Archive for January, 2010

Photo safari – African hunting dogs

By Ed Yong | January 31, 2010 12:54 pm

This, sadly, isn’t part of the South African series. We weren’t quite lucky enough to see any hunting dogs there. For that, I had to make a trip to London Zoo yesterday. They were worth the price of admission in themselves though.

To me, these are the most beautiful of Africa’s predators. They are also the most successful, by some considerable margin. Attacking in large groups and built for long chases, around 80% of wild dog hunts end in a kill. This compares to a measly success rate of (I think) around 25% for the big cats.

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CATEGORIZED UNDER: Animals

Solving the San Francisco plankton mystery

By Ed Yong | January 30, 2010 12:00 pm

This article is reposted from the old WordPress incarnation of Not Exactly Rocket Science.

Look into the oceans past the sharks, seals and fish and you will find the tiny phytoplankton. These small organisms form the basis of life in the seas but if their populations get to big, they can also choke the life from it by forming large and suffocating algal blooms.

Solving the San Francisco plankton mysteryThe waters of San Francisco Bay have never had big problems with these blooms and if anything, scientists worried that the waters didn’t have enough phytoplankton. All that changed in 1999, when the phytoplankton population started growing. It has doubled in size since.

Now, scientists from the United States Geological Survey (USGS) have found that the blooms are the result of a long chain of ecological changes in the area. The plankton are just players in a large ensemble drama involves clams, mussels, fish, crabs and a cold snap.

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Rotifers find answer to parasites by blowing on the wind

By Ed Yong | January 28, 2010 2:00 pm

When our lives are in danger, some humans go on the run, seeking refuge in other countries far away from the threats of home. Animals too migrate to escape danger but one group – the pond-living bdelloid rotifers – have taken this game of hide-and-seek to an extreme.

If they are threatened by parasitic fungi, they completely remove any trace of water in their bodies, drying themselves out to a degree that their parasites can’t stand. In this desiccated state, they ride the wind to safety, seeking fresh pastures where they can establish new populations free of any parasites.

This incredible strategy may be partially responsible for another equally remarkable one – the complete abandonment of sex. For over 80 million years, the bdelloids (pronounced with a silent ‘b’) have lived an asexual existence. Daughters are identical clones of their mothers, budded off from her body. No males have ever been discovered. For this reason, Olivia Judson once described bdelloid rotifers as an “evolutionary scandal”. Their sexless lifestyles simply shouldn’t work in the long run.

Ditching sex allows an animal to efficiently pass all of its genes to the next generation without having to seek out a mate. This should give asexual animals a big advantage but not so. Sex provides fuel for evolution. Every time two individuals meet in flagrante, their chromosomes are joined, shuffled and re-dealt to the next generation. In this way, sex begets diversity, remixing genes into exciting new combinations.

This diversity is a vital weapon in the never-ending war against parasites. Parasites, with their large populations and short generations, are quick to evolve new ways of exploiting their hosts. They could have their run of a genetically uniform population and soon bring it to its knees. A sexually active species is a harder target. With genes that shuffle every generation, new anti-parasite adaptations are always just one bout of mating away. And so it goes, again and again, with hosts constantly having to outrun their parasites and sex acting as the getaway vehicle.

So asexual reproduction, for all its immediate gains, should be a poor long-term strategy compared to the dynamic nature of sex. Bdelloids have clearly addressed this problem and thanks to the last few years of research, we know how. They have evolved ways of achieving every single one of the many benefits of sex, without actually doing the deed. Escape parasites? They’ve got that covered. Shuffle their genes? They do that too. Generate genetic diversity? Check. 

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Terminally ill ants choose to die alone

By Ed Yong | January 28, 2010 12:00 pm

Captain_Oates.jpgIn 1912, Antarctic explorer Captain Lawrence Oates willingly walked to his death so that his failing health would not jeopardise his friends’ odds of survival. Stepping from his tent into a raging blizzard, he left his men with the immortal words, “I am just going outside and may be some time.” It was a legendary act of heroism but one that is mirrored by far tinier altruists on a regular basis – ants.

