of California, Berkeley

In recent memory, the most exciting and surprising series of confirmed discoveries were the detection of Pluto’s packed system of four small moons outside its very large moon Charon. They were unexpected, are in a surprisingly delicate configuration, and their origin and survival remains challenging for theorists to explain. They’re also particularly exciting in light of the fact that we now get to explore them up close when New Horizons visits the Pluto system next year!

Carolyn Porco, planetary scientist and Cassini imaging lead, Space Science Institute

I was part of the Voyager mission to the outer solar system.  Every stop was packed with surprises. But the best surprise of all was the spectacular geysering activity we on Cassini have found at the south pole of Enceladus.  We suspected that moon might have geysers of some sort.  But never did we imagine they’d be the phenomenally dramatic and huge things they turned out to be. It all comes down to a failure of imagination and our inability to divine the variety and spectacle of the phenomena that Mother Nature can create.

Christopher Russell, Geophysicist, Dawn mission principal investigator, UCLA

I will give you three answers, all from the moons of the outer solar system: The magnetic field of Ganymede (which seems to be generated by a magnetic dynamo similar to that in the Earth – no other moon is like that today, although our moon once was), the plume of Enceladus and the lakes on Titan. These moons were like small planets.

Mark Showalter, planetary astronomer, SETI Institute

I’ll vote for Saturn’s F ring as first imaged by Voyager 1. It showed the so-called “braids” (which aren’t really braids, of course) and it was the first time we all realized that a ring didn’t have to be circular and uniform.

Let me pass along a quick anecdote. At the moment that first image came down, one of the Imaging team scientists was doing an on-camera interview, which I was watching. Somewhat befuddled, he blurted out, “This is high on the list of things we didn’t expect to see!” I always wondered what else was on that list.

Linda Spilker, Cassini project scientist, Jet Propulsion Laboratory

For me, the discovery of the icy jets spewing out of the south polar region of Saturn’s tiny moon Enceladus was a big surprise. Enceladus is only 500 km in diameter and should have frozen solid long ago yet today it lofts icy particles and gas into space, creating Saturn’s diffuse E ring. The discovery of liquid methane lakes and seas at the north pole of Saturn’s giant moon Titan was another big surprise. Titan has a thick nitrogen atmosphere and methane plays the role on Titan, with clouds and rain, that water plays on Earth, creating river channels and filling lakes and seas which contain more than 100 times as much hydrocarbons than all of the oil and gas on Earth.

Alan Stern, New Horizons principal investigator, Southwest Research Institute

River valleys on Mars, volcanoes on Io, and the discovery that dwarf planets dominate the population of planets in our solar system. More generally, we should not be surprised at being surprised at the richness of nature — that’s a hallmark of planetary science.

Anne Verbiscer, planetary scientist, University of Virginia

I know this sounds awfully self-serving, but the discovery that surprised me the most was that of Saturn’s Phoebe Ring!  Yes, we planned our Spitzer observations with the intent of finding a ring, but we were really surprised (and delighted) to find that it was there!

Orbit diagram for the outer solar system. The Sun and Terrestrial planets are at the center. Jupiter, Saturn, Uranus and Neptune are in purple solid circles. The Kuiper Belt (including Pluto) is the dotted light blue region just beyond the giant planets. Sedna's orbit is shown in orange, and 2012 VP113's orbit is shown in red. (Scott Sheppard, Carnegie Institution for Science)

New orbit diagram for the outer solar system. The Sun and Terrestrial planets are at the center. Jupiter, Saturn, Uranus and Neptune are in purple solid circles. The Kuiper Belt (including Pluto) is the dotted light blue region just beyond the giant planets. Sedna’s orbit is shown in orange, and 2012 VP113′s orbit is shown in red. (Scott Sheppard, Carnegie Institution for Science)

This post has been updated to include more responses

31 Mar 08:00

And Sometimes You Just Move On

by Christopher Wright
Tertiarymatt

Poe's Law.

29 Mar 17:13

The Absolute Weirdness of Miranda

by Nadia Drake
Tertiarymatt

Click thru for picture.

Miranda looks like it’s been Frankensteined together. The small, lumpy moon orbits Uranus and has a surface covered by patches of intersecting ridges, weirdly bumpy terrain and pockmarked plains, and dark, irregular canyons. It’s kind of like a badly crafted moon-quilt, except there’s nothing warm and fuzzy about a barren chunk of icy rock with grooves that make the Grand Canyon look like a paper cut.

Earlier this week, I asked a bunch of scientists to share what they’ve been the most surprised by in the solar system. “The absolute weirdness of Miranda,” was one of the responses from planetary scientist Bill Bottke of the Southwest Research Institute. There are a number of bizarre satellites in the solar system, so Bottke pointing to Miranda meant it was worth a closer look.

Miranda was spotted in 1948 by Gerard Kuiper, but it wasn’t until Voyager 2 swung by the solar system’s most unfortunately named planet in 1986 that we got a good look at its little moon. Miranda is only 500 kilometers across, or about one-seventh the size of our moon.

Basically, Miranda appears as though it’s made out of pieces that don’t quite fit together properly, sort of like poor, lurchy Frankenstein. How the moon came to be like this is still a mystery. One theory suggests that in its first incarnation, Miranda was a less-grotesque, more-normal version of itself — until a giant impact or five came along and blew the moon apart. The pieces eventually reassembled, but not in a way that made much sense. Another hypothesis suggests that meteorite impacts locally melted the moon, and slush rising to the surface formed the giant, ridged patches scientists call “coronae.” Other theories have thrown in a little icy volcanism and internal heating caused by gravitational interactions with Uranus and its other moons. Or, Miranda could have begun to differentiate, with its internal layers separating into something like a core, mantle, and crust — but froze before it finished the job.

30 Mar 18:51

Tiny convention painting: Monkey King!



Tiny convention painting: Monkey King!

30 Mar 18:28

The Gospel According to Genius

Tertiarymatt

You know, I'm actually really liking using a MBP, but I still don't think I could bring myself to ever give Apple money.

Howdy! I've been given a chance to do a weekly Apple-centric comic over on Macworld.com. We're calling it Multi-Touch Theater and this is the second installment. (Last week's is here.) If the traffic is good, I can hopefully keep doing these on a weekly basis. Doing comics like this for other sites really helps me keep Diesel Sweeties running and ad-free, so please go give them both a read if you have a moment.

New strips will continue to run on Fridays, Steve willing. I'll keep running them in my feed as long as I'm able.

Thanks!

what's a gmail

27 Mar 11:51

Thursday round-up

by Amy Howe
Tertiarymatt

Kind of a big deal.

The Court heard oral arguments in one case yesterday and issued an opinion in another, but the big news out of the Court continues to be Tuesday’s oral argument in the challenges to the Affordable Care Act’s contraception mandate.  At Talking Points Memo, Sahil Kapur has additional coverage of the oral argument here and here.  Commentary on the case comes from Noah Feldman at Bloomberg View, who focuses on what he describes as “two important wrinkles in the oral argument that . . . might tell us a lot about both the court’s potential holding and the tenor of the possible dissent”; from Andrew Cohen at The Week, who concludes that “the decision will be more a reflection of the court’s current ideology than about the stability of first amendment precedent or the text of the Religious Freedom Restoration Act”; from Daniel Fisher of Forbes, who predicts that “courts will soon be a lot busier trying to figure out whether a company is trying to avoid a law or regulation out of sincere religious beliefs or to save a buck”; from Brandon Garrett at ACSblog, who argues that the Court on Tuesday “could have pushed harder on a constitutional question that comes first: whether the lawsuit even belongs in a federal court”; from Kent Greenfield at The Prospect, who contends that, if the Court were to rule for Hobby Lobby,  “[j]ust like before the Civil Rights Act, each individual business will be able to pick and choose whether to assert a religious right to discriminate or refuse to provide insurance or pay a minimum wage”;  and from Michael Dorf at Verdict, who observes that, in the past, “claims like the one made by the current plaintiffs were less ideologically charged. Indeed, to the extent that there was any discernible ideological pattern, it was the opposite.”

Yesterday the Court issued a decision in United States v. Castleman, holding that Castleman’s state conviction for misdemeanor domestic assault qualifies as a “misdemeanor crime of domestic violence” and thereby prohibits him from having a gun.  Coverage of the Court’s decision comes from Nina Totenberg of NPR, Jess Bravin of The Wall Street Journal’s Law Blog, and Kent Scheidegger of Crime and Consequences.

After the decision in Castleman, the Court heard oral arguments in Wood v. Moss, in which the Court is considering claims by protesters opposed to the policies of then-President George W. Bush against the Secret Service agents who moved their protests away from the president.  Lyle Denniston covered the oral argument for this blog; other coverage comes from Nina Totenberg of NPR, Jess Bravin of The Wall Street Journal, and Ruthann Robson at the Constitutional Law Prof Blog.

Briefly:

  • At Reason.com, Damon Root discusses the cert. petition filed recently in Courtney v. Danner, a challenge to a Washington law that gives “de facto monopoly privileges to companies providing commercial ferry service.”
  • At Concurring Opinions, Ronald K.L. Collins (also of this blog) reports that Shaun McCutcheon, the plaintiff in the challenge to the federal limits on aggregate campaign contributions, plans to write a book, to be released shortly after the Court’s decision in his case.

In association with Bloomberg Law

28 Mar 12:56

Friday round-up

by Amy Howe
Tertiarymatt

In case you want to read more about Hobby Lobby's sham case before the court.

Commentary on the challenges to the Affordable Care Act’s contraception mandate continues to dominate Court-related news.  At Big Think, Steven Mazie discusses what he describes as the alliance of “strange bedfellows” supporting Hobby Lobby and Conestoga, the challengers in the case, while at Balkinization David Gans urges the Court to “recognize that the rights of Hobby Lobby’s thousands of employees – who have deeply held beliefs and convictions of their own – are at stake here, too.”  At First Things, Travis Weber urges the Court to strike down the mandate, arguing that it “puts the jobs, livelihoods, and healthcare of millions of Americans at risk by forcing those who stand up for their consciences to choose between paying crippling fines that could shut down their businesses or dropping the healthcare of their employees.” David Cortman echoes these arguments in an op-ed for The Washington Times, in which he writes that, “[i]f the government’s mandate is allowed to stand, people might be out of a job, have no insurance coverage and have less or no money to pay for these items should they choose to buy them.”  At The Volokh Conspiracy, Michael McConnell weighs in on some of the legal questions raised at Tuesday’s oral argument; he concludes by predicting that, in “the cold light of legal principle, the challenge to the contraceptive mandate will carry the day.”  And at Forbes, Trevor Burrus cautions that supporters of the mandate “who are opposing Hobby Lobby’s suit as an attempt to undercut women’s rights or as an attempt to let your boss choose your health care, should be thinking instead about the next big government mandate that could affect a business’s right of conscience that they actually care about.”

Briefly:

  • At Fortune, Roger Parloff previews next week’s oral arguments in Alice Corporation v. CLS Bank International, in which the Court will consider whether the Patent Act authorizes patents on software – more specifically, on computer-implemented inventions.   (Ronald Mann previewed the case for this blog earlier this month.)

In association with Bloomberg Law

28 Mar 19:09

Patent law’s deep questions and the government’s answers

by Eric Citron

Many lawyers come to the law for its deep philosophical questions—questions of morality, jurisprudence, and the public good.  These people usually think that patent law is exclusively for dorks, and that they should avoid it like the plague (in its generic, metaphorical sense—they aren’t really interested in the microbiology).  This is ironic, because patent law has a tendency to pose some of the hardest and most interesting philosophical questions the law has to offer:  What does it mean to invent a composition of matter or a new thing?  Where do we draw the line between the laws of nature and the application of those laws in some product of human ingenuity?  Think a computer is obviously a new and patentable machine?  (That’s got to be right.)  Well how will you deal with the fact that every piece of new software arguably makes it new again, capable of doing something no other machine has done before?  That thing the computer is doing may be very close to a patent-ineligible abstract idea or law of nature.  Should the software nonetheless be patent-eligible?  Always, often, sometimes, never?  This year’s intellectual property blockbuster, Alice Corp. v. CLS Bank International, poses some of these questions.

But while these are deep and interesting questions that lawyers should love to puzzle over, like many such ideas in science, they might be dangerous.  Intellectual property is hugely important to a number of the Nation’s biggest companies, is a massive economic driver in today’s economy, and poses a critical public policy issue about the balance between encouraging innovation and allowing for competition.  There is an abiding concern that questions about patent-eligibility posed at a high degree of generality represent a threat of unforeseen consequences to the very practical world of patent practice and product innovation.

The government’s position—set forth in its brief in Alice—is a study in the balancing act that the patent office and the courts often confront.  The government seems to view its take on software patent eligibility as a fairly narrow, middle-ground approach that scales down the deeply philosophical questions inevitably raised in cases like this.  For the government, this case is not about software patents so much as it is about business-method patents—which the government loosely defines throughout its brief as patents on “methods of organizing transactions and other human activities” or relationships.  These, the government says, are not eligible for patents because they are abstract ideas, not concrete inventions.  And furthermore, when you have such an abstract idea, you cannot make it concrete just by telling someone to do it on a computer.  Some software should be patent eligible, but at least not that.

This sets up a critical distinction for the government between two kinds of software inventions:  those that are patent eligible because they “disclose technological, scientific, or industrial innovations” and otherwise “improve the way computers function” (yay!); versus those that “are directed to organizing abstract concepts and relationships using a computer” (boo!).  Put otherwise, the government thinks you can get a patent on an idea for making computers more awesome, but you cannot necessarily patent your idea for making the world more awesome just because it uses a computer.

The government’s position is that this distinction tracks existing skepticism about business-method patents while still preserving a realm of “technical” innovation in computing that might seem intuitively patent-eligible.  The government even proposes a two-step approach where one first asks whether the core invention is a patent-ineligible abstract idea, and only considers the software application issues if that is so.  Accordingly, even some abstract ideas may be patent eligible as implemented through computer software, and conversely, software never loses its patent eligibility unless it at least embodies an abstract idea.  The hope seems to be that this position will preserve the ability of the patent office to work out a distinction between software that meaningfully moves forward the field of computing and software that merely takes a business method and turns it into ones and zeroes.

