Archive for December, 2009

Happy New Year!

By Ed Yong | December 31, 2009 4:00 pm

This has been A Good Year TM. I won an award, had fun reporting on the eye-opening World Conference of Science Journalists, finally joined Twitter, spoke at Science Online London and was promoted at work.

On top of that, this blog has gone from strength to strength thanks to the promotional efforts of the folks here at ScienceBlogs and the word-spreading antics of you readers. This last month, the blog has seen the largest amount of traffic it has ever seen, about four times the level of the same time last year.

So thank you to everyone for continuing to read what I churn out. It means a lot. If you want to get more of my ramblings, you can also follow me on Twitter or become a fan of this blog on Facebook.

I’ll endeavour to provide the same quality of news coverage with perhaps a few more opinion pieces on journalism and science communication, and one or two satirical send-ups. And I want to point out that Not Exactly Rocket Science has been, and always will be, free. In an age where paywalls are popping up around news sources all over the place, this blog will continue to be a place where people can get their science news solely for the price of their time.

Finally, I need to thank my amazing wife Alice, whose photo graces the sidebar. None of this would be possible without her support.

So Happy New Year everyone. I hope that, as the 21st century enters its difficult second album, you all have yourselves A Good Year TM.


Evolution without genes – prions can evolve and adapt too

By Ed Yong | December 31, 2009 2:00 pm

If you search for decent definitions of evolution, the chances are that you’ll see genes mentioned somewhere. The American Heritage Dictionary talks about natural selection acting on “genetic variation”, Wikipedia discusses “change in the genetic material of a population… through successive generations”, and TalkOrigins talks about changes that are inherited “via the genetic material”. But, as the Year of Darwin draws to a close, a new study suggests that all of these definitions are too narrow.

Prions.jpgJiali Li from the Scripps Institute in Florida has found that prions – the infectious proteins behind mad cow disease, CJD and kuru – are capable of Darwinian evolution, all without a single strand of DNA or its sister molecule RNA.

Prions are rogue version of a protein called PrP. Like all proteins, they are made up of chains of amino acids that fold into a complex three-dimensional structure. Prions are versions of PrP that have folded incorrectly and this misfolded form, called PrPSc, is social, evangelical and murderous. It converts normal prion proteins into a likeness of its abnormal self, and it rapidly gathers together in large clumps that damage and kill surrounding tissues.

Li has found that variation can creep into populations of initially identical prions. Their amino acid sequence stays the same but their already abnormal structures become increasingly twisted. These “mutant” forms have varying degrees of success in different environments. Some do well in brain tissue; others thrive in other types of cell. In each case, natural selection culls the least successful ones. The survivors pass on their structure to the “next generation”, by altering the folds of normal prion proteins.

This process follows the principles of Darwinian evolution, the same principles that shape the genetic material of viruses, bacteria and other living things. In DNA, mutations manifest as changes in the bases that line the famous double helix. In prions, mutations are essentially different styles of molecular origami. In both cases, they are selectively inherited and they can lead to adaptations such as drug resistance. In prions, it happens in the absence of any genetic material. 

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CATEGORIZED UNDER: Evolution, Medicine & health

Not Exactly Rocket Science Review of 2009

By Ed Yong | December 30, 2009 9:30 am

I don’t really like end-of-the-year lists. They seem a bit too self-knowing and forced, and there are just so many of them, particularly because we’re heralding the end of a decade too. I half-expect someone to create a Top Ten Years of the Decade list (and Time Out would probably put 1977 in there just to be edgy).

This might seem like a funny way of introducing an end-of-the-year list, but I’ve tried to make this one a bit different. This is not a collection of the “top” scientific discoveries of the year. I’m not calling them “breakthroughs”. I’m not judging them on such abstract and subjective measures as “quality” or “significance”. There is no Ardi and no ice on the moon.  

Instead, this is a list of stories that have made you and I widen our eyes in collective excitement. It was chosen by you readers through a series of nine polls. It reflects the fact that science has a value that goes well beyond practical applications. The coolest discoveries expand our knowledge about the world around us and our place in it. They make us wonder. They make us want to know more. I’ve learned a great deal through writing for this blog over the last 12 months and I hope that I’ve been able to share at least some of that successfully with you lot.

