Archive for July, 2010

Pocket Science: plague-running mice, and how to watch mutations in real time

By Ed Yong | July 30, 2010 9:00 am

Not Exactly Pocket Science is a set of shorter write-ups on new stories with links to more detailed takes, where available. It is meant to complement the usual fare of detailed pieces that are typical for this blog.

Prairie_dog

Plague-running mice create epidemics

The bacterium behind bubonic plague – Yersinia pestis has a notorious track record for massacring humans, creating at least three major pandemics including the Black Death of the 14th century. But it’s mainly a disease of rodents and it regularly infects the black-tailed prairie dogs of North America. It’s an enigmatic killer. It will remain relatively silent for years before suddenly exploding into an epidemic that kills nearly all the prairie dogs in infected colonies within a few weeks. Now Daniel Sakeld from Stanford University has found the culprit behind these lurk-and-kill cycles – the tiny grasshopper mouse.

Prairie dog colonies, and their diseases, are generally isolated from one another. Even though Yersinia is very persistent, it eventually fades away unless it finds a new group of hosts. The grasshopper mouse provides it with just such an opportunity by acting as an alternative and highly mobile host for Yersinia. It’s a plague-runner. By scampering across the grasslands, it inadvertently creates a network between otherwise unconnected colonies, opening up corridors for Yersinia to spread.

By creating a mathematical model, and observing both rodents in the wild, Sakeld found that when the mouse is absent, only a small proportion of prairie dogs are plagued by plague. In these conditions, infections spread very slowly during fights and hostile takeovers between neighbours. When mouse numbers pass a threshold, fatal plague epidemics are virtually guaranteed.

The numbers of grasshopper mice in the grasslands rises and falls over time, a cycle that could spell life or death for the prairie dog. These patterns of lengthy lurking and sudden death are also shared by many other deadly diseases like anthrax and hantaviruses. In these cases, alternate hosts like the grasshopper mouse might also be involved in the sudden rise of deadly epidemics.

Reference: PNAS http://dx.doi.org/10.1073/pnas.1002826107

Mutation

Events occur in real time – watching the birth of mutations

Life is a massive game of Chinese whispers – information is constantly being passed on and as this happens, errors build up. Every time a cell divides in two, its genetic information is copied and there’s a small chance that mistakes (or ‘mutations’) will creep in. Some of these mutations will be beneficial, others will be fatal. Either way, they provide fuel for evolution, producing the variation that natural selection acts upon.

Now, Marina Elez from University Paris Descartes Medical School has found a way to spot mutations in real time. She can look at dividing cells and literally watch the moment when mutations show up across the entire genome. The technique works in bacteria, and it could be expanded to study the birth of mutations in more complex cells or even cancers.

Studying mutations isn’t easy. They’re very rare and most don’t produce any noticeable effects that would give away their presence. More often not, they’re repaired by proofreading proteins, which watch for errors in copied DNA and edit them back into shape. Elez realised that these proofreaders could lead her to the location of mutations – all she needed to do was follow. She focused on one bacterial proofreader called MutL, which forms large clusters around mutations that it can’t repair. Elez tagged MutL with a molecule that glows in the dark. The result: bacteria that give off tiny pinpricks of light at every point of their genome with an irreparable mutation.

By counting these bright dots, Elez could estimate the mutation rate in her bacteria. And fortunately, her estimate was a good match for the predictions of earlier studies. Elez also thinks that the approach should work in other living things because proofreading proteins like MutL are very similar from species to species. The technical challenges might be greater in more complicated cells, but the principle of watching mutations in real time is sound. And that opens up all sorts of possibilities. You could, for example, look at tumours, to see when and where the genetic changes that create a cancer will emerge.

Reference: Current Biology http://dx.doi.org/10.1016/j.cub.2010.06.071

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On the Origin of Science Writers

By Ed Yong | July 29, 2010 9:38 am

Writing
Every now and then, I get an email from someone who’s keen to get into science writing and wants to know how I started. Whenever I reply, and I always try to, I’m always left with the nagging feeling that my experience is but one of a multitude of routes that people have taken. Science writing (whether you want to call it journalism, blogging, communication and so on) is a diverse field, as are the people working in it. It would be far more illuminating for a newbie to see a variety of stories rather than just one.

This was the origin of this thread of origins. I will be asking science writers around the world to do what they do best – tell a story – about the thing they know best – themselves. This will be a perpetual thread that I hope will act as a lasting resource for the writers of tomorrow to take inspiration from.

Some kind individuals have already submitted their stories and I hope that many more will chip in. You can already see that they’re a varied bunch. Some stumbled into it by accident. Some came from traditional journalistic backgrounds. Others were bitten by a radioactive Carl Sagan. The more the stories accumulate, the better this diversity reveals itself.