Like Captain Oates, workers of the ant species Temnothorax unifasciatus will also walk off to die in solitude, if they’re carrying a fungal infection. In fact, Jurgen Heinze and Bartosz Walter found that workers, regardless of the reason for their demise, take their last breaths in a self-imposed quarantine. A Temnothorax worker may spend its life in the company of millions, but it dies alone.

In nature, old age is a luxury that few individuals can afford. Most often, death comes at the hands of predators or parasites. In the latter case, dying individuals pose a massive threat to their peers. In the closely-packed, humid environment of a nest, infections can spread like wildfire. Metarhizium only becomes infectious a few days after its host succumbs – it takes that long to produce new spores. And by that point, the ants are long gone.

Heinze and Walter treated 70 workers with spores of the parasitic fungus Metarhizium anisopliae. Three-quarters of them were dead within ten days. Of these, at least 70% voluntarily left the colony either hours or even days before that point and died well away from their nestmates. Another 21% were found dead outside the nests. It wasn’t clear if they had left themselves or been evicted but certainly, the other ants don’t treat infected workers any differently.

The tiny hermits never try to return home. They don’t forage for food or water. They never try to get in touch with nestmates. If they’re returned home, they’ll actively try to flee again. As Heinze and Walter say, this appears to be “an active and, in most cases, adaptive response of the dying ant to its own condition.”

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MORE ABOUT: alone, ant, die, solitude, temnothorax

What colours were dinosaur feathers?

By Ed Yong | January 27, 2010 1:00 pm

Sinosauropteryx.jpg

Dinosaur books have become more colourful affairs of late, with the dull greens, browns and greys of yesteryear replaced by vivid hues, stripes and patterns. This has largely been a question of artistic licence. While fossils may constrain an artist’s hand in terms of size and shape, they haven’t provided any information about colour. But that is starting to change.

The fossils of some small meat-eating dinosaurs were covered in filaments that are widely thought to be the precursors of feathers. And among these filaments, a team of Chinese and British scientists have found the distinctive signs of melanosomes, small structures that are partly responsible for the colours of modern bird feathers.

Melanosomes are packed with melanins, pigments that range from drab blacks and greys to reddish-brown and yellow hues. Their presence in dinosaur filaments has allowed Fucheng Zhang to start piecing together the colours of these animals, millions of years after their extinction. For example, Zhang thinks that the small predator Sinosauropteryx had “chestnut to reddish-brown” stripes running down its tail and probably a similarly coloured crest down its back. Meanwhile, the early bird Confuciusornis had a variety of black, grey, red and brown hues, even within a single feather.

Zhang’s discovery also launches another salvo into a debate over the very nature of “feathered” dinosaurs. Beautiful fossils, mainly from China, show that several species of dinosaur had feathers akin to the flight-capable plumes of modern birds. Species like Caudipteryx and the four-winged Microraptor had true feathers with asymmetric vanes arranged around a central shaft.

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Rebooting science journalism – thoughts from Timmer

By Ed Yong | January 26, 2010 9:30 am

Rebooting-science-journalis.jpg

Colour? Science journalists care not for colour.

It’s been more than a week since ScienceOnline 2010. Like many other people who went, I’m recovering from the disease that has become known as Scio10 plague, or sciflu, or Ed Yong plague (curse you, Skloooot!) and the depression of not being surrounded entirely by passionate, enthusiastic, ground-breaking people. Which explains why it’s taken me this long to post reflections on the Rebooting Science Journalism session that I chaired. This will come but, for now, my co-panellist John Timmer has kindly provided his own ruminations. This is, incidentally, the first guest post that anyone’s ever done for this blog but I’ll happily make an exception for a journalist of John’s calibre. Here he:

One of the odd things about actually being on the Rebooting Science Journalism panel is a product of the fact that we turned over everything to the audience after we’d had our say. We never got the chance to ask each other questions, or try to sum up everything that was said during the session. But one of the ideas we all seemed to agree on is that the medium doesn’t matter, so I’m going to borrow Ed’s blog to try to piece together my take on what was said and see if I can get my fellow panelists and anyone else who may be interested to let me know what they think.