But without criticizing the government’s position at all—and indeed, while avoiding any comment on the merits of the case before the Supreme Court or what the Justices might do with it—it is worth saying that the government’s approach may turn out to be something of a greased-up watermelon: a thing that looks like it has real heft, but is almost impossible to firmly grasp.  Do programs that allow you to ask your computer natural language questions and get accurate answers (you may have met him or her) represent what the government calls “improvements in a computer’s operation as a computer,” or are they just computer-implemented embodiments of the world’s most common human interaction?  How about a computer that plays chess—a machine we have pursued since the famous hoax of the Mechanical Turk?  This all seems to trade on some deep, ontological account of what it means for a computer to function “as a computer,” which is just the kind of philosophical imponderable that makes these cases so hard, but also so much fun.

The reason this isn’t a criticism is that, as many scholars and judges have pointed out, every proposal for pinning down the distinction between patent-ineligible abstract ideas and patent-eligible innovations seems to slip out of your hands when you try to pick it up and work with it; the distinction between “technical” software innovations and software that simply implements an abstract idea may be the same.  The government has a “non-exhaustive list” of at least six factors you might consider in solving such puzzlers, but they do not seem easy to apply in any kind of mechanical way, and may be frustrating to the kinds of lawyers who like to respond to legal questions with answers rather than a new set of considerations.

For similar reasons, the government’s view of software patent eligibility may be more innocuous in name than it is in practice from the standpoint of existing patents (or not, or vice versa).  A lot would come to turn on a distinction that seems difficult to rigorously define ex ante.  Plain-English categorizations of alleged software inventions do not obviously fit into one or another of the proposed boxes:  For example, does a program that gets a computer to do something it has never done before make it function better “as a computer?”  (And while you are thinking about that, consider that your own intuitions about what makes a computer “a computer” might be largely a product of the software through which you have experienced its computational power.)  It is thus hard to know the exact zigs and zags even the government’s proposed course would cut through the existing software patent portfolios of the many companies watching this case with interest.  Perhaps the best that can be predicted is that, whatever comes of Alice, the patent office and the courts will end up drawing lines in practice with a lot of reflective equilibrium, much as they do now.

In association with Bloomberg Law

29 Mar 12:02

U.S. bypasses Korematsu plea (UPDATED)

by Lyle Denniston
Tertiarymatt

This sort of tickles my inner conspiracy theorist.

UPDATE:  Saturday 2:05 p.m.  The government’s new brief is now available and can be read here.

————

The Obama administration, urging the Supreme Court to turn aside a new challenge to presidential power to detain individuals suspected of terrorism links, chose not to support a years-long campaign to get the Court to repudiate one of its most heavily criticized opinions from the World War II era.

In a brief filed this week in Hedges v. Obama (docket 13-758), the U.S. Solicitor General’s office said nothing about the 1944 ruling in Korematsu v. United States – a decision that upheld the conviction of a Japanese American for refusing to go to a wartime detention camp.

In January, government lawyers had been urged to use their reply to the Hedges petition to try to persuade the Court either to overrule outright the Korematsu decision, or at least to tell the Court that the government did not regard that precedent as support for any current detention authority.

The brief, filed Wednesday, did neither, focusing its argument mainly on the point that the individuals who filed the challenge — journalists, authors and political activists — did not have a right to sue because they actually were not threatened with detention and thus could not claim legal injury.

The Hedges case, if granted review, would put before the Court a significant controversy over what Congress meant three years ago in spelling out anew the power of the president to order the capture and possible long-term confinement of potential terrorists.  The controversy centers on whether that added new authority, or simply reaffirmed the power Congress had given the president right after the terrorist attacks on the U.S. in 2001.

To compromise a dispute over whether a restatement of detention authority would extend it to U.S. citizens, Congress wrote into a military defense bill a statement that nothing in the bill “shall be construed to affect existing law or authorities relating to the detention of United States citizens, lawful residents of the United States, or any other persons who are captured or arrested in the United States.”

A federal judge in New York City temporarily barred enforcement of the law after finding that the challengers had a “realistic fear” that they might be detained.  The judge said the challengers were likely to win the case after a full trial, on the theory that it violated First Amendment free-speech rights.  The judge later issued a permanent order against enforcement “in any manner, as to any person.”

The government then appealed to the U.S. Court of Appeals for the Second Circuit, which overturned the judge’s order.  It did so, however, only on the premise that — as the government claimed — the challengers could not sue because they could not prove that they were genuinely at risk of being detained under the 2011 provision.

In the court of appeals, the children of Fred Korematsu and two other Japanese Americans who were convicted of violating the wartime curfew and imprisonment orders — Gordon Hirabayashi and Minoru Yasui — urged the three-judge panel to rule that no part of detention authority relied upon the Korematsu precedent.  (In 1984, four decades after that ruling, all three of those men had had their convictions overturned in a highly unusual federal court decision.)

The Second Circuit did not react to that plea, instead ruling that the challengers contesting the new detention power lacked “standing” to sue.

When the lawyers for the challengers filed their petition in the Supreme Court last December, they asked the Supreme Court to take the case.  They raised First Amendment issues and “standing” issues, as well as a plea for the Court to overrule the Korematsu decision, if it were found to be any part of the justification for detention.

On the basis of that overruling plea, private lawyers who had succeeded in getting the three men’s wartime convictions overturned wrote to Solicitor General Donald B. Verrilli, Jr., asking him to use the government’s response in the case to support overruling Korematsu.

Although a response to that plea was not a part of the brief filed Wednesday, Verrilli argued at length that the four individual challengers were not at any risk of being detained, that the 2011 provision did not add to presidential authority, and that the Justices should deny review on the basis of a lack of “standing” to make the challenge.

After the challengers’ lawyers have a chance to reply to the government’s brief, the Court will decide whether to grant or deny review.  That action may come sometime in April or May.

In association with Bloomberg Law

29 Mar 19:29

Tiny convention painting #2: Elsa from Frozen!

Tertiarymatt

The color version.



Tiny convention painting #2: Elsa from Frozen!

28 Mar 21:58

Tiny convention painting #1

Tertiarymatt

Teehee.



Tiny convention painting #1

28 Mar 07:19

angeliska: I had a conversation with my Dad tonight that...

Tertiarymatt

I was a big fan of the color kittens back in the day.



angeliska:

I had a conversation with my Dad tonight that reminded me of one my most favorite bedtime stories: The Color Kittens!

Man, I had forgotten all about the color kittens until this moment.

20 Mar 18:00

We Can Distinguish Between At Least A Trillion Smells

by Ed Yong
Tertiarymatt

Take-away from this: some people smell way better than others.

Guesses have a strange way of disguising themselves as facts, and taking root in popular knowledge. Consider the claim that the human nose can distinguish between 10,000 different smells. The statement crops up in all manner of websites, along with textbooks and scientific publications.

The figure came from a paper published in 1927, which suggested that people could tell the difference between odours according to four different qualities—fragrant, acidic, caprylic, and burnt—along a nine-point scale. That gives us 6,561 distinguishable smells, which was later rounded up to 10,000!

And that’s it.

There wasn’t any evidence for any of these assumptions, but that didn’t stop an uneducated guess from becoming enshrined as fact.

When Andreas Keller at Rockefeller University learned about this, he was dissatisfied. He wanted to come up with a better estimate—one rooted in actual experiments.

Similar estimates already exist for vision. We know that our eyes are sensitive to wavelengths of light between 390 and 700 nanometres—that is, from red to violet. By doing comparisons within that range, scientists have shown that we can tell the difference between 2.3 million and 7.5 million colours.

The same applies to sound. We can hear frequencies between 20 and 20,000 Hertz—from four octaves below middle C to many octaves above it. Within that range, we can discriminate between around 340,000 tones.

But colours and tones are easy to probe. Both vary along a single dimension: wavelengths of light and frequencies of sound, respectively. Smells don’t have an equivalent. They are complicated cocktails of molecules; a rose, for example, owes its scent to some 275 ingredients. There’s no single metric that we can measure these against; instead, we’re forced to describe them with subjective adjectives. And unlike light and sound, which we can perceive within certain boundaries, there is potentially no limit to the combinations of molecules that could make up an odour.

To estimate the bounds of our sense of smell, Keller had to get creative.

He gave volunteers three jars, two of which contained the same smell. Their job was to find the odd one out. The team made the smells from the same pool of 128 ingredients, which were mixed together in groups of 10, 20 or 30. They then paired these mixtures up so that some pairs had no ingredients in common, some were almost identical, and most were somewhere in between. Each volunteer sat through 260 of these discrimination tests.

After crunching the numbers, the team found that when the pairs of mixtures overlapped by less than 51 percent, most of the volunteers could tell the difference between them. And if they overlapped by less than 57 percent, most of them were distinguishable. This means that the average person can tell the difference between 1.7 trillion (that’s 1,700,000,000,000)different combinations of 30 ingredients.

“It’s one of those moments you live for as a scientist: reframing a problem and finding the solution out in left field,” says Avery Gilbert, a smell scientist who first tracked down the origins of the spurious 10,000 number.

The 1.7 trillion figure is an average. At least one person in the study had an exquisitely sensitive nose that could potentially discriminate between more than 10 million trillion trillion combinations of 30 ingredients. Another volunteer could only make out around 70 million of them.

There’s good reason for this variability. The genes that create smell receptors—the proteins that recognise the molecules we inhale—are the largest family of genes in our genome. They’re also more variable than other genes. “As a consequence, everybody smells the olfactory environment with a different set of receptors and therefore perceives it differently,” says Keller.

The 1.7 trillion figure is also a gross underestimate. “There are probably billions of odorous molecules and we only worked with 128 of them,” says Keller. “Furthermore, we only mixed 30 components. There are many more mixtures with 40 or 50 components.”

Still, a trillion smells is still many more than the number of colours or tones we can perceive. There’s good reason for that too. “Smell evolved to help us detect small differences between different smells: the smell of my baby compared to the smell of my neighbour’s baby, or the smell of fresh milk compared to the smell of spoiled milk,” says Keller. “There really is no need to discriminate trillions of smells, but there is a need to discriminate very similar smells. As a consequence, we can discriminate very many different smells.”

“The numbers are staggering yet not that surprising,” says Gilbert. “Smell is, above all, a combinatoric sense. There is a large but finite number of odorous molecules in the world and they occur in an endless array of mixtures and concentrations. Yet here we are, sniffing at them and making these incredibly fine discriminations on a daily basis. We handle the complexity pretty well.”

“If we couldn’t discriminate a trillion different mixtures where would we be?” he adds. “We’d know when to take the garbage out, but we wouldn’t be able to tell one vintage of Bordeaux from another. In fact, if we couldn’t discriminate millions of combinations we wouldn’t have bothered to create Bordeaux in the first place.”

Reference: Bushdid, Magnasco, Vosshall & Keller. 2014. Humans Can Discriminate More than 1 Trillion Olfactory Stimuli. Science http://dx.doi.org/10.1126/science.1249168

13 Mar 06:46

A Guide to Lonely Planets in the Galaxy

by Nadia Drake
Tertiarymatt

Stuff like this always shows up how science fiction falls often short at guessing about the universe.

Rogue planets are homeless worlds. They have neither sunrises nor sunsets, because unlike the planets we’re more familiar with, these lonely worlds aren’t tethered to a star. Instead, they travel in solitary arcs around the Milky Way’s core.

Earlier this week, Cosmos: A Spacetime Odyssey, introduced many of its viewers to the concept of these lonely planets.

“The galaxy has billions of them, adrift in perpetual night. They’re orphans, cast away from their mother stars during the chaotic birth of their native solar systems,” Neil DeGrasse Tyson says, as a planet emerges from the darkness. “Rogue planets are molten at the core, but frozen at the surface. There may be oceans of liquid water in the zone between those extremes. Who knows what might be swimming there?”

In the days that followed the show’s premiere, social media sites lit up with questions from viewers wondering what, exactly, these rogue worlds are — and could there really be billions of them, as Tyson said?

(The answer is yes. Probably.)

For decades, astronomers hypothesized that free-floating planets existed. But scientists needed a way to find them. The two most well-known ways of finding exoplanets rely on telltale signals coming from the planets’ stars – either wobbles caused by the gentle tugs of an orbiting planet’s gravity, or the slight dimming produced when a planet passes between Earth and its star.

So how do you find planets that have no stars?

For now, the best methods include looking for a young rogue’s heat in the infrared, and a technique called gravitational microlensing that works well for older, cooler planets, says astronomer David Bennett of the University of Notre Dame. Microlensing takes advantage of gravity’s ability to bend and mess with light. If a massive object – say, a rogue planet – passes between a star and Earth, the planet can act as a lens, curving and tweaking the star’s light as seen from Earth. In general, the more massive the planet, the more affected the light.

So far, using either method, we can’t easily detect starless planets that are smaller than a Jupiter, or at least 300 times the mass of Earth.

ESO/P. Delorme

Free-floating planet CFBDSIR 2149-0403 is the blue spot marked by crosshairs in the center of the infrared image. Click to enlarge. ESO/P. Delorme

Anyway, early observational hints of these untethered worlds turned up in the late 1990s, when a team of Japanese astronomers found evidence for warm, planetary mass objects in the Chamaeleon cluster, about 500 light-years away. Other teams soon reported more rogue candidates, in a cluster near the star sigma-Orionis, in the Orion nebula, in the Taurus star-forming region. More recently, in 2012, astronomers described a hot (700 degrees Celsius) homeless planet, clunkily named CFBDSIR2149-0403, just 100 light-years away.

Evidence for the “billions” parts of Tyson’s statement arrived in 2011. A microlensing study published in Nature suggested the Milky Way contains at least 400 billion star-less worlds, that the lonely planets are more common than stars like our sun. Data from two microlensing consortiums, known by the acronyms OGLE and MOA, pointed toward 10 possible free-floating planets, spotted over a two-year-long survey aimed toward the Milky Way’s galactic bulge.

Based on comparisons between the surveys’ detection efficiency, the probability of microlensing events, and the expected amount of lensing caused by planets and stars, the team concluded that these planetary lenses were everywhere. “There are statistical uncertainties in the analysis,” says Bennett, a member of the MOA consortium. “Four hundred billion planets is probably a good lower limit.”

But not everyone is convinced. Despite careful work by the authors, it’s still possible the objects detected are just very far from their stars, that they’re brown dwarfs (a type of low-mass pseudo-star that failed to ignite nuclear burning in its core), or that the galactic population estimates are off.