Who should contribute to this thread?

Anyone who regularly writes about science, and preferably has been doing it for a couple of years now. I originally wanted to focus on science journalists but because all these definitions are bleeding into one, I’m opening it to all manner of science writers. From blogger to book writer, beginner to veteran, Asimov to Zimmer, tell us your story.

What should I say?

You’ll see from the existing entries (which are virtually unedited) that there’s a lot of variety in content, tone and length. This is as it should be – science writers are a diverse bunch and it would be a shame to edit them into uniformity. But essentially, there are two basic questions:

  • how did you make your start
  • what advice would you give to people in the same position?

What do I do?

Just  stick a comment in with your story, who you are and what you do. If there are multiple links, it’ll be diverted to my spam folder, but just email or tweet me and tell me to rescue it. Alternatively, feel free to email your story and I’ll put it up on your behalf.

How do I tell people about this?

Obviously, the URL is above, but you can also link to this page from tinyurl.com/sciwriters and bit.ly/sciwriters

What about regular comments?

I’m not going to restrict people from posting regular comments initially, but I’d ask that readers keep them to a minimum. The thread’s value relies on the stories taking centre-stage.

Other than that, go for it.

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CATEGORIZED UNDER: Journalism

A warmer ocean is a less green one

By Ed Yong | July 28, 2010 1:00 pm

Phytoplankton

The Earth’s oceans are mysterious and largely unexplored. Many of their inhabitants are familiar to us but their whereabouts and numbers are far less clear. This is starting to change. In two new studies, Boris Worm from Dalhousie University has revealed an unprecedentedly detailed portrait of the planet’s marine life, from tiny plankton to mighty whales. And with that knowledge comes concern, for neither study paints an optimistic picture about the fate of tomorrow’s seas, as changing climate slowly raises their temperature.

Graduate student Daniel Boyce focused on some of oceans’ smallest but most important denizens – the phytoplankton. These tiny creatures are the basis of marine food webs, the foundations upon which these watery ecosystems are built. They produce around half of the Earth’s organic matter and much of its oxygen. And they are disappearing. With a set of data that stretches back 100 years, Boyce found that phytoplankton numbers have fallen by around 1% per year over the last century as the oceans have become warmer, and if anything, their decline is getting faster.  Our blue planet is becoming less green with every year.

Meanwhile, post-doc Derek Tittensor has taken a broader view, looking at the worldwide distributions of over 11,500 seagoing species in 13 groups, from mangroves and seagrasses, to sharks, squids, and corals. His super-census reveals three general trends – coastal species are concentrated around the western Pacific, while ocean-going ones are mostly found at temperate latitudes, in two wide bands on either side of the equator. And the only thing that affected the distribution of all of these groups was temperature.

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Missing post

By Ed Yong | July 27, 2010 5:47 pm

If anyone saw an RSS notification for a post about science writers that doesn’t seem to exist, it’s because I published it by mistake before it was ready. I’ve now deleted it. Currently, the plan is to get it up on Thursday.

Cheers,

Ed

CATEGORIZED UNDER: Uncategorized

Jellyfish eye genes suggest a common origin for animal eyes

By Ed Yong | July 27, 2010 8:45 am

Cladomena

Jellyfish may seem like simple blobs but some have surprisingly sophisticated features, including eyes. These are often just light-sensitive pits but species like the root-arm medusa have complex ‘camera’ eyes, with a lens that focuses light onto a retina. Not only are these organs superficially similar to ours, they’re also constructed from the same genetic building blocks.

Hiroshi Suga from the University of Basel has been studying the eyes of the root-arm medusa (Cladonema radiatum). His work strongly suggests that all animal eyes share a common origin, whether they belong to a human or an insect, an octopus or a jellyfish. The details may be different but they’re all under the control of closely related ‘master genes’ that themselves evolved from a common ancestor.

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MORE ABOUT: eyes, jellyfish, Pax

Sniff-detector allows paralysed people to write messages, surf the net and drive a wheelchair

By Ed Yong | July 26, 2010 3:00 pm

In Israel’s Loewenstein Rehabilitation Hospital, the patient known as LI1 is a prisoner of her own body. She is a 51-year-old woman who was paralysed by a stroke several months ago. Suffering from “locked-in syndrome”, she is completely aware but unable to move or speak. She cannot even control the blinks of her eyes. And yet LI1 has recently been able answer questions from her doctors and communicate with her family through written messages. All she has to do is sniff.