I came away with two pairs of related concepts. The first set came from David Dobbs, who noted there’s two things about science that really motivate our writing: “wow, that’s neat,” and “hrm, that’s strange.” As Ed noted, if someone’s feeling that motivation, it doesn’t matter if they’re a blogger, podcaster, print journalist, etc.–the distinctions really aren’t clear, and we’ve had too many examples of both excellent and awful things done in all formats to find any of them inherently superior.

Ed mentioned that he starting writing this blog because he kept getting his story ideas turned down, and it’s clear from the content here that he’s got no shortage of good ideas and good writing, regardless of what editorial decisions he’s suffered through. In the same way, Carl described how a story he wanted to do got turned down by the Times; when he put it on his blog, complete with a video of duck erections, it got over a hundred thousand views.

These are examples of what you might call “pull”–stories so compelling that they’ll bring readers in to see what’s happening no matter where they appear. I tried (with less success than I’d like) to argue that we also need push, sites that put science in front of a set of readers that aren’t necessarily looking for it, and in fact may find it seriously uncomfortable. (Bora argues for the same thing in this video, but focuses on TV and the radio. I think pushing works in all media.) I think we need a bit of both if we’re going to provide the sort of functions that we generally agree that science journalism should: provide accurate information to the public about a field that has important things to say about everything from human nature to policy decisions.

(What I was attempting to argue was that we’ve got all these researchers who are now interested in writing for a popular audience, and a lot of sites that are like Ars, with a large readership that might be open to reading more quality science journalism. We need to do more to try to get the two together–to do more to push science writing. Unfortunately, I had the sense that I was running badly over my time limit, and never got around to making this explicit.)

Thinking about it since, I’ve been convincing myself that these two pairs of ideas–neat/strange and pull/push–are somewhat related. It’ll take a couple of paragraphs to explain why, but I’ll start with this: the popularity of stories like Carl’s duck sex videos requires an interplay between the pull–a compelling topic and Carl’s excellent writing–and dozens of small pushes. I’m not sure of the ratio among them, but the people who read stories like that find them through a combination of word-of-mouth (or modern equivalents, like Twitter), social news sites like Digg, and news aggregators like Slashdot and Boing Boing.

We don’t really have much control over word-of-mouth and, in part because of the dismal understanding of science, stories that do well on places like Digg often have only a passing resemblance to science (something that the “wisdom of the crowd” advocates would do well to note). But I’d argue that the aggregators are probably a major factor in determining which stories go big, and they fall roughly within the push category. So, the difference between pushing and pulling stories, like so many things in life, isn’t a simple binary distinction.

I’ll now loop back to my idea, which is the fact that we’ve got a ton of quality people interested in communicating science, and a lot of sites that are staffed by people with only the vaguest familiarity with what constitutes good science. I’m consistently amazed by the sheer volume of garbage that winds up being featured within the science category at Slashdot. If someone with a good science background went to the people responsible for one of those sites and offered to help provide a degree of credibility to the science section, would those managers respond positively? I’d bet some of them would, though I’d be interested in hearing whether anybody’s actually tried and been turned down.

All of which sets me up to loop back to David’s pair of motivations for science coverage, the “neat vs. something odd” tension. I worry that the increasing reliance on pulling readers places an undue emphasis on the stories about something neat. The stories we write when something smells funny are equally important, and can help the public understand the limits of what we can say about many areas of science, so de-emphasizing them comes at a real cost. This is especially true for the stories that are a bit of both: sounds neat, but smells odd. A lot of the more popular, “pull” coverage of these tends to emphasize the neatness at the expense of highlighting issues with data or interpretation, and that’s a significant loss when it comes to public understanding.