Since 2011, though, MOA has been hard at work analyzing larger data sets and refining estimates for how many free-floating planets populate the Milky Way. So far, Bennett says, new estimates appear to support the original finding that these rogue planets are really common. And, there are hints that we may soon be able to find smaller, untethered planets about the mass of Neptune – much too small to be mistaken for a failed star.

Southwest Research Institute

Artist’s conception of the solar system’s lost giant planet. Southwest Research Institute

Now, about those chaotic early years. Astronomers suspect that many free-floating planets are wandering through interstellar space because they’ve been kicked out of their home stellar systems. This process tends to happen early in a system’s history, says astrophysicist Greg Laughlin of the University of California, Santa Cruz. As planets in young systems settle into their orbits, their gravitational jostling can end up sending a sibling or two into space.

It’s possible that something like this happened in our solar system. Theories describing the early solar system don’t really work unless a fifth giant planet – another Uranus or Neptune – were present at the start (one of the problems with these models is that Earth sometimes ends up running into Venus, which we know didn’t happen). Later, as the planets begin to migrate, that fifth giant is kicked out of the solar system and sent flying into space.

Where it is now is anyone’s guess. “The damn thing could be half-way across the galaxy, for all we know,” says Konstantin Batygin, a post-doc at the Harvard-Smithsonian Center for Astrophysics.

Ok. What about the second part of Tyson’s quote? Could these worlds really have molten cores and subsurface oceans?

Perhaps surprisingly, the answer is yes. This part of the narrative echoes a paper published in 1999 by Caltech planetary scientist David Stevenson, who considered how Earth-mass planets cast from their solar systems might fare in outer space. Stevenson suggests that if these planets retained a hydrogen atmosphere, they could stay warm enough to have liquid water on their surface. A subsurface ocean could be present even without an atmosphere. And, larger planets are generally warmer than smaller planets, says Stevenson, who calculated that a cast-off Jupiter would only cool by about 15 Kelvin at its surface.

Let’s hope there are critters — preferably plesiosaurs or laser sharks — swimming in those rogue, subsurface seas.

 ESO/L. Calçada/P. Delorme/R. Saito/VVV Consortium

Artist’s representation of rogue planet CFBDSIR2149-0403. ESO/L. Calçada/P. Delorme/R. Saito/VVV Consortium

 

25 Mar 21:29

Birth control, business, and religious beliefs: In Plain English

by Amy Howe
Tertiarymatt

Blerg.

Almost two years ago to the day, the Supreme Court heard oral arguments in a challenge to the Affordable Care Act’s individual mandate, which requires virtually everyone in the United States to buy health insurance or pay a penalty.  This morning, it heard a new and different challenge arising out of the Affordable Care Act:  can a business be required to provide its female employees with health insurance that includes access to free birth control, even if doing so would violate the strong religious beliefs of the family that owns the business?  After the oral argument today, it looked like the Court’s answer may well be no, although the decision may not prove as sweeping as some of the challengers might prefer.  And as is so often the case, it looks like Justice Anthony Kennedy may hold the key vote in the case.  Let’s talk about the proceedings at the Court today in Plain English.

Justices Sotomayor, Ginsburg and Kagan (Art Lien)

Justices Sotomayor, Ginsburg and Kagan (Art Lien)

As Lyle explained in his preview of today’s oral arguments, the two cases at the Court today (which were treated as one ninety-minute argument) were filed by two deeply religious families and their family businesses:  the Green family owns the craft chain Hobby Lobby and the Christian bookstore chain Mardel; the Hahn family owns the cabinet company Conestoga Wood Specialties.  Regulations issued under the Affordable Care Act require the companies to provide their female employees with health insurance that includes no-cost access to twenty forms of birth control.  The families, however, object on religious grounds to providing four of those forms – two brands of the emergency “morning after” pill and two kinds of interuterine devices (IUDs) – that prevent embryos from implanting in a woman’s uterus.  Because they believe that human life begins at conception, the families therefore believe that if the corporations were to cover those four forms of birth control, they would in essence be “complicit in abortion.”

The families and the companies went to court, arguing that the “birth control” mandate violated the Religious Freedom Restoration Act (RFRA), a 1993 law that Congress enacted as a response to a 1990 Supreme Court decision holding that an individual’s religious beliefs do not excuse him from having to follow a law that applies to everyone – in that case, a state law prohibiting the use of the hallucinogenic drug peyote.  (The Court also agreed to review whether the mandate violated the Hahn family and Conestoga’s religious rights under the First Amendment, but there was very little discussion of that question today.)  Under RFRA, the government cannot impose a “substantial burden” on the exercise of religion unless that burden uses the narrowest possible way to promote a very important interest of the government.

Former Solicitor General Paul Clement argued first today, on behalf of the challengers to the mandate (collectively referred to as “Hobby Lobby”), and the initial battle lines were quickly drawn.  Three of the Court’s more liberal Justices focused on the potential scope of the rule that Clement and his clients were advocating.  If Hobby Lobby prevailed, Justice Sonia Sotomayor asked, could employers refuse to cover other medical procedures, like blood transfusions?  Or, Justice Elena Kagan added, what about vaccinations?  Clement responded that any procedure to which an employer objected on religious grounds could be reviewed under the RFRA “substantial burden” test.  Hobby Lobby’s case, he argued, was an easy one, he argued:  the fact that the government has excused other employers – such as churches, small businesses, and religious non-profit groups – from having to comply with the mandate demonstrates that the government’s interest in having Hobby Lobby comply with the mandate is not very significant.  By contrast, he noted, an employer who objected to providing coverage for vaccinations, he noted, might have a tougher time meeting the RFRA test because of the very strong government interest in having as many people as possible vaccinated to prevent the spread of disease.  That answer did not seem to satisfy Kagan, who lamented that, if every medical treatment to which someone objects must be evaluated on a case-by-case basis,” everything would be piecemeal, nothing would be uniform.”

(Art Lien)

(Art Lien)

Kagan then turned to the prospect that a decision in Hobby Lobby’s favor would have sweeping effects on RFRA even more broadly, raising a point to which both Justice Ruth Bader Ginsburg and she would return to several times.  RFRA, Kagan suggested, was an uncontroversial law when Congress – by an almost unanimous vote – enacted it. That overwhelming support for the law strongly implies, she contended, that Congress certainly did not expect the law to apply to for-profit corporations, allowing them to seek religious exemptions from, for example, laws governing the minimum wage, child labor, or family leave.  And even if, as Clement assured the Court, courts have not previously seen such claims by for-profit corporations, Kagan predicted that a ruling in Hobby Lobby’s favor would cause religious objectors to “come out of the woodwork.”

After spending a few minutes on questions from Sotomayor about how the mechanics by which a corporation exercises religion, the Justices then plunged into the nitty-gritty of Hobby Lobby’s options under the ACA and the mandate, focusing in particular on whether the company faced a “substantial burden” for exercising its religious beliefs.  Kagan and Sotomayor suggested that the company could choose not to provide insurance for its employees at all, which would subject it to a penalty of $2,000 per employee – which, Kagan speculated, is probably less than it would have to pay to provide insurance for an employee.   And if that’s the case, Kagan continued, where is the substantial burden?   This theory seemed to pique the interest of Justice Anthony Kennedy, who is often regarded as a key vote in high-profile cases.  Assuming hypothetically that the costs to the company are the same whether it provides its employees with health insurance or instead pays the penalty and compensates the employees so that they can buy their own insurance, Kennedy asked Clement, what would your case be?  Clement countered that Hobby Lobby would still face a burden because, if it didn’t provide its employees with insurance, it wouldn’t be able to attract workers.

(Art Lien)

(Art Lien)

If Paul Clement faced tough and persistent questions from Justices Kagan, Sotomayor, and Ginsburg, Solicitor General Don Verrilli found Chief Justice John Roberts and Justices Alito and Scalia to be difficult sells during his forty-five minutes at the lectern.  Verrilli emphasized several points.  The first was that, in determining whether an exemption is available under RFRA, courts must consider the effect that the exemption will have on others – here, Hobby Lobby’s female employees, for whom contraceptive coverage will not be available.  Significantly, that argument seemed to carry at least some weight with Justice Anthony Kennedy, who earlier in the argument had expressed concern that an employer’s religious beliefs could trump the rights of female employees.  But other Justices were skeptical, asking Verrilli to identify language in RFRA that would even allow courts to consider the interests of the female employees.

Verrilli also urged the Court to focus, in deciding whether Hobby Lobby is even entitled to bring a lawsuit under RFRA, on whether the company is a “person” that can “exercise religion.”  And it would be, he argued, a “vast expansion” of the law for the Court to hold that for-profit corporations can make claims for religious exemptions from generally applicable laws.  But the Chief Justice suggested that the Court’s holding might not necessarily be that broad:  the Court could limit its decision in this case to whether corporations like Hobby Lobby, Mardel, and Conestoga, which are owned entirely by one family, have to comply with the mandate, without deciding whether a larger, publicly owned company can object to a law or regulation on religious grounds.

Several Justices also expressed doubt about whether, even if a corporation can exercise religion for purposes of RFRA, the government has a compelling interest in requiring corporations like Hobby Lobby to provide insurance that includes access to free birth control or the mandate is the narrowest possible way to do so.  On the first point, the Justices emphasized that the government has, for a variety of reasons, declined to require other employers – including churches and religious non-profits but also for-profit companies whose health insurance plans are grandfathered in – to comply with the mandate, thereby undermining the government’s argument regarding the mandate’s importance.  And on the second, Justice Antonin Scalia suggested that it wouldn’t be “terribly expensive” for the government, rather than the employers, to pay for the four forms of birth control at issue in this case.

Justice Stephen Breyer, who is often regarded as the fourth member of the Court’s more liberal wing, asked relatively few questions today, and the questions that he did ask for the most part did not tip his hand.  But, although the government will almost certainly need Breyer’s vote to prevail, that won’t be enough; it will need a fifth Justice, presumably Justice Kennedy.  Although Kennedy’s other comments and questions had suggested that his vote might be in play, any optimism that the government may have harbored probably faded when, toward the end of Verrilli’s argument, Kennedy told Verrilli that, under the government’s view of the case, a for-profit corporation like Hobby Lobby could also be required to pay for insurance that would cover abortions.

Will Justice Kennedy – as it appeared today – provide the key vote, or will we get a June surprise the way we did two years ago, in the Court’s ruling on the individual mandate?  We likely won’t know anything more until June, but whenever we do, we will be back to cover the ruling in Plain English.

In association with Bloomberg Law

21 Mar 16:00

How Will Science Confirm Those Cosmic Signals From the Infant Universe?

by Nadia Drake
Tertiarymatt

Two things: One, I personally hope the BICEP2 results aren't confirmed, and two, it's incredible to me that shit we've got at the South Pole.

Announced on Monday, the detection of primordial gravitational waves – ripples in the fabric of the universe that tell us about the first trillionth of a trillionth of a trillionth of a second after the Big Bang – is already one of the biggest science discoveries of the year. In fact, it’s hard to think of something that can realistically top that.

That statement might sound a little hyperbolic, but it isn’t. Many cosmological ideas depend on the events in those very first, violent instants. Until now, we haven’t had much direct observational evidence pointing toward one theory or another.

“Most signs of what happened back then get obliterated,” says MIT physicist Frank Wilczek. “But gravitational waves interact so weakly with everything else that they propagate, they give us a record. What the team is seeing, or claims to be seeing, is the imprint of gravitational waves on the microwave background.”

A team using the BICEP2 detector at the South Pole found the waves’ imprints in the thermal radiation that’s left over from the Big Bang. Called the cosmic microwave background, this radiation forms the fabric that primordial gravitational waves press their fingerprints into, leaving swirly signatures that scientists call B-mode polarizations.

b_over_b_rect_BICEP2

Gravitational waves from inflation generate a faint but distinctive twisting pattern in the polarization of the CMB, known as a “curl” or B-mode pattern. (Harvard University)

These signatures are predicted by a theory known as cosmological inflation, proposed in 1980.

Inflation suggests that the universe we observe today – flat, smooth, relatively uniform – is the result of an unbelievably rapid and accelerating expansion that lasted for a fraction of a second after the Big Bang. Just how fast was it? Wilczek calculates that the acceleration of the expansion was somewhere in the neighborhood of 1048 centimeters/second2 – a number so big it’s basically impossible to comprehend. (Appropriately, inflation theory is connected to one of everyone’s favorite mind-boggling outcomes: The multiverse.)

The gravitational wave discovery has been described in news stories this week as “The Big One,” “a window back to almost the beginning of time,” “as big as it gets,” “worthy of a Nobel prize,” and “a grand slam.”

But along with those descriptions are qualifiers like “if the discovery is confirmed” and “if it is real” – statements that suggest caution is still needed.

That’s not because the data are shaky, necessarily, though there are some sticky spots that need clearing up. Among other things, three data points are sitting in a weird place and contamination by other sources of polarization cannot yet be definitively ruled out.

“The quality of the observing team is widely known to be excellent,” says Matt Strassler, a physicist at Harvard University. “But there are enough little funny things in the data, so I’d feel a lot better when a second independent team sees the same [signal] that BICEP2 sees where they are supposed to see it, and not the same funny things in the data which shouldn’t be there if the interpretation as gravitational waves is right.”

One of the principles of empirical science is that an experiment or an observation must be repeatable. You must be able to replicate a result. Too often, though, nobody bothers to independently verify another team’s science (there are some notable exceptions, like this one); in this case, I think we’ll see a number of teams looking to replicate the BICEP2 observations, and quickly. Here, scientists will be working to rule out other sources of B-mode polarizations, verify the signal in other patches of sky, and see if it’s observable on more than one microwave frequency.

“The result can be checked within the next year or two, in a number of ways,” says Neil Turok, director of the Perimeter Institute for Theoretical Physics, noting one significant caveat to the discovery. “It is very important to check that the B-mode signal is not contaminated by — or entirely due to — radiation from dust or particles in our galaxy.”

734356main_PIA13953

Artist’s concept of the Planck satellite. (ESA/NASA/JPL-Caltech)

Turok and others suggest that the Planck space observatory, launched in 2009 and tasked with mapping the cosmic microwave background, could help clear this up. Gravitational waves aren’t the only astrophysical phenomena that can produce B-mode polarizations in the observed background; others include atmospheric distortions, synchrotron radiation, and galactic dust.