LI1 uses a ‘sniff controller’, an incredible new technology that allows paralysed patients to control machines with their noses. It’s the brainchild of Anton Plotkin and Lee Sela at the Weizmann Institute of Science. Whenever a patient sniffs, the device measures the change in pressure inside their noses. It converts these into electrical signals that are passed to a computer via a simple USB connection. With just a sniff, people can move a cursor on a screen, allowing locked-in patients to write messages. Quadriplegics can even use the device to surf the web, or drive a wheelchair.

This technology was developed almost by accident in the lab of Noam Sobel, who studies the way of brains process our sense of smell. The group use a device called an olfactometer, which produces waves of smell to see how sensitive a person’s senses are. For one of their experiments, the team rigged the olfactometer so that volunteers triggered the odour pulse themselves when they sniffed. “We noticed that sniffs are a very good and fast trigger,” says Sobel. “It then simply dawned on us that instead of triggering odor, we could trigger anything: letters in a text writer or turns of a wheelchair.  The rest just flowed (or rather, rushed) from there.” It’s a fantastic example of the useful and unpredictable roads that basic scientific research can lead to.

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I've got your missing links right here (24th July '10)

By Ed Yong | July 24, 2010 12:00 pm

News

You can just engineer a crime scene.” Scientists can fabricate blood and saliva samples containing DNA from a person other than the donor of the blood and saliva. (Andrew Pollack, NYT)

New research suggests one reason women are underrepresented in science and math is they see such careers as impeding their desire to help others. (Tom Jacobs, Miller-McCune)

Researchers implant false symptoms: we can be convinced we reported symptoms of mental illness that we never mentioned and, as a result, we can actually start believing we have the symptom itself. (Vaughan Bell, Mind Hacks)

Eradicating any organism would have serious consequences for ecosystems — wouldn’t it? Not when it comes to mosquitoes. (Janet Fang, Nature)

Is Torosaurus just an older version of Triceratops? (Brian Switek, Smithsonian Dinosaur Tracking)

Mark Henderson has had his genes tested three times by three different companies. Read about his surprising and sometimes alarming comparison. (Times; paywall (but it’s worth it))

More after the jump…

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CATEGORIZED UNDER: Links, Uncategorized

Pocket Science – belly-flopping frogs, and fattening marmots

By Ed Yong | July 23, 2010 9:00 am

Not Exactly Pocket Science is a set of shorter write-ups of new stories with links to more detailed takes by the world’s best journalists and bloggers. It is meant to complement the usual fare of detailed pieces that are typical for this blog.

Frogs evolved to jump before they perfected landings

Most frogs are can leap large distances in a single bound, jumping forward with a thrust of their powerful hind legs and landing gracefully on their front ones. But it wasn’t always like this. A study of one of the most primitive groups of frogs suggests that the first frogs landed in an awkward belly-flop. These animals evolved to jump before they perfected their landings.

Virtually all frogs jump and land in the same way. But Richard Essner Jr from Southern Illinous University discovered a unique leaping style in the Rocky Mountain tailed frog. This species belongs to a group called the leiopelmatids, more commonly (and accurately) known as the “primitive frogs”. Using high-speed video footage, Essner showed that the tailed frog’s landings are an awkward mix of belly-flops, face-plants and lengthy skids. Only when it grinds to a halt does it gather its outstretched limbs together. By contrast, two more advanced species – the fire-bellied toad and the northern leopard frog – rotate their limbs forward in mid-air to land gracefully. The tailed frog managed to jump a similar distance, but its recovery time was longer.

These results support the idea that frogs eventually evolved their prodigious jumping abilities to escape from danger by rapidly diving into water. Landings hardly matter when you’re submerged and the ability to pull them off elegantly only evolved later. Essner thinks that doing so was fairly simple – if the tailed frog starts pulling its legs in just slightly earlier, it would land with far more poise. This simple innovation was probably a critical one in frog evolution. The primitive frogs never got there, but they have other ways of coping with their clumsy crash-landings. They’ve stayed very small to limit the injuries they sustain, and they have large shield-shaped piece of cartilage on their undersides to protect their soft vital organs.

Reference: Naturwissenschaften http://dx.doi.org/10.1007/s00114-010-0697-4; Video by Essner; soundtrack by me.

More on frogs: Tree frogs shake their bums to send threatening vibes, pesticide-stricken frogs, ‘Wolverine’ frogs, a lungless frog, and seven habits of highly successful toads

Marmot

Changing climate fattens marmots

The media is rife with tales of animals from polar bears to corals suffering as a result of climate change. But some species stand to gain from the rising global temperatures. In Colorado’s Rocky Mountains, warmer climes allow the yellow-bellied marmot to awaken from its winter hibernation earlier. With more time available to eat, they become bigger and so do their populations. In just three decades, their numbers have tripled.