Of course, these are just the ideas that I came away with, and I’d expect that my fellow panelists might have been drawn in other directions, or have some thoughts on the above. If so, I’m looking forward to hearing them.

CATEGORIZED UNDER: Journalism

Review: The Immortal Life of Henrietta Lacks by Rebecca Skloot

By Ed Yong | January 25, 2010 6:04 pm

Look in any biomedical laboratory, and you will find HeLa cells. Over 50 million tonnes of these cells have been grown in churning vats of liquid all over the world. They have been one of the most important tools in modern medicine, pushing forward our understanding of cancer and other diseases, and underpinning the polio vaccine, IVF, cloning, and more. None of these advanced would have been feasible without HeLa. Most scientists have used or seen them but most have no idea about their origin. It’s time to find out.

In early 1951, there was only one place in the world where HeLa cells could be found – the cervix of a poor, black tobacco farmer called Henrietta Lacks. She was treated for cervical cancer at Johns Hopkins Hospital where, without her knowledge or consent, doctors took some cells from her tumour and cultured them. They became HeLa – the immortal line of cells that would change the world. Henrietta died in the same year. Her family only learned of her “immortality” more than 20 years later, when scientists started using them in research, again without informed consent, to better understand Henrietta’s cells. The cells launched a multimillion-dollar industry that sells human biological materials but her family cannot afford health insurance.

The remarkably story of Henrietta’s life, cells and family are now coming to light, narrated in an equally remarkable book – Rebecca Skloot’s The Immortal Life of Henrietta Lacks. Skloot is a veteran science journalist and first-time author and her debut is thrilling and original non-fiction that refuses to be shoehorned into anything as trivial as a genre. It is equal parts popular science, historical biography and detective novel. It reads as evocatively as any work of fiction, with dialogue, characters and settings vividly reconstructed from archived material, legal documents and thousands of hours of interviews. Like a mystery, the chronology flits back and forth from the first and last days of Henrietta’s life, the decades of discovery that followed her death and Skloot’s own modern-day quest to uncover the story.

Indeed, Skloot repeatedly appears as a character in her own book, narrating her journey from first hearing about HeLa cells in a classroom to her attempts to contact and support the Lacks family. This literary device could easily have come across as self-aggrandising but Skloot fully earns her status as the story’s third protagonist. Her narration reveals the trials that the Lacks family have undergone since Henrietta’s cells went global, and the sheer amount of trust it took to uncover the details of this story.

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CATEGORIZED UNDER: Uncategorized

Echolocation in bats and whales based on same changes to same gene

By Ed Yong | January 25, 2010 12:00 pm

Millions of years before humans invented sonar, bats and toothed whales had mastered the biological version of the same trick – echolocation. By timing the echoes of their calls, one group effortlessly flies through the darkest of skies and the other swims through the murkiest of waters. It’s amazing enough that two such different groups of mammals should have evolved the same trick but that similarity isn’t just skin deep.

The echolocation abilities of bats and whales, though different in their details, rely on the same changes to the same gene – Prestin. These changes have produced such similar proteins that if you drew a family tree based on their amino acid sequences, bats and toothed whales would end up in the same tight-knit group, to the exclusion of other bats and whales that don’t use sonar.

This is one of the most dramatic examples yet of ‘convergent evolution’, where different groups of living things have independently evolved similar behaviours or body parts in response to similar evolutionary pressures.

It is one of a growing number of studies have shown that convergence on the surface – like having venom, being intelligent or lacking enamel – is borne of deeper genetic resemblance. But this discovery is special in a deliciously ironic way. It was made by two groups of scientists, who independently arrived at the same result. The first authors even have virtually identical names. These are people who take convergence seriously!

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South African wildlife – Cape buffalo

By Ed Yong | January 23, 2010 12:00 pm

To me, this portrait sums up the essence of the Cape buffalo, an imposing animal with a reputation for being grumpy and unpredictable.