Unlike BICEP2, Planck is in space, which means it has less to contend with in terms of Earth’s atmosphere mucking up observations of the microwave background. Planck also studies a larger patch of sky, and has collected a pile of data about polarization caused by dust and galactic foreground radiation. Those observations will be crucial for ruling out these other sources of B-mode signals. Now, the Planck team is analyzing its polarization data and preparing a release for later this year. “Planck should be able to confirm or refute this result,” says physicist Paul Steinhardt of Princeton University.

Mark Kamionkowski, a theoretical physicist at Johns Hopkins University, notes that while Planck could be helpful, it wasn’t designed specifically to look for B-mode polarization in the cosmic microwave background. As a result, he says, there are some tricky instrumental effects that will need to be accounted for.

Instead, Kamionkowski points to a handful of experiments that are designed specifically to look for gravitational wave signatures. Among these are SPIDER and EBEX, which both rely on balloon-borne detectors, launched into the south polar atmospheric vortex from McMurdo Station in Antarctica. For several weeks near the height of southern summer, the Antarctic sky hosts a cadre of enormous science balloons; these two will be looking specifically for the curled imprints of gravitational waves (others study such things as cosmic rays).

But SPIDER, EBEX, and BICEP are not alone at the South Pole. There’s also the South Pole Telescope, right next door to BICEP at Amundsen-Scott South Pole Station. Last summer, the team running an experiment there called SPTPol announced the detection of a different kind of cosmic gravitational signature, known as lensing. Now, the telescope is searching for primordial B-modes, although in a slightly different way than BICEP.

“I am not entirely sure, but there is a good chance that the B-mode signal could be detected in SPTPol in cross-correlation with BICEP2,” Kamionkowski said. “I hope that the SPTPol and BICEP2 people can get together to look into this ASAP.”

The BICEP2 telescope's focal plane consisting of an array of 512 superconducting bolometers, designed to operate at 0.25 K (0.25 degrees Celsius above absolute zero) in order to reduce thermal noise in the detectors. (Anthony Turner, JPL)

The BICEP2 telescope’s focal plane consisting of an array of 512 superconducting bolometers, designed to operate at 0.25 K (0.25 degrees Celsius above absolute zero) in order to reduce thermal noise in the detectors. (Anthony Turner, JPL)

Also at the South Pole is BICEP2’s successor, called the Keck Array. The array is more sensitive than BICEP2 – it has 2,560 detectors in it, compared to BICEP2’s 512 detectors. It also studies the sky at a different frequency (100GHz) than BICEP2 (150GHz), and will be looking to confirm the presence of gravitational wave signatures at the second frequency.

At slightly less southerly latitudes, in the Chilean Atacama, a cluster of other experiments are ready to peer closely at the cosmic microwave background. Here, ACTPol, CLASS, ABS, and POLARBEAR take advantage of the bone-dry sky to stare at radiation from the beginning of time.

Just last week, POLARBEAR released the first direct detection of B-modes due to gravitational lensing, a different kind of distortion in the background radiation that’s caused by structure (things like galaxies and clumps of dark matter) in the universe.

“We were focused on the lensing because we knew that signal was there. We wanted to see it and prove our instrument was working well,” says observational cosmologist Adrian Lee of the University of California, Berkeley. Now, the team is gearing up to study gravitational wave B-modes.

“POLARBEAR is going to be looking for this signal,” Lee says. “We’re really motivated to try and confirm the results they’re seeing.”

How long will it be until we know whether BICEP2’s data can be confirmed? It’s hard to say. Estimates range from a few weeks to a few years. Until those data come down, physicists will remain what Strassler describes as cautiously optimistic.

“We will look for confirmation from all of these experiments,” Kamionkowski says.

The Dark Sector Lab (DSL), located 3/4 of a mile from the Geographic South Pole, houses the BICEP2 telescope (left) and the South Pole Telescope (right). (Steffen Richter, Harvard University)

The Dark Sector Lab (DSL), located 3/4 of a mile from the Geographic South Pole, houses the BICEP2 telescope (left) and the South Pole Telescope (right). (Steffen Richter, Harvard University)

17 Mar 19:00

How to Turn Gut Bacteria Into Journalists

by Ed Yong
Tertiarymatt

#biopunk

The gut is a dark and hidden world. We usually only know what’s happening within it when something goes badly wrong. But there are trillions of microbes in our guts; with their first-hand experience, they’re perfectly positioned to tell us about what’s going on inside ourselves. Pamela Silver from Harvard Medical School is now training them to do that. Her team is transforming gut bacteria into journalists—microscopic reporters who cover the bowel beat.

So far, they have loaded E.coli—a common gut microbe—with a genetic circuit that allows it to detect and remember the presence of an antibiotic. These engineered bacteria can colonise the guts of mice to no ill effect. If the mice get the antibiotic in their diet, the bacteria all flip to a different state, which the team could assess by analysing the rodents’ poo.

It’s a simple proof-of-principle, and detecting an antibiotic isn’t massively useful. But the study lays the groundwork for more exciting applications, which the team are already starting to pursue. Imagine microbial reporters that can spot the chemical signatures of inflammation, disease-causing bacteria, or environmental toxins.

The project is part of the growing field of synthetic biology. Its practitioners bring the ethos of engineering into the world of living things, by combining different genetic “parts” or “modules” to create organisms with new abilities. Many of the initial successes were cute demos, like photographic bacteria, but the field is now moving towards more serious applications, like yeast that can brew antimalarial drugs, cells that self-destruct if they turn cancerous, or bacteria that make plant roots grow longer. “We’re tired of making toy systems that don’t necessarily have an application,” says Silver.

To create her reporter bacteria, Silver teamed up with two partners—Jeffrey Way at Harvard’s Wyss Institute, and a virus called lambda. Lambda is a bacteriophage—a virus that infects bacteria. Its life cycle has two stages—one where it actively reproduces and kills its host, and another where it wheedles its way into its host’s genome and sits there, dormant and harmless.

It flips between these two states using a genetic switch involving two genes—cI and cro—which mutually block each other. If cI wins this battle and Cro is inactive, the phage opts for the dormant, hidden lifestyle. If Cro wins and cI is inactive, the phage goes for the more lethal route. Environmental influences, like hunger or radiation, can change the balance between the two genes, flipping the phage from one lifestyle to another.

The lambda switch was perfect for Silver and Way’s needs—it provided a way of changing between two states, depending on an outside signal. It also came with two huge advantages.

First, in the 1970s and 80s, scientists like Mark Ptashne unpicked exactly how switch works at the most intimate level; Silver once worked in Ptashne’s lab, and Way was in a lab next door. “We understood it in a level of detail that you can’t get from a textbook,” he says.

Second, the lambda switch never fails. A cell is a chaotic environment, and genes get switched on by accident all the time. But that would be disastrous for lambda—if it flips from dormancy to active killing at the wrong moment, it risks going down with its host. So natural selection has fashioned a switch that goes all-or-nothing in two possible directions, and is extraordinarily stable. It just doesn’t flip by accident. “I’d challenge you to find a human-designed circuit that works that well,” says Silver.

The team took the switch out of the lambda genome and implanted it into E.coli. They tweaked it so that it starts in the cI state, and stably flips to the Cro state in response to an antibiotic called tetracycline. In the Cro state, the bacteria switch on another gene that turns them blue if they’re grown in the right conditions. The upshot: if you grow these bacteria in the lab, their colour will tell you if they’ve seen tetracycline. They detect, they remember, and they report.

At first, team members Jonathan Kotula and Jordan Kerns tested this modified switch in laboratory strain of E.coli. But eventually, they showed that it also works in a wild one that actually lives in mouse guts. When they fed this strain to the mice, it established itself nicely and behaved exactly as the team wanted. Both phases are important—the team need to be able to test future genetic circuits in lab-reared microbes that won’t cause problems for natural ones, but that will eventually work in natural strains once they have been perfected.

Chris Voigt from MIT is impressed, especially because the circuit “worked so robustly in the messy gut of a mouse”. Many synthetic biologists have tried to programme cells with specific genetic circuits, and while these often work in the lab, they fail in real environments. “This is one of the few examples—if not the only one—of a circuit working out of a test tube or fermenter,” says Voigt.

Silver and Way are now hard at work on their next applications, all of which use the lambda switch at their core. Their ultimate vision is to engineer bacteria that will not only detect changes in the gut but also respond to them. Imagine a strain that detects the early signs of inflammation and makes an anti-inflammatory drug, or that sense a harmful species of microbe and makes an antibiotic. They would be journalists and doctors.

“We know it’ll work,” says Silver. “We already have some preliminary data. Once we know the fundamentals of this device, we can keep on tweaking it, putting in downstream things like therapeutics or upstream thing like sensors.”

These applications may take many years to realise; for now, the team’s work is already a testament to the value of basic science. Back in the 1970s and 1980s, none of the scientists who were studying phages would ever have guessed that their work could be used in this way.

Even Way wasn’t convinced. “There were a huge amount of picky details that seemed like they could never possibly be relevant, or weren’t necessary for demystifying life,” he says. “But those picky details have been really useful in doing this engineering. The textbook level isn’t good enough, which is why a lot of attempts at synthetic biology fail, or create non-robust systems.” Nature makes things look simple, but to emulate it, we need to understand its details.

Reference: Kotula, Kerns, Shaket, Siraj, Collins, Way & Silver. 2014. Programmable bacteria detect and record an environmental signal in the mammalian gut. PNAS http://dx.doi.org/10.1073/pnas.1321321111

More on synthetic biology: Can We Save the World by Remixing Life?

26 Mar 18:01

The Humble Heroes of Weight-Loss Surgery: Stomach Acids and Gut Microbes

by Virginia Hughes
Tertiarymatt

This is a really weird effect. There's such an enormous volume of stuff we don't know about how the body works.

Update, 3/31: Today Schauer’s group released an updated study of the STAMPEDE bariatric surgery clinical trial results three years out. Participants who underwent surgery not only had near-normal levels of blood glucose after three years, but also reported higher quality-of-life scores compared with people who did not get surgery. 

*

If you heard of a treatment that effectively cured 40 percent of people with a devastating common disease — cancer, say, or Alzheimer’s — that would be front-page news, right? People would be gathering around water coolers across the world to gush about the progress of medical science.

We actually do have one such success story, though most people don’t think of it in such glowing terms: weight-loss surgery. A clinical trial published in 2012 studied obese people with diabetes after receiving either intensive medical therapy (which included lifestyle coaching, home glucose monitoring, diabetes medications, and a push to join Weight Watchers) or intensive medical therapy and weight-loss surgery. About 40 percent of those who got the surgery no longer had diabetes a year later, compared with 12 percent who had medical therapy alone. The vast majority of people who had surgery stopped taking their diabetes medications altogether. And the surgery group lost around 25 percent of their weight, whereas the medical therapy group lost just 5 percent.

When the study came out, “it did shake up the conventional thinking about diabetes, because it showed you can’t achieve these outcomes with drugs,” says Philip Schauer, director of the Bariatric and Metabolic Institute at the Cleveland Clinic, who led that trial.

And yet, despite the dramatic, scientifically supported advantages of bariatric surgery, relatively few obese patients have an operation. Around 200,000 bariatric surgeries are performed each year in the U.S., which Schauer (who’s a surgeon) points out is only about 1 percent of the 20 million Americans with severe obesity. “Surgery is definitely underutilized,” he says.

There are many reasons for this. Like all surgeries, this one comes with medical risks (about 1 in 300 patients die, and others get blood clots, gastrointestinal leaks, or bowel blockages). It’s no more risky than gallbladder or appendix surgery, but many patients and doctors perceive it to be worse, according to Schauer. Another hurdle is financial: The surgery costs up to $25,000, and about half of all insurance policies don’t cover it. Of the policies that do, many require patients to jump through hoops — such as first going on a nine-month, medically supervised diet — in order to qualify.

Even if there were no risks and no insurance barriers, bariatric surgery is probably not a practical solution for the escalating public-health problem of diabetes. Take one city: Cincinnati, Ohio. “According to our projections, by 2025 one-quarter of the population of Cincinnati will have type-2 diabetes,” says Randy Seeley, a neuroscientist at the University of Cincinnati and the director of the Cincinnati Diabetes and Obesity Center. Even if every diabetic who qualified for weight-loss surgery wanted to get it, “we don’t have enough surgeons and surgery tables.”

In today’s issue of Nature, Seeley and his colleagues have published a mouse study suggesting that, one day, doctors might be able to mimic the beneficial effects of surgery without actually doing the surgery.

That premise will seem crazy to most surgeons, and that’s because the conventional explanation for bariatric surgery’s effectiveness is mechanical. In the two most common procedures (known as Roux-en-Y gastric bypass, and vertical sleeve gastrectomy, or VSG), surgeons make the stomach drastically smaller:


“The common-wisdom explanation is that this is the intestinal equivalent of wiring your jaw shut,” Seeley says. That is: With a much smaller stomach, patients simply can’t absorb as many calories, so they lose weight and the weight-loss cures their diabetes. But Seeley doesn’t think this explanation makes sense. “It’s bologna,” he says.

He points out that, anecdotally, patients don’t feel as hungry after surgery as they used to. What’s more, within days of surgery — long before any substantial weight loss has occurred — many patients show such improvement in blood glucose levels that they can stop taking diabetes medications. All of this suggests that surgery changes not just the structure of the stomach, but its biochemistry.

Older studies have shown, in both humans and mouse models, that these surgeries increase the level of circulating bile acids — fluids made by the liver that help break down fats. Nobody knows why bile acids go up after surgery, but Seeley’s study suggests that they play a key role in its beneficial effects.

In addition to breaking down fats, bile acids are hormones, or signaling molecules that bind to receptors in cells all over the gut, including one called the farsenoid-X receptor, or FXR.

To see whether bariatric surgery influenced FXR activity, Seeley’s group overfed two types of mice: normal animals, and those genetically engineered to lack the FXR gene. After ballooning in size, both types of obese mice underwent VSG surgery.

One week after surgery, both types of mice dropped a ton of weight compared with controls that had had a sham surgery. The normal mice sustained most of that weight loss for the duration of the experiment, about 14 weeks. In contrast, the animals lacking the FXR gene gained the weight back by the fifth week.

In other words, the mice lacking FXR went through the same mechanical changes as the others — their stomachs shrunk in exactly the same way — and yet didn’t benefit from weight-loss surgery.