Arpat Ozgul from Imperial College London studied a 33-year census of Colorado’s marmots, where individuals have been tracked over their entire lifetimes. These rodents spend the winter hibernating in their burrows. But since 1976, they have been waking up earlier and earlier in the year, presumably because of a rise in warm days. That gives them more time to eat and grow before their next hibernation, and the adults have become around 10% heavier. Ozgul found that being fatter offers many advantages for a marmot – females are more likely to breed, youngsters grow more quickly, and adults are more likely to survive their next bout of hibernation.

It’s no surprise that their population has shot up dramatically, although surprisingly, this wasn’t a gradual process. Their numbers seemed to be fairly stable but they passed a tipping point in 2000 and have skyrocketed ever since. By modelling the changes in their bodies over time, Ozgul concluded that the marmots haven’t changed much genetically – their extra pounds are the result of their response to environmental changes. For example, the bluebells that they like to eat declined after 2000, which might have prompted them to seek other fattier foods.

But Ozgul worries that this boom period has a bust on the horizon – it’s a short-term response to warmer climate. These are animals that are adapted to chilly mountainous temperatures and they don’t fare well in heat. If temperatures continue to rise and summers get longer and drier, their health might suffer and their populations might crash.

More on this story from Jess McNally at Wired and Lucas Laursen at Nature

Reference: Nature http://dx.doi.org/10.1038/nature09210; image by Ben Hulsey

More on climate change and animal populations: The rise of “weedy” mice, the mystery of the shrinking sheep, lost clownfish, marching emperor penguins, and declining amphibians and reptiles

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Mosses use explosive cannons and mushroom clouds to spread their spores

By Ed Yong | July 22, 2010 2:00 pm

Sphagnum-moss

As you read this, forceful explosions are rocking the planet, covering it in mushroom clouds. Thankfully, nuclear winter isn’t going to befall us quite yet. These explosions are caused by biological cannons rather than man-made bombs and the clouds they produce are mere millimetres high. They are the means by which peat mosses disperse their spores.

There are over 285 species of peat moss, all belonging to the genus Sphagnum. They are among the most common plants in the world, growing in the cold, moist parts of the Earth and covering about 1% of its land. They rely on the wind to disperse their spores and all of them face a similar problem. They grow in flat mats, which hug the ground at a level where the air is relatively still. Ideally, they need to get their spores into the ‘turbulent boundary layer’ – a zone up to 10cm off the ground, where swirls of air and sideways currents can carry the spores over long distances.

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CATEGORIZED UNDER: Plants

How I got my genes tested, and the birth of Science Writer Disease Risk Top Trumps

By Ed Yong | July 21, 2010 9:00 am

23andmekit

Thanks to genetic testing, I now know that If it were biologically possible to have a baby with Mark Henderson, Science Editor of the Times, that baby would be certain to have wet earwax. And he or she would definitely not have cystic fibrosis. Science!

This is all in aid of a session at the UK Conference of Science Journalists exploring the world of genetic testing, hosted by Mark, Daniel Macarthur from Genomes Unzipped and others. As part of the session, various journalists were offered the chance to get their genes tested for free by one of the three leading companies providing such services. I had a brief chat to Daniel about it, got his recommendations, and signed up. Four days later, a testing kit from 23andme arrived on my desk. I knew that 23andme had recently swapped some samples in a technical blunder but after reading Daniel’s blog, I was convinced that it was unlikely to happen again. If it did, I would enjoy finding out that I was secretly a black woman.

An hour later, I had delivered a dollop of my finest sputum into the tube they provided… and realised that I was only about a third of the way up to the fill-line. Doing this in the middle of the office was not a smart move. Ten further minutes later, and to a crescendo of laughter from my colleagues, the tube was full, sealed in a biohazard bag (I try not to take this as an indictment of my breath) and sealed in a Fed-ex envelope.  Four weeks later, the results arrived. The whole process couldn’t have been simpler.

In fact, it was perhaps too easy. Signing up to the 23andme site, verifying the code on my testing kit and preparing the sample took little more than an hour. I had to read and agree to documents that reassured me about the privacy of my information and provide consent to analyse my samples. The same documents warn about the possible psychological consequences of finding out your data and the limtiations of the resulting information (more on these later; meanwhile, I’ve uploaded the full consent form to Posterous so you can see it for yourself). Nonetheless, I was well aware of these risks. I could have found out that I have substantially high odds of developing life-threatening diseases. I could have discovered that I’m not actually related to my parents. This is not a bottle one can re-cork.

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MORE ABOUT: 23andme, gene testing
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