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CATEGORIZED UNDER: Animals, South African wildlife

Slime mould attacks simulates Tokyo rail network

By Ed Yong | January 21, 2010 2:00 pm

In a Japanese laboratory, a group of scientists is encouraging a rapidly expanding amoeba-like blob to consume Tokyo. Thankfully, the blob in question is a “slime mould” just around 20cm wide, and “Tokyo” is represented by a series of oat flakes dotted about a large plastic dish. It’s all part of a study on better network design through biological principles. Despite growing of its own accord with no plan in mind, the mould has rapidly produced a web of slimy tubes that look a lot like Tokyo’s actual railway network.

The point of this simulation isn’t to reconstruct the monster attacks of popular culture, but to find ways of improving transport networks, by recruiting nature as a town planner. Human societies depend on good transport networks for ferrying people, resources and information from place to place, but setting up such networks isn’t easy. They have to be efficient, cost-effective and resistant to interruptions or failure. The last criterion is particularly challenging as the British public transport system attests to, every time a leaf or snowflake lands on a road or railway.

Living thing also rely on transport networks, from the protein tracks that run through all of our cells to the gangways patrolled by ant colonies. Like man-made networks, these biological ones face the same balancing act of efficiency and resilience, but unlike man-made networks, they have been optimised through millions of years of evolution. Their strategies have to work – if our networks crash, the penalties are power outages or traffic jams; if theirs crash, the penalty is death.

To draw inspiration from these biological networks, Atsushi Tero from Hokkaido University worked with the slime mould Physarum polycephalum. This amoeba-like creature forages for food by sending out branches (plasmodia) from a central location. Even though it forms vast, sprawling networks, it still remains as a single cell. It’s incredibly dynamic. Its various veins change thickness and shape, new ones form while old ones vanish, and the entire network can crawl a few centimetres every hour.

For a mindless organism, the slime mould’s skill at creating efficient networks is extraordinary. It can find the most effective way of linking together scattered sources of food, and it can even find the shortest path through a maze. But can it do the same for Tokyo’s sprawling cityscape?

Tero grew Physarum in a wet dish at a place corresponding to Tokyo, with oat flakes marking the locations of other major cities in the Greater Tokyo Area. Physarum avoids bright light, so Tero used light to simulate mountains, lakes and other prohibitive terrain on his miniature map. The mould soon filled the space with a densely packed web of plasmodia. Eventually, it thinned out its networks to focus on branches that connected the food sources. Even by eye, these final networks bore a striking similarity to the real Tokyo rail system.

The mould’s abilities are a wonder of self-optimisation. It has no sense of forward-planning, no overhead maps or intelligence to guide its moves. It creates an efficient network by laying down plasmodia indiscriminately, strengthening whatever works and cutting back on whatever doesn’t. The approach seems as haphazard as a human planner putting railway tracks everywhere, and then removing the ones that aren’t performing well. Nonetheless, the slime mould’s methods (or lack thereof) produced a network with comparable cost, efficiency and tolerance for faults to the planned human attempt.

Tero tried to emulate this slime mould’s abilities using a deceptively simple computer model, consisting of an randomly meshed lattice of tubes. Each tube has virtual protoplasm flowing through it, just as the branches of the slime mould do. The faster the flow rate, the wider the tube becomes. If the flow slows, the tubes thin and eventually disappear.

Tweaking the specific conditions of the model produced networks that were very similar to those of both live Physarum and Tokyo’s actual rail system. Tweaking it further allowed Tero to boost the system’s efficiency or resilience, while keeping its costs as low as possible. This, perhaps, is the engineering of the future – a virtual system inspired by a biological one that looks a lot like a man-made one.

Reference: Tero et al. 2010. Rules for Biologically Inspired Adaptive Network Design. Science 10.1126/science.1177894

More on slime moulds: Predatory slime mould freezes prey in large groups

Images: from AAAS/Science

CATEGORIZED UNDER: Biotechnology, Technology
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