“It’s really superb science,” Schauer says, though it’s far too early to know whether the same thing is happening in people. Nevertheless, it’s an important study because it suggests that drug therapies might one day be designed to mimic these changes in FXR and possibly replace surgery altogether, he says. “Even as a surgeon, I would say, yeah, that would be a big advance.”

It probably won’t be as simple as turning up the FXR dial, though. FXR is a complicated gene whose activity changes depending on tissue type and environmental circumstances. For example, mice lacking FXR are actually resistant to getting obese in the first place. FXR codes for a transcription factor, a protein that itself regulates dozens of other genes. “It’s doing lots of different things in different tissues,” Seeley says. “One of the things we don’t know is, which population of FXR matters?”

To add yet another level of complexity, the gene also has a big influence on gut bacteria. Seeley’s study found several bacterial strains that change in response to surgery in the normal animals but not in those lacking FXR. A strain called Roseburia, for example, went up 12-fold in normal mice after surgery but did not change in the mutants. This is provocative because two studies have shown that people with type-2 diabetes carry abnormally low levels of this bug in their guts. And this is just one of many other recent reports linking gut microbes to obesity and diabetes. A study published a year ago showed that in mice, gastric bypass surgery changes the microbial make-up of the gut, and that this shift might explain the animals’ subsequent weight loss. “We’re starting to see a picture emerge,” Seeley says.

Seeley is a lab rat; he’s not a surgeon and not a doctor. So I was surprised to hear him passionately riff on the overwhelming benefits of weight-loss surgery, and bemoan our stubborn cultural stigma against obese people. “People tend to think of surgery as a tool to help people’s compliance, and that’s a problem,” he says. In his view, surgery is not about physically preventing obese people from eating more. It’s about fundamentally changing their metabolism so that they no longer need to eat more.

And why, I asked him, is the average Joe so resistant to this idea?

“Lean people want to take credit for being lean. They want to say it’s because I control my environment, I don’t go to McDonald’s, I work out,” he says. “But you can’t say that and not blame the obese individual for being obese.”

This is, in my opinion, a tragedy. As I’ve written about before, an overwhelming amount of evidence now suggests that obesity has little to do with willpower. More than a decade ago, researchers at 16 clinics in the United States enrolled thousands of overweight and obese people with diabetes on a strict weight-loss regimen that focused on diet and exercise. As published last year, this intensive, long-term intervention did very little in terms of weight loss, and had no effect on death rates from heart disease.

Sometimes, Seeley says, he wishes he were a cancer researcher. When cancer researchers tell their seat neighbor on an airplane what they study, “they don’t have to hear that person’s personal hypothesis of the cell cycle,” he says. But with obesity, everybody’s got a story. “We all have a highly embedded idea of this in our own heads,” he says. “So it’s tricky to have a discussion about it as a biomedical issue.”

25 Mar 15:33

Can We Beat Drug-Resistant Malaria At Its Birthplace?

by Ed Yong
Tertiarymatt

Long, but really quite good piece on the on-going war against malaria in Southeast Asia.

In the war against malaria, one small corner of the globe has repeatedly turned the tide, rendering our best weapons moot and medicine on the brink of defeat. I travelled to Thailand and Burma to meet the scientists who are trying to eliminate resistant malaria before it defeats our best remaining drug. This story originally appeared in Mosaic and is republished under a CC-BY 4.0 licence.  

The meandering Moei river marks the natural boundary between Thailand and Myanmar. Its muddy waters are at their fullest, but François Nosten still crosses them in just a minute, aboard a narrow, wooden boat. In the dry season, he could wade across. As he steps onto the western riverbank, in Myanmar, he passes no checkpoint and presents no passport.

The air is cool. After months of rain, the surrounding jungle pops with vivid lime and emerald hues. Nosten climbs a set of wooden slats that wind away from the bank, up a muddy slope. His pace, as ever, seems relaxed and out of kilter with his almost permanently grave expression and urgent purpose. Nosten, a rangy Frenchman with tousled brown hair and glasses, is one of the world’s leading experts on malaria. He is here to avert a looming disaster. At the top of the slope, he reaches a small village of simple wooden buildings with tin and thatch roofs. This is Hka Naw Tah, home to around 400 people and a testing ground for Nosten’s bold plan to completely stamp out malaria from this critical corner of the world.

Malaria is the work of the single-celled Plasmodium parasites, and Plasmodium falciparum chief among them. They spread between people through the bites of mosquitoes, invading first the liver, then the red blood cells. The first symptoms are generic and flu-like: fever, headache, sweats and chills, vomiting. At that point, the immune system usually curtails the infection. But if the parasites spread to the kidneys, lungs and brain, things go downhill quickly. Organs start failing. Infected red blood cells clog the brain’s blood vessels, depriving it of oxygen and leading to seizures, unconsciousness and death.

When Nosten first arrived in South-east Asia almost 30 years ago, malaria was the biggest killer in the region. Artemisinin changed everything. Spectacularly fast and effective, the drug arrived on the scene in 1994, when options for treating malaria were running out. Since then, “cases have just gone down, down, down,” says Nosten. “I’ve never seen so few in the rainy season – a few hundred this year compared to tens of thousands before.”

But he has no time for celebration. Artemisinin used to clear P. falciparum in a day; now, it can take several. The parasite has started to become resistant. The wonder drug is failing. It is the latest reprise of a decades-long theme: we attack malaria with a new drug, it mounts an evolutionary riposte.

Back in his office, Nosten pulls up a map showing the current whereabouts of the resistant parasites. Three coloured bands highlight the borders between Cambodia and Vietnam, Cambodia and Thailand, and Thailand and Myanmar (Burma). Borders. Bold lines on maps, but invisible in reality. A river that can be crossed in a rickety boat is no barrier to a parasite that rides in the salivary glands of mosquitoes or the red blood cells of humans.

History tells us what happens next. Over the last century, almost every frontline antimalarial drug – chloroquine, sulfadoxine, pyrimethamine – has become obsolete because of defiant parasites that emerged from western Cambodia. From this cradle of resistance, the parasites gradually spread west to Africa, causing the deaths of millions. Malaria already kills around 660,000 people every year, and most of them are African kids. If artemisinin resistance reached that continent, it would be catastrophic, especially since there are no good replacement drugs on the immediate horizon.

Nosten thinks that without radical measures, resistance will spread to India and Bangladesh. Once that happens, it will be too late. Those countries are too big, too populous, too uneven in their health services to even dream about containing the resistant parasites. Once there, they will inevitably spread further. He thinks it will happen in three years, maybe four. “Look at the speed of change on this border. It’s exponential. It’s not going to take 10 or 15 years to reach Bangladesh. It’ll take just a few. We have to do something before it’s too late.”

Hundreds of scientists are developing innovative new ways of dealing with malaria, from potential vaccines to new drugs, genetically modified mosquitoes to lethal fungi. As Nosten sees it, none of these will be ready in time. The only way of stopping artemisinin resistance, he says, is to completely remove malaria from its cradle of resistance. “If you want to eliminate artemisinin resistance, you have to eliminate malaria,” says Nosten. Not control it, not contain it. Eliminate it.

That makes the Moei river more than a border between nations. It’s Stalingrad. It’s Thermopylae. It’s the last chance for halting the creeping obsolescence of our best remaining drug. What happens here will decide the fate of millions.

The world tried to eliminate malaria 60 years ago. Malaria was a global affliction back then, infecting hundreds of thousands of troops during World War II. This helped motivate a swell of postwar research. To fight the disease, in 1946 the USA created what is now the Centers for Disease Control and Prevention (CDC), the country’s premier public health institute. After a decisive national eradication programme, the nation became malaria-free in 1951. Brazil had also controlled a burgeoning malaria epidemic with insecticides.

Meanwhile, new weapons had emerged. The long-lasting insecticide DDT was already being widely used and killed mosquitoes easily. A new drug called chloroquine did the same to Plasmodium. Armed with these tools and buoyed by earlier successes, the World Health Organization formally launched the Global Malaria Eradication Programme in 1955. DDT was sprayed in countless homes. Chloroquine was even added to table salt in some countries. It was as ambitious a public health initiative as has ever been attempted.

It worked to a point. Malaria fell dramatically in Taiwan, Sri Lanka, India, the Caribbean, the Balkans, and parts of the south Pacific. But ultimately the problem was too big, the plan too ambitious. It barely made a dent in sub-Saharan Africa, where public health infrastructure was poor and malaria was most prevalent. And its twin pillars soon crumbled as P. falciparum evolved resistance to chloroquine and mosquitoes evolved resistance to DDT. The disease bounced back across much of Asia and the western Pacific.

In 1969, the eradication programme was finally abandoned. Despite several successes, its overall failure had a chilling impact on malaria research. Investments from richer (and now unaffected) countries dwindled, save for a spike of interest during the Vietnam War. The best minds in the field left for fresher challenges. Malaria, now a tropical disease of poor people, became unfashionable.

§

 

François Nosten always wanted to travel. His father, a sailor on merchant ships, returned home with stories of far-flung adventures and instilled a deep wanderlust. Nosten’s original plan was to work on overseas development projects, but one of his teachers pushed him down a different path. “He said the best thing you can do if you want to travel anywhere is to be a doctor. That’s why I started medical school.” As soon as he graduated, he joined Médecins Sans Frontières and started living the dream. He flew off to Africa and South-east Asia, before arriving in Thailand in 1983. There, he started treating refugees from Myanmar in camps along the Thai border.

In 1985, an English visitor arrived at the camps and Nosten took him for a random tourist until he started asking insightful questions about malaria. That man was Nick White. A British clinician, he was drawn to Bangkok in 1980 by the allure of the tropics and a perverse desire to study something unfashionable. The University of Oxford had just set up a new tropical medicine research unit in collaboration with Bangkok’s Mahidol University, and White was the third to join.

“The rosbif and the frog”, as Nosten puts it, bonded over an interest in malaria, a desire to knuckle down and get things done, and a similar grouchy conviviality. They formed a close friendship and started working together.

In 1986, they set up a field station for White’s Bangkok research unit: little more than a centrifuge and microscope within Nosten’s rickety house. Three years later, Nosten moved to Shoklo, the largest refugee camp along the Thai–Myanmar border and home to around 9,000 people. Most were Karen – the third largest of Myanmar’s 130 or so ethnic groups – who were fleeing persecution from the majority Bamar government. Nosten worked out of a bamboo hospital – the first Shoklo Malaria Research Unit.

Malaria was rife. Floods were regular. Military leaders from both Thailand and Myanmar occasionally ordered Nosten to leave. Without any electricity, he often had to use a mirror to angle sunlight into his microscope. He loved it. “I’m not a city person,” he says. “I couldn’t survive in Bangkok very well. I wasn’t alone in Shoklo but it was sufficiently remote.” The immediacy of the job and the lack of bureaucracy also appealed. He could try out new treatments and see their impact right away. He trained local people to detect Plasmodium under a microscope and help with research. He even met his future wife – a Karen teacher named Colley Paw, who is now one of his right-hand researchers (White was the best man at their wedding). These were the best years of his life.

The Shoklo years ended in 1995 after a splinter faction of Karen started regularly attacking the camps, in a bid to force the refugees back into Myanmar. “They came in and started shooting,” says Nosten. “We once had to hide in a hole for the night, with bullets flying around.” The Thai military, unable to defend the scattered camps, consolidated them into a single site called Mae La – a dense lattice of thatch-roofed houses built on stilts, which now contains almost 50,000 people. Nosten went with them.

He has since expanded the Shoklo Unit into a huge hand that stretches across the region. Its palm is a central laboratory in the town of Mae Sot, where Nosten lives, and the fingers are clinics situated in border settlements, each with trained personnel and sophisticated facilities. The one in Mae La has a $250,000 neonatal care machine, and can cope with everything short of major surgery. Nosten has also set up small ‘malaria posts’ along the border. These are typically just volunteer farmers with a box of diagnostic tests and medicine in their house.

“I don’t know anybody else who could have done what François has done,” says White. “He’ll underplay the difficulties but between the physical dangers, politics, logistical nightmares, and the fraught conditions of the refugees, it’s not been easy. He’s not a shrinking violet.”

Thanks to Nosten’s network, locals know where to go if they feel unwell, and they are never far from treatments. That is vital. If infected people are treated within 48 hours of their first symptoms, their parasites die before they get a chance to enter another mosquito and the cycle of malaria breaks. “You deploy early identification and treatment, and malaria goes away,” says Nosten. “Everywhere we’ve done this, it’s worked.”

*****

Victories in malaria are often short-lived. When Nosten and White teamed up in the 1980s, their first success was showing that a new drug called mefloquine was excellent at curing malaria, and at preventing it in pregnant women. Most drugs had fallen to resistant parasites and the last effective one – quinine – involved a week of nasty side-effects. Mefloquine was a godsend.

But within five years, P. falciparum had started to resist it too. “We tried different things like increasing the dose, but we were clearly losing the drug,” says Nosten. “We saw more and more treatment failures, patients coming back weeks later with the same malaria. We were really worried that we wouldn’t have any more options.”

Salvation came from China. In 1967, Chairman Mao Zedong launched a covert military initiative to discover new antimalarial drugs, partly to help his North Vietnamese allies, who were losing troops to the disease. It was called Project 523. A team of some 600 scientists scoured 200 herbs used in traditional Chinese medicine for possible antimalarial chemicals. They found a clear winner in 1971 – a common herb called qing hao (Artemisia annua or sweet wormwood). Using hints from a 2,000-year-old recipe for treating haemorrhoids, they isolated the herb’s active ingredient, characterised it, tested it in humans and animals, and created synthetic versions. “This was in the aftermath of the Cultural Revolution,” says White. “Society had been ripped apart, there was still a lot of oppression, and facilities were poor. But they did some extremely good chemistry.”

The results were miraculous. The new drug annihilated even severe forms of chloroquine-resistant malaria, and did so with unparalleled speed and no side-effects. The team named it Qinghaosu. The West would know it as artemisinin. Or, at least, they would when they found out about it.

Project 523 was shrouded in secrecy, and few results were published. Qinghaosu was already being widely used in China and Vietnam when the first English description appeared in the Chinese Medical Journal in 1979. Western scientists, suspicious about Chinese journals and traditional medicine, greeted it with scepticism and wasted time trying to develop their own less effective versions. The Chinese, meanwhile, were reluctant to share their new drug with Cold War enemies.

During this political stalemate, White saw a tattered copy of the 1979 paper. He travelled to China in 1981, and returned with a vial of the drug, which he still keeps in a drawer in his office. He and Nosten began studying it, working out the right doses, and testing the various derivatives.

They realised that artemisinin’s only shortcoming was a lack of stamina. People clear it so quickly from their bodies that they need seven daily doses to completely cure themselves. Few complete the full course. White’s ingenious solution was to pair the new drug with mefloquine – a slower-acting but longer-lasting partner. Artemisinin would land a brutal shock-and-awe strike that destroyed the majority of parasites, mefloquine would mop up the survivors. If any parasites resisted the artemisinin assault, mefloquine would finish them off. Plasmodium would need to resist both drugs to survive the double whammy, and White deemed that unlikely. Just three days of this artemisinin combination therapy (ACT) was enough to treat virtually every case of malaria. In theory, ACTs should have been resistance-proof.

Nosten started using them along the Thai–Myanmar border in 1994 and immediately saw results. Quinine took days to clear the parasites and left people bed-ridden for a week with dizzy spells. ACTs had them returning to work after 24 hours.

But victories in malaria are often short-lived. In the early 2000s, the team started hearing rumours from western Cambodia that ACTs were becoming less effective. White tried to stay calm. He had heard plenty of false alarms about incurable Cambodian patients, but it always turned out that they were taking counterfeit drugs. “I was just hoping it was another of those,” he says.

It was not. In 2006, Harald Noedl from the Medical University of Vienna started checking out the rumours for himself. In the Cambodian village of Ta Sanh, he treated 60 malaria patients with artesunate (an artemisinin derivative) and found that two of them carried exceptionally stubborn parasites. These infections cleared in four to six days, rather than the usual two. And even though the patients stayed in a clinic outside any malaria hotspots, their parasites returned a few weeks later.

“I first presented those data in November 2007 and as expected, people were very sceptical,” says Noedl. After all, a pair of patients is an epidemiological blip. Still, this was worrying enough to prompt White’s team to run their own study in another nearby village. They got even worse news. The 40 people they treated with artesunate took an average of 3.5 days to clear their parasites, and six of them suffered from rebounding infections within a month. “Rapid parasite clearance is the hallmark of artemisinins,” says Arjen Dondorp, one of White’s colleagues based in Bangkok. “That property suddenly disappeared.”

Despite the hopes that ACTs would forestall artemisinin’s expiry, resistance had arrived, just as it had done for other antimalarials. And, as if to rub salt in the wound, it had come from the same damn place.

*****

Why has a small corner of western Cambodia, no bigger than Wales or New Jersey, repeatedly given rise to drug-beating parasites?

White thinks that the most likely explanation is the region’s unregulated use of antimalarial drugs. China supplied artemisinin to the tyrannical Khmer Rouge in the late 1970s, giving Cambodians access to it almost two decades before White conceived of ACTs. Few used it correctly. Some got ineffective doses from counterfeit pills. Others took a couple of tablets and stopped once their fever disappeared. P. falciparum was regularly exposed to artemisinin without being completely wiped out, and the most resistant parasites survived to spread to new hosts. There is a saying among malariologists: “The last man standing is the most resistant.”

Genetic studies hint at other explanations. Early last year, Dominic Kwiatkowski from the University of Oxford showed that some P. falciparum strains from west Cambodia have mutations in genes that repair faults in their DNA, much like some cancer cells or antibiotic-resistant bacteria. In other words, they have mutations that make them prone to mutating. This might also explain why, in lab experiments, they develop drug resistance more quickly than strains from other parts of the world. Evolution is malaria’s greatest weapon, and these ‘hypermutators’ evolve in fifth gear.

Kwiatkowski’s team also found that P. falciparum is spookily diverse in west Cambodia. It is home to three artemisinin-resistant populations that are genetically distinct, despite living in the same small area. That is bizarre. Without obvious barriers between them, the strains ought to regularly mate and share their genes. Instead, they seem to shun each other’s company. They are so inbred that they consist almost entirely of clones.

Kwiatkowski suspects that these parasites descended from some lucky genetic lottery winners that accumulated the right sets of mutations for evading artemisinin. When they mate with other strains, their winning tickets break up and their offspring are wiped out by the drug. Only their inbred progeny, which keep the right combinations, survive and spread.

It undoubtedly helps that South-east Asia does not have much malaria. In West Africa, where transmission is high, a child might be infected with three to five P. falciparum strains at any time, giving them many opportunities to mate and shuffle their genes. A Cambodian child, however, usually sees one strain at a time, and is a poor hook-up spot for P. falciparum. The region’s infrastructure may also have helped to enforce the parasites’ isolation: local roads are poor, and people’s movements were long constrained by the Khmer Rouge.

West Cambodia, then, could be rife with P. falciparum strains that are especially prone to evolving resistance, that get many opportunities to do so because antimalarial drugs are abused, and that easily hold on to their drug-beating mutations once they get them.

These are plausible ideas, but hard to verify since we still know very little about how exactly the parasites resist a drug. Earlier cases of resistance were largely due to mutations in single genes – trump cards that immediately made for invincible parasites. A small tweak in the crt gene, and P. falciparum can suddenly pump chloroquine out of its cells. A few tweaks to dhps and dhfr, the genes targeted by sulfadoxine and pyrimethamine, and the drug can no longer stick to its targets.

Artemisinin seems to be a trickier enemy. Curiously, P. falciparum takes a long time to evolve resistance to artemisinin in lab experiments, much longer than in the wild. Those strains that do tend to be weak and unstable. “I suspect you need a complicated series of genetic changes to make a parasite that’s not lethally unfit in the presence of these drugs,” says White. “It would be unusual if this was a single mutation.”

Practices such as unregulated drug use and misuse may help encourage and accelerate the rate of such changes out in the field. Kwiatkowski’s study suggests that the parasites may have evolved artemisinin resistance several times over, perhaps through a different route each time. Several groups are racing to find the responsible mutations, with news of the first few breaking in December 2013. That’s the key to quickly identifying resistant parasites and treating patients more efficiently. (Currently, you can only tell if someone has artemisinin-resistant malaria by treating them and seeing how long they take to get better.) “We want to be able to track resistance using blood spots on filter paper,” says Chris Plowe at the University of Maryland School of Medicine, whose group is one of those in the race.

But time is running out. From its origins in Cambodia, resistance has reached the Thai–Myanmar border. Nosten has shown that the proportion of patients who are still infected after three days of ACT has increased from zero in 2000 to 28 per cent in 2011. Most are still being cured, but as artemisinin becomes less effective, its partner drug will have to mop up more surviving parasites. Plasmodium will evolve resistance to the partner more quickly, driving both drugs towards uselessness.

This is already happening in western Cambodia, where ACTs are failing up to a quarter of the time and many people are still infected a month later. Long-lasting infections will provide parasites with more chances to jump into mosquitoes, and then into healthy humans. Malaria cases will rise. Deaths will follow. “This is the silence before the storm,” says Arjen Dondorp. “The threat is still slightly abstract and there’s still not that much malaria, which doesn’t help with a sense of urgency. If we suddenly see malaria exploding, then it’ll be a clear emergency, but it’ll also be too late.”

*****

In his office at Mahidol University, Nick White is surrounded by yellowing monographs of old malaria research and overlooked by a wall-mounted mosaic of drug packets made by his daughter. He is now the chairman of the Mahidol–Oxford Tropical Medicine Research Unit and a mentor to the dozens of researchers within. He is gently ranting.

“Everything to do with change in malaria meets with huge resistance,” he says. He means political resistance, not the drug kind. He means the decade it took for the international community to endorse ACTs despite the evidence that they worked. He means the “treacle of bureaucracy” that he and Nosten swim through in their push to eliminate malaria.

“The global response to artemisinin resistance has been a bit pathetic. Everyone will tell you how important it is and there have been any number of bloody meetings. But there is little appetite for radical change.” He misses the old days when “you could drive a Land Rover across borders in your khaki shorts and spray things and do stuff”.

From the outside, things look rosier. Malaria is fashionable again, and international funding has gone up by 15 times in the last decade. Big organisations seem to be rallying behind the banner of elimination. In April 2013, the World Health Organization published a strategy called The Emergency Response to Artemisinin Resistance

“It’s a marvellous plan,” he says drily. “It says all the right things, but we haven’t done anything.” It follows two other strategies that were published in 2011 and 2012, neither of which slowed the spread of artemisinin resistance. Elimination became a dirty word after the noisy failures of the 1950s and 60s, and the new strategies look like the same old tactics for controlling malaria, presented under the guise of eradicating it. “They’re prescriptions for inertia,” says White.

Worse, they are channelling funds into ineffective measures. Take insecticide-treated bednets, a mainstay of malaria control. “We’ve had meetings with WHO consultants who said, ‘We don’t want to hear a word against bednets. They always work.’ But how cost-effective are they, and what’s the evidence they work in this region? The mosquitoes here bite early in the evening. And who’s getting malaria? Young men. Are they all tucked up in their bednets by 6 o’clock? No. They’re in the fields and forests. Come on! It’s obvious.”

He says that resources could be better devoted to getting rid of fake drugs and monotherapies where artemisinin is not paired with a partner. That would preserve ACTs for as long as possible. The world also needs better surveillance for resistant parasites. White is helping with that by chairing the World-Wide Anti-Malarial Resistance Network – a global community of scientists who are rapidly collecting data on how quickly patients respond to drugs, the presence of resistance genes, the numbers of fake drugs, and more.

White also wants to know if artemisinin-resistant parasites from South-east Asia can spread in African mosquitoes. Hundreds of mosquito species can transmit malaria, but P. falciparum is picky about its hosts. If resistant strains need time to adapt to new carriers, they might be slow to spread westwards. If they can immediately jump into far-off species, they are a plane ride away from Africa. “That changes your containment strategy,” says White, “but stupidly, it’s cut out of every research application we’ve ever made.”

He is pessimistic. “I’m pretty confident we won’t win but I think we should try a lot harder than we have been. If we didn’t pull out all the stops and kids start dying of artemisinin-resistant malaria, and we can trace the genetic origins of those parasites to South-east Asia, we shouldn’t sleep easy in our beds.”

*****

The Mosquito breederWhen Nosten’s team first arrived at Hka Naw Tah in February, they slept and worked from the village’s unassuming temple. Using development funds from their grant, they put up a water tower and supplied electricity for the local school. In return, the villagers built them a clinic – a spacious, open-sided hut with a sloping tin roof, benches sitting on a dirt floor, a couple of tables holding boxes of drugs and diagnostic kits, treatment rooms, and a computer station. It took just two days to erect.

The Karen respect strong leadership but there is an easy-going camaraderie in the clinic. When we arrive, one of the research assistants is napping across a bench. Nosten walks over and sits on him. “You see, and I think this is a good sign, that it’s hard to tell who’s the boss and who’s the patient,” he says.

Most of the villagers don’t seem sick, but many of them have malaria nonetheless. Until recently, Nosten’s team had always searched for the parasites by examining a drop of blood under a microscope. If someone is sick, you can see and count the Plasmodium in their red blood cells. But in 2010, they started collecting millilitres of blood – a thousand times more than the usual drops – and searching for Plasmodium’s DNA. Suddenly, the proportion of infected people shot up from 10–20 per cent to 60–80 per cent. There are three, four, maybe six times as many infected people as he thought.

“We didn’t believe it at first,” says Nosten, “but we confirmed it and re-confirmed it.” Perhaps the tests were giving false positives, or picking up floating DNA from dead parasites? No such luck – when the team treated people with ACTs, the hidden parasites disappeared. They were real.

These ‘sub-microscopic infections’ completely change the game for elimination. Treating the sick is no longer good enough because the disease could bounce back from the hordes of symptomless carriers. The strike will have to be swift and decisive. If it’s half-hearted, the most resistant parasites will survive and start afresh. In malarial zones, you need to treat almost everyone, clearing the parasites they didn’t even know they had. This is Nosten’s goal in the border villages like Hka Naw Tah. He has support from the Bill and Melinda Gates Foundation, one of the few large funders to have truly grasped the urgency of the situation and who are “very much in the mood for elimination”.

Killing the parasites is easy: it just involves three days of ACTs. Getting healthy people to turn up to a clinic and take their medicine is much harder. The team have spent months on engagement and education. The clinic is dotted with posters explaining the symptoms of malaria and the biology of mosquitoes. Earlier this morning, Honey Moon, a Karen woman who is one of Nosten’s oldest colleagues, knocked on the doors of all the absentees from the last round to persuade them to come for tests. As a result, 16 newcomers turned up for treatments, bringing the team closer to the full 393. Nosten is pleased. “In this village, I’m quite optimistic that most people will be free of the parasite,” he says.

Another village down the river is proving more difficult. They are more socially conservative and have a poorer understanding of healthcare. There are two factions of Karen there, one of which is refusing to take part to spite their rivals. “It’s a good lesson for us,” says Nosten. “These situations will be elsewhere.” Eliminating malaria is not just about having the right drug, the deadliest insecticide, or the most sensitive diagnostic test. It is about knowing people, from funders to villagers. “The most important component is getting people to agree and participate,” says Nosten. It matters that he has been working in the region for 30 years, that the Shoklo unit is a familiar and trusted name in these parts, that virtually all his team are Karen. These are the reasons that give Nosten hope, despite the lack of political will.

If the strategy looks like it is working after a year, they will start scaling up. Eventually, they hope to cover the entire sinuous border. I ask Nosten if he would ever consider leaving. He pauses. “Even if I wanted to go somewhere else, I’m more or less a prisoner of my own making,” he says. He would need to find a replacement first – a leader who would command respect among both the Karen and malaria researchers, and would be willing to relocate to a place as remote as Mae Sot. It is hard to imagine a second person who would tick all those boxes. Surrounded by airborne parasites, spreading resistance, and border-hopping refugees, François Nosten is stuck. He would not have it any other way.

 

17 Mar 00:30

Solar System’s Smallest Planet Is Shrinking

by Nadia Drake
Tertiarymatt

The solar system is endlessly weird.

Mercury is getting smaller. Over its roughly 4.5 billion years of existence, the dense little planet’s diameter could have shrunk by as much as 14 kilometers, a study published today in Nature Geoscience reports.

It might sound strange, but a shriveling Mercury is not unexpected. In fact, theories describing how the planet’s core cools over time predicted that by now, Mercury’s diameter should have lost around 10 kilometers. But until this new analysis, teams had only been able to measure a 7-kilometer contraction at most. Now, scientists have used data gathered by NASA’s MESSENGER probe, which has been orbiting Mercury since 2011, to calculate how much Earth’s odd little neighbor has shrunk.

A lobate scarp about 400 kilometers long runs vertically near Mercury's horizon in this 2008 MESSENGER image. These scarps are signs that Mercury is shrinking. (NASA/Johns Hopkins University Applied Physics Laboratory/Carnegie Institution of Washington

A lobate scarp about 400 kilometers long runs vertically near Mercury’s horizon in this 2008 MESSENGER image. These scarps are signs that Mercury is shrinking. (NASA/Johns Hopkins University Applied Physics Laboratory/Carnegie Institution of Washington)

Unlike Earth’s, Mercury’s lithosphere – essentially, a planet’s outermost shell – isn’t broken up into a patchwork of tectonic plates that could slip beneath one another to accommodate shrinkage. It’s just one big lid. So instead, Mercury’s surface crinkles, forming puckered geological features called lobate scarps, which are long, steep cliffs with curved edges, wrinkle ridges – less pronounced than lobate scarps – and high-relief ridges.

“Some scarps, like Enterprise Rupes, in Mercury’s southern hemisphere, are truly gigantic – 600 miles long and 2 miles high,” says study author Paul Byrne, a planetary geologist at the Carnegie Institution for Science in Washington, D.C. “Other scarps are much smaller.”

Conceptually, these surface wrinkles are similar to those that appear on the skin of a prune or a raisin as the originally plump fruit dries and shrivels. But Mercury isn’t shrinking because of water loss. It’s getting smaller because its enormous metallic core is cooling and contracting.

In general, more contraction produces taller, longer, and possibly steeper scarps, Byrne says. Measuring the length and height of these features lets scientists calculate how much shrinking the planet has been doing. In the new study, Byrne and his colleagues identified and measured a total of 5,934 scarps and ridges on Mercury’s surface. Then, based on that data set, they calculated that the planet’s diameter could have shrunk by as little as 9.2 kilometers, or by as much as 14.2 kilometers.

In other words, these observations are much more in line with predictions, and are helping resolve a discrepancy between theory and observation that has existed since Mariner 10 first swooped in and took some photos of the little planet in the mid-1970s. (Related: “Mercury, the Smallest Planet, Is Getting Even Smaller, Scientists Say.”)

What’s perhaps unexpected is the observation that the planet is not uniformly contracting – the scarps and wrinkles aren’t evenly distributed on Mercury’s surface. Some regions, like the Northern volcanic plains, show more evidence of shrinkage than others.

“I think it’s probably the result of variations in the strength of rocks across and within the planet,” Byrne says. “Some parts of the planet’s lithosphere are likely stronger than others, and so the outcome of their response to stresses due to global contraction will probably look different – either in terms of shapes of structure, distribution of structures, or both.”

It’s just another of our weird little neighbor’s quirks; indeed, the first rock from the sun has proven to be reliably enigmatic. Mercury is extremely dense. Its metal core, which occupies about 85 percent of the planet’s radius (in contrast to Earth’s core, which comprises roughly 50 percent) – has a layered architecture that isn’t seen anywhere else in the solar system. Mercury’s orbit is the most elliptical of all the sun’s planets, and the planet rotates asynchronously, completing three rotations for every two trips around the sun. Put more simply, one year on Mercury lasts 88 Earth-days, and one day on Mercury is just a bit longer than 58 Earth-days. That would make for a confusing calendar.

And, surprisingly, there’s water ice at the roasted little planet’s poles.

26 Mar 20:52

Accessing iNaturalist data

Tertiarymatt

R for citizen science.

The iNaturalist project is a really cool way to both engage people in citizen science and collect species occurrence data. The premise is pretty simple, users download an app for their smartphone, and then can easily geo reference any specimen they see, uploading it to the iNaturalist website. It let's users turn casual observations into meaningful crowdsourced species occurrence data. They also provide a nice robust API to access almost all of their data. We've developed a package rinat that can easily access all of that data in R. Our package spocc uses iNaturalist data as one of it's sources, rinat provides an interface for all the features available in the API.

Searching Currently you can get access to iNaturalist occurrence records from our package spocc, which works great for scenarios where you want lot's of data from many sources, but rinat will get you full details on every record and offers other searching on terms other than species names. First let's see how this matches with what you can get with spocc.

options(stringsAsFactors = F)
library(spocc)
## Loading required package: ggplot2
library(rinat)
out <- occ(query = "Accipiter striatus", from = "inat")
inat_out <- get_inat_obs(taxon = "Accipiter striatus", maxresults = 25)
### Compare Id's and see that results are the same without viewing full tables
cbind(out$inat$data$Accipiter_striatus$Id[1:5], inat_out$Id[1:5])
##        [,1]   [,2]
## [1,] 581369 581369
## [2,] 574433 574433
## [3,] 570635 570635
## [4,] 555214 555214
## [5,] 551405 551405

The results are the same, the rinat package will offer a bit more flexiblity in searching. You can search for records by a fuzzy search query, a taxon (used above in spocc), a location in a bounding box, or by date. Let's say you just want to search by for records of Mayflies, you can use the taxon parameter to search for all lower level taxonomic matches below order.

may_flies <- get_inat_obs(taxon = "Ephemeroptera")
## See what species names come back.
may_flies$Species.guess[1:10]
##  [1] "Mayfly"               "Heptageniidae"        "Ephemerella subvaria"
##  [4] "Ephemerella subvaria" "Mayflies"             "Stream Mayflies"     
##  [7] "Mayflies"             "Mayflies"             "Mayflies"            
## [10] "Hexagenia"

You could also search using the fuzzy query parameter, looking for mentions of a specific habitat or a common name. Below I'll search for one of my favorite habitats, vernal ponds and see what species come back. Also we can search for common names and see the scientific names (which should be all the same).

vp_obs <- get_inat_obs(query = "vernal pool")
vp_obs$Species.guess[1:10]
##  [1] "Docks (Genus Rumex)"                    
##  [2] "Blennosperma bakeri"                    
##  [3] "Rails, Gallinules, and Coots"           
##  [4] "Western Spadefoot"                      
##  [5] "Western Spadefoot"                      
##  [6] "Eupsilia"                               
##  [7] "upland chorus frog"                     
##  [8] "Wood Frog"                              
##  [9] "Striped Meadowhawk (Sympetrum pallipes)"
## [10] "Ambystoma maculatum"
# Now le'ts look up by common name:

deer <- get_inat_obs(query = "Mule Deer")
deer$Scientific.name[1:10]
##  [1] "Odocoileus hemionus" "Odocoileus hemionus" "Odocoileus hemionus"
##  [4] "Odocoileus hemionus" "Odocoileus hemionus" "Odocoileus hemionus"
##  [7] "Odocoileus hemionus" "Odocoileus hemionus" "Odocoileus"         
## [10] "Odocoileus hemionus"

All of these general searching functions return a dataframe that is m x 32 (where m is the requested number of results). The column names are mostly self-explanatory, including, common names, species names, observer id's, observer names, data quality, licenses and url's for images so you can go look at the photo a user took.

Filtering

All searches can also be filtered by space and time. You can search for records within a specific bounding box, or on a specific date (but not a range). We can redo our deer search using a bounding box for the western United States.

bounds <- c(38.44047, -125, 40.86652, -121.837)
deer <- get_inat_obs(query = "Mule Deer", bounds = bounds)
cat(paste("The number of records found in your bunding box:", dim(deer)[1], 
    sep = " "))
## The number of records found in your bunding box: 47

By checking the dimensions, we can see only 47 records were found. We could try the samething for a given day, month or year. Let's try searhing for cumulative totals of observations of Ephemeroptera and see if we can detect seasonality.

library(ggplot2)
out <- rep(NA, 12)
for (i in 1:12) {
    out[i] <- dim(get_inat_obs(taxon = "Ephemeroptera", month = i, maxresults = 200))[1]
}
out <- data.frame(out)
out$month <- factor(month.name, levels = month.name)
ggplot(out, aes(x = month, y = out, group = 1)) + geom_point() + stat_smooth(se = FALSE) + 
    xlab("Month") + ylab("Cumulative of Mayfly observations") + theme_bw(16)

plot of chunk filter_date

Exactly as you'd expect observations of this season insect tend to peak in the summer and then slowly decline. Except for September peak, it follows the expected trend.

User and project data

There are several other functions from the API that allow you to access data about projects and users. You can grab detailed data about projects, users and observations. Let's look at the EOL state flowers project. First we can grab some basic info on the project by searching for it based on it's "slug". You can find this in the URL of the project: "http://www.inaturalist.org/projects/state-flowers-of-the-united-states-eol-collection", which is the section of text after "projects/", so in this case it would be "state-flowers-of-the-united-states-eol-collection"

Let's grab some info on the project by getting observations but set the type as "info"

eol_flow <- get_inat_obs_project("state-flowers-of-the-united-states-eol-collection", 
    type = "info", raw = FALSE)
## 204  Records
## 0
### See how many taxa there are, and how many counts there have been
cat(paste("The project has observed this many species:", eol_flow$taxa_number, 
    sep = " "))
## The project has observed this many species: 20
cat(paste("The project has observed this many occurrences:", eol_flow$taxa_count, 
    sep = " "))
## The project has observed this many occurrences: 204

We can grab all the observations from the project as well just by setting the type as "observations". Then it's easy to to get details about specific observations or users.

eol_obs <- get_inat_obs_project("state-flowers-of-the-united-states-eol-collection", 
    type = "observations", raw = FALSE)
## 204  Records
## 0-100-200-300
## See just the first few details of an observation.
head(get_inat_obs_id(eol_obs$Id[1]))
## $captive
## NULL
## 
## $comments_count
## [1] 0
## 
## $community_taxon_id
## [1] 48225
## 
## $created_at
## [1] "2013-04-08T15:49:15-07:00"
## 
## $delta
## [1] FALSE
## 
## $description
## [1] ""
## See the first five species this user has recorded
head(get_inat_obs_user(as.character(eol_obs$User.login[1]), maxresults = 20))[, 
    1]
## [1] "Lynx rufus"              "Melanerpes formicivorus"
## [3] "Lontra canadensis"       "Buteo lineatus"         
## [5] "Icteridae"               "Pelecanus occidentalis"

There are many more details that you can get, like counts of observations by place ID (extracted from the project or observation, but not well exposed to users), the most common species by date, or by user. There is almost no end to the details you can extract. If you ever wanted to do a case study of a citizen science project, you could get data to answer almost any question you had about the iNaturalist project with rinat.

Finally, what species occurrence package wouldn't be complete without some basic mapping. This function will generate a quick map for you based on a data frame of observations from rinat. These can be from functions such as get_inat_obs, or get_inat_obs_project. Let's end by plotting all the observations from the EOL state flowers project.

### Set plot to false so it returns a ggplot2 object, and that let's us modify
### it.
eol_map <- inat_map(eol_obs, plot = FALSE)
### Now we can modify the returned map
eol_map + borders("state") + theme_bw() + xlim(-125, -65) + ylim(25, 50)

plot of chunk eol_plot

25 Mar 12:52

Opens Roundup (March 25)

by Catriona MacCallum
Tertiarymatt

A lot of good stuff in here.

 

In this issue, the US FIRST act meets opposition on all fronts, David Wiley (champion of open education) on the 5Rs of openness, Wellcome releases its report on how to promote an effective market for APCs, PeerJ one year on, ten tips for navigating publishing ethics, the power of post-publication review, altmetrics for developing countries, the pros and cons of publishing in arXiv, a fantastic crowdsourcing project in the humanities, John Ioannidis on the look-out for a journal near you…., and more

With thanks to Allison Hawxhurst and Katie Fleeman for tips and links.

POLICY DEVELOPMENTS

US FlagUS: Why FIRST is a Trojan Horse

March 11: If you haven’t read PLOS’s reaction to the introduction of the FIRST Bill then here is another opportunity to read Cameron’s post (main link) as well as that of EFF published the same day and SPARC a couple of days before that. But it wasn’t just open access advocates objecting to the public access language in Section 303 (which could see embargo lengths increase to three years after publication). Science insider also lists the growing opposition coming from scholarly societies and various research and university groups noting that the overwhelming feeling is that the bill represents a missed opportunity for the US to maintain its scientific lead, in particular because of constraints on the amount of funding for NSF and the restrictions the bill imposes on the type of research it would fund. The bill, introduced by republicans, has been particularly divisive and at odds with the original  America Competes Act introduced by democrats. The ensuing markup of the FIRST Bill on the 12th was lively but an impassioned plea by Rep. Zoe Lofgren to strike the public access language in Section 303 was narrowly defeated by 9-8 along party lines. The bill still has a long way to go.

AND IN OTHER NEWS

Legal Dispute between a Professional Association and Press

March 16: On H Net, a listserv for the humanities, Phil Brown from H-Asia calls attention to an article in the Chronicle of Higher Education (available to subscribers only) discussing a dispute between the Social Science History Association and Duke University Press over control of the Association’s journal, Social Science History. Here’s the nub of what he says in full:

(After notifying Duke of its intent to solicit bids for a new publication contract):

In June 2012, not having gotten a bid from Duke, the association sent the press a letter saying it would be moving on and ending the contract; Duke disputed its right to do that. According to the association, Duke interprets that phrase “participation in the journal” to mean that the association has only two choices:  “continue with Duke as the sole publisher in perpetuity or give up its ownership of the journal altogether and allow Duke to continue to publish the journal,” even though the university “has no ownership or intellectual-property rights” in it. “

The full details of the suit are available.

Clarifying the 5th R

Image by Sean MacEntee (CC-BY 2.0)

Image by Sean MacEntee (CC-BY 2.0)

March 15: David Wiley, a proponent for open educational resources (OER), introduced the concept of the 4Rs as a way to think about openness in 2007. He described the four main activities enabled by open content as Reuse, Rework, Remix and Redistribute, which is what the creative commons attribution license permits. The 4Rs have been influential as a framework for educational resources  and what being open means more generally . On March the 4thhe added a 5th R – Retain – to the mix. This is the right to make, own and control a copy of the work. This addition was in response to the fact that while many OER publishers permit access to their content they “do not make it easy to grab a copy of their OER that you can own and control forever”. “How many OER publishers enable access but go out of their way to frustrate copying? How many more OER publishers seem to have never given a second thought to users wanting to own copies, seeing no need to offer anything beyond access?”

Some (e.g. David Draper and Mike Caulfield) have subsequently questioned the need for a 5th R – surely being able to own and control a copy of the work is implicit in any licence that permits the 4Rs in the first place? Wiley agrees with this but believes that ownership per se has never been explicitly addressed in the discussion of open content (main link) and this has direct consequences: “If the right to Retain is a fundamental right, we should be building systems that specifically enable it. When you specifically add ‘Enable users to easily download copies of the OER in our system’ to your feature list, you make different kinds of design choices” – ones that most designers of OER systems have failed to think about.

The implications of the 5th R are fundamentally important as they change the context of what we’re doing – it’s no longer enough to state that others can reuse, remix or redistribute your work. It suggests that those involved in providing open content also need to help build or facilitate the infrastructure that enables the content to be easily reused by others. In other words, we have a responsibility to reduce the friction around the content we make open (e.g.  Cameron’s article in PLOS Biology about this). And this applies not just to libraries and institutions with an educational remit but to funders and publishers as well.

Metaphysicians: Sloppy researchers beware. A new institute has you in its sights

March 15: Article in the economist about a new institution at Stanford called the Meta-Research Innovation Center (Metrics) to be run by John Ioannidis (author of the famous ‘Why most published findings are false’ paper in PLOS Medicine, currently viewed almost 980,000 times). The new laboratory aims to find out whether attempts to reproduce studies actually work and to guide policy on how to improve the validation of research more generally. Among the initiatives is also “a ‘journal watch’ to monitor scientific publishers’ work and to shame laggards into better behaviour. And they will spread the message to policymakers, governments and other interested parties, “in an effort to stop them making decisions on the basis of flaky studies.”

PeerJ’s $99 open access model one year on

PeerJMarch 13: A brief review in Times higher of how PeerJ is doing. “PeerJ co-founder Jason Hoyt said that the journal had fulfilled its year-one aims of “staying alive”, starting to grow and “laying the groundwork to show this business model could be sustainable”. It is on track to be self-sustaining by early 2015, and there are no plans to raise prices. “If anything we would like to lower them if we can figure out some other revenue stream,” Dr Hoyt said.” PeerJ was also explicitly references in the Wellcome Trust report into and effective APC market by Björk and Solomon mentioned below. That report concludes that “PeerJ has published around 220 articles in the first nine months of operation. It is not clear at this point if the journal will scale up to a level that will make it financially sustainable but it offers an innovative funding model”.

Institutional repositories provide an ideal medium for scholars to move beyond the journal article

Academic Commons Use-per-item graph (CC BY 3.0)

Academic Commons Use-per-item graph (CC BY 3.0)

March 12: Leyla Williams, Kathryn Pope, and Brian Luna Lucero from Columbia University make the case for institutional repositories to collect all the work of their scholars rather than focusing on only peer reviewed journal articles or monographs. They discuss how their IR ‘Academic Commons’ hosts conference videos, presentations, and technical reports and other “grey literature” (as the figure shows). “IRs are crucial for authors whose work may not fit within the scope of any one scholarly journal.”, they note. “They are also vital for researchers with data that lies outside the parameters of disciplinary data repositories, for dissertation authors who want to make supplemental materials available, and for undergraduates.” They discuss examples where deposition in their repository has helped young researchers find a job and how the lively twitter feed around what’s deposited helps disseminate the work.

Top 10 tips for navigating ethical challenges in scholarly publishing

Plaigiarism By Brett jordan

Image by Brett Jordan (CC BY)

March 12: Jackie Jones, Executive Journals Editor at Wiley provides her top tips on publication ethics to coincide with the 2nd edition of Wiley’s “Best Practice Guidelines on Publishing Ethics: A Publisher’s Perspective”.  The guidelines (available online or as a PDF) are published under a Creative Commons Non-Commercial license and have drawn on a range of expertise including from COPE. They form a useful addition to the more in-depth guidelines and forums that COPE already provides and signal the increasing accountability that all reputable publishers have to ensure high ethical standards in scholarly publishing. In a subsequent post, Udo Schuklenk an editor of the journal Bioethics and Developing World Bioethics lists some of the infringements he’s seen as editor with respect to plagiarism:  “Over the years you begin to delude yourself into thinking that you have seen the full range of ethics infringements.  It’s particularly ironic, I guess, when you edit bioethics journals: you would hope that your authors would be clued in to publication ethics issues.” Unfortunately no journal can escape these issues.

Fostering a transparent and competitive market for open access publishing

Image by 401(K) 2013 (CC-BY-SA 2.0)

Image by 401(K) 2013 (CC-BY-SA 2.0)

March 12: A range of funders, led by the Wellcome Trust, released a report by Bo-Christer Björk of the Hanken School of Economics, Finland, and Professor David Solomon of Michigan State University on the structure and shaping of the APC market. It’s worth skimming the whole report as it has a lot of good information as well as giving a sense of the directional thinking of funders. The report contains useful figures and data.

The key conclusions are that the full OA market is competitive and functioning with varied pricing depending on field and impact. The market for APCs of articles in hybrid journals run by subscription publishers is dysfunctional with relatively flat pricing (and low uptake). A set of analyses of the report have started to appear and look out for a some comments and a summary here over the next few days.

Science self-corrects – instantly

Image by Boston Public Library (CC BY 2.0)

Image by Boston Public Library (CC BY 2.0)

March 11:  The  blog for PubPeer, an online post-publication commenting service, discusses two papers published in Nature in January purporting to provide a revolutionary simple technique for producing pluripotent stem cells, termed STAP cells. A post by Paul Knoepfler on his own blog expressed initial doubts which were fuelled by comments on PubPeer exposing problems with the figures in the paper. Knoepfler then hosted a post to crowdsource researchers trying to replicate the apparently simple production of mouse STAP cells – so far with little success. And then comments posted last week suggested that some of the figures in one of the Nature papers were duplicated from seemingly different experiments in the lead author’s doctoral thesis. Not long after, the Wall Street journal reported that the senior co- author from RiKEN (a leading Japanese research institute) asked for the papers to be retracted though a co-author at Harvard continues to support the work. Nature also reported on the press conference with RIKEN, who announced the findings of an interim investigation but have not made any decision about retracting the papers. The story rumbles on – this week, RIKEN withdrew the original press release about the paper stating “The reports described in the CDB news story “STAP cells overturn the pluripotency paradigm” published on Jan 30, 2014 are currently under investigation. Due to a loss of confidence in the integrity of these publications, RIKEN CDB has withdrawn press release from its website.”

The moral of the story is not just whether the papers in Nature hold up but whether commenting platforms like PubPeer and blogs provide a valid means to scrutinise bold claims. While there are cases where issues are identified there is also concern about the potential for personal attacks, particularly given the anonymity that some of these platforms provide.

This is especially important given the increasing number of times pre-publication review actually fails. In a recent and related post in Nature, Richard van Noorden discusses how to choose among the many venues now available for researchers to discuss work after publication, focusing on a discussion of the same papers by Kenneth Lee on ResearchGate. ResearchGate provided Lee with a more structured review form, they’re calling Open Review. PLOS Labs has also recently set up a similar innovative initiative, called ‘Open Evaluation’. As PubPeer conclude at the end of the post (main link) “Science is now able to self-correct instantly. Post-publication peer review is here to stay”

How is it possible that Elsevier are still charging for copies of open-access articles?

March 11: Mike Taylor provides a run-down of the charges that Elsevier still try to apply for reusing their ‘Open Access’ Articles. Apparently, it’s all to do with a problematic technical fix that Elsevier has been trying to solve for a couple of years now. And this week Peter Murray Rust publishes a letter he received from Elsevier’s Director of Access and Policy Alicia Wise, about how they have now taken steps to fix the problem and compensate individuals who have been mis-sold Open Access products….

Should we eliminate the Impact Factor?

March Issue: An interesting take on the impact factor by the Editor in Chief of Biotechniques, Nathan Blow. He reviews the pros and cons of the impact factor versus other article level metrics and concludes that there is an equal danger of misuse if researchers get wedded to any single alternative metric. And he thinks they will because scientists need something on which to base their publishing decisions. What he ends up calling for is a bit more sense in the way we use metrics, and a bit less laziness: “we need to change the way scientists view such metrics: While it might be good to publish in a top tier journal with an Impact Factor of 30—if your article only gets 2 citations, what does this mean? And the opposite is also true—if the journal has an Impact Factor of 2, but your article receives 500 citations in 2 years, should you be penalized for where you publish? And fundamentally, what does it mean to get 2 versus 500 citations? The validity of any statistic or analysis tool depends on careful and appropriate application by an informed user. Maybe scientists need to look beyond sheer numbers towards the “community” impact of their studies. Here, network analysis showing the reach of an article based on a deeper citation analysis might provide stronger insights into its impact. Tenure committee members also need to look beyond the simple “30-versus-2” Impact Factor debate and use their experience and knowledge to see the true contribution that a scientist is making to their field and beyond—you cannot ask a young scientist to do something that you are not willing to do yourself! In the end, measures such as the Impact Factor are only “lazy” statistics because we make them lazy.”

While I agree with much of what he says, I think he omits another factor that scientists should consider when they choose where to publish and that’s the service the journal (or platform) provides Are there the checks and balances that ensure your work is properly reported, what sort of  peer- review service do they have, does the publisher help ensure that the data underlying the paper’s findings are available, is the metadata in a form that means your article or the components within it can be found by anyone interested regardless of subject or geographic location, and can the content be reused easily if others do find it. Making sure your work can be validated, disseminated and is searchable and reusable is what really counts. The metrics will follow.

Is a Rational Discussion of Open Access Possible?

Image by Vaguery (CC-BY 2.0)

Image by Vaguery (CC BY 2.0)

March 10: A dedicated blog set up by Rick Anderson to host the slides and transcripts of a talk he gave at the Smithsonian Libraries. Rick is perhaps better known as a chef for Scholarly Kitchen (where he’s posted a link to the video of his talk). Both blogs have a lively set of comments – largely supportive ones from Mike Taylor for example even though he was criticised in the talk and some insights from Jan Velterop (who started BMC with Vitek Tracz).

Altmetrics could enable scholarship from developing countries to receive due recognition

March 10: Fantastic post by Juan Pablo Alperin on the potential impact of altmetrics for researchers in developing countries. One of the issues he raises is the perception that researchers in developing countries don’t produce as much research but this is largely because the research they do produce is not represented in abstracting and indexing services such as Thomson Reuters’ Web of Science. This means that the work doesn’t get cited as much and the journals don’t even gain entry into the notorious impact factor game. Resources like SciELO are trying to redress this balance but are still working with only a subset of the 5000+regional journals (largely from S. America). He provides a striking image (below) of the world scaled by the number of papers in  Web of Science by authors actually living there which puts the lack of representation in these countries into stark relief.

World Scaled  Image by Juan Pablo Alperin (cC-BY)

World Scaled Image by Juan Pablo Alperin (CC BY)

But whether altmetrics can help redress this balance is open to question. The potential is huge but to realise the promise, he argues, altmetrics (and the ALM community more generally) need to engage with scholars from developing regions. He cautions that if altmetrics are used as just another means to rank scholars then the danger is that they will evolve to cater only for those in locations where they are most heavily used (i.e. not in developing countries). However he is part of the Public Knowledge Project working with the PLOS’ ALM application to provide a free altmetrics service to journals being run and hosted in developing countries (via the OJS platform). “As the field begins starting to consolidate, I remain optimistically pro-altmetrics for developing regions, and I have faith in the altmetrics community to serve all scholars. Which directions altmetrics should go, how they should be used, or how the tools should be implemented is not for me to prescribe, but if we exclude (or do not seek to include) scholars from developing regions, altmetrics will become another measure from the North, for the North. And we already know that story.”

Dubiously online

March 08: Article about the need to police open access journals in India by an Indian Academic, Rudrashis Datta: “Unless the higher education authorities step in to stem the rot, serious open access publishing, so important in the Indian academic context, runs the risk of dying a natural death, leaving serious researchers and academics without the advantage of having to showcase their scholarly contributions to readers across the world.“

The price of publishing with arXiv

March 05: Mathematician discussing the advantages and disadvantages of publishing in arXiv: “The advantage: I had a lot of fun. I wrote articles which contain more than one idea, or which use more than one field of research. I wrote articles on subjects which genuinely interest me, or articles which contain more questions than answers. I wrote articles which were not especially designed to solve problems, but to open ones. I changed fields, once about 3-4 years.”….”The price: I was told that I don’t have enough published articles…”

“But, let me stress this, I survived. And I still have lots of ideas, better than before, and I’m using dissemination tools (like this blog) and I am still having a lot of fun.”

Making it Free, Making it Open: Crowdsourced transcription project leads to unexpected benefits to digital research

Image by Ewan Munro (CC BY-SA)

Image by Ewan Munro (CC BY-SA)

March 03: Melissa Terras Professor of Digital Humanities at University college London.discusses how they used crowdsourcing to transcribe all of philosopher and reformer, Jeremy Bentham’s writings.  The ‘Trancscribe Bentham’ site is hosted by UCL. It is a fantastic project and seems likely to follow the success of similar crowdsourcing initiatives in the sciences like GalaxyZoo. As Mellisa notes, “This week we hit over 7000 manuscripts transcribed via the Transcription Desk, and a few months ago we passed the 3 million words of transcribed material mark. So we now have a body of digital material with which to work, and make available, and to a certain extent play with. We’re pursuing various research aims here – from both a Digital Humanities side, and a Bentham studies side, and a Library side, and  Publishing side. We’re working on making canonical versions of all images and transcribed texts available online.  Students in UCL Centre for Publishing are (quite literally) cooking up plans from what has been found in the previously untranscribed Bentham material, unearthed via Transcribe Bentham. What else can we do with this material?” And there are lots of doors opening for them too – such as looking into Handwritten Text Recognition (HTR) technologies.

Experiment in open peer review for books suggests increased fairness and transparency in feedback process

Feb 28: Hazel Newton, the Head of Digital Publishing at Palgrave Macmillan describes their current peer review pilot investigating how open feedback functions in monograph publishing and gets feedback from authors involved in project. Great to see open peer review experiments in the humanities as well as the sciences.

The post Opens Roundup (March 25) appeared first on PLOS Opens.

27 Mar 02:05

Art of the day: linework for a tiny painting (seriously...



Art of the day: linework for a tiny painting (seriously tiny…2.5”x3.5”), of Elsa from Frozen.