So without any further fanfare, the list:

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Treating tinnitus with an individually tailored piece of music

By Ed Yong | December 29, 2009 9:30 am

Many of us have just spent the Christmas season with a persistent and irritating ringing noise in our ears. But now that the relatives have gone home for the year, it’s worth remembering that a large proportion of the population suffers from a more persistent ringing sensation – tinnitus. It happens in the absence of noise, it’s one of the most common symptoms of hearing disorders, and it’s loud enough to affect the quality of life of around 1-3% of the population. 

There have been many suggested treatments but none of them have become firmly established and most simply try to help people manage or cope with their symptom. Now, Hidehiko Okamoto from Westfalian Wilhelms University has developed a simple, cheap and enjoyable way of reducing the severity of the ringing sound. The treatment has showed some promise in early trials and even better, it is personally tailored to individual patients. 

The method is simple. Find out the main frequency of the ringing sound that the patient hears – this becomes the target. Ask the patient to select their favourite piece of music and digitally cut out the frequencies one octave on either side of this target. Get the patient to listen to this “notched” piece of music every day. Lather, rinse and repeat for a year.

Okamoto tried this technique in a small double-blind trial of 23 people, eight of whom were randomly selected to receive the right treatment. Another eight listened to a piece of music that had a random set of frequencies cut out of it, while seven were just monitored. The treatment seemed to work. After a year, the treatment group felt that their ringing sensation was around 30% quieter, while the other two groups showed no improvements.

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MORE ABOUT: Music, notched, tinnitus

Three desert lizards evolve white skins through different mutations to the same gene

By Ed Yong | December 28, 2009 5:30 pm

In the White Sands National Park of New Mexico, there are three species of small lizard that all share white complexions. In the dark soil of the surrounding landscapes, all three lizards wear coloured coats with an array of hues, stripes and spots. Colours would make them stand out like a beacon among the white sands  so natural selection has bleached their skins. Within the last few thousand years, the lesser earless lizard, the eastern fence lizard and the little striped whiptail have all evolved white forms that camouflage beautifully among the white dunes.

Erica Bree Rosenblum from the University of Idaho has found that their white coats are the result of changes to the same gene, Mc1r. All of these adaptations arose independently of one another and all of them reduce the amount of the dark pigment, melanin, in the lizards’ skin.  It’s a wonderful example of convergent evolution, where the same environmental demands push different species along the same evolutionary paths. But Rosenblum has also found that there are many ways to break a gene.

Each of the three lizards has a different mutation in their Mc1r gene, that has crippled it in diverse ways. These differences may seem slight, but they affect how dominant and widespread the white varieties are, and how likely they are to branch off into new species of their own. Even when different species converge on the same results – in this case, whitened skin – and even when the same gene is responsible, their evolutionary paths can still be very different.

The Mc1r gene encodes a protein called the melanocortin 1 receptor (MC1R). It’s a messenger that sits astride the cell’s membrane and transmits messages across it. It triggers a sequence of events that stimulates the production of the dark pigment melanin. In this way, it affects the skin colour of many animals and faulty copies of the gene tend to result in lighter colours. In humans, for example, around 80% of redheads owe their hair colour to common faulty variant of Mc1r.

In each of the White Sands lizards, just one of the MC1R protein’s many amino acids has been swapped (red circles above), and it’s a different one in each species. All three amino acids lie within the part of the protein that straddles the cell membrane. These regions are important for keeping the protein together, and for channelling signals from one side of the membrane to another.

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CATEGORIZED UNDER: Evolution, Lizards, Reptiles

Vote for your story of the year – final mopping-up round

By Ed Yong | December 28, 2009 9:30 am

This is the final round of voting for the NERS stories-of-the-year polls. So far, there have been eight polls, each covering a different scientific field and I’m going to collate the results of these in the next couple of days. But before I do, there have been a few straggler stories that may deserve a place on the list. Here’s your pick:

What’s your favourite story of the last month?(polls)


The 13,000-year old tree that survives by cloning itself

By Ed Yong | December 26, 2009 12:00 pm

In California’s Jurupa Mountains, there is a very unusual group of tree – a Palmer’s oak. Unlike the mighty trees that usually bear the oak name, this one looks like little more than a collection of small bushes. But appearances can be deceiving. This apparently disparate group of plants are all clones of a single individual, and a very old one at that.

By repeatedly cloning itself, the Palmer’s oak has lived past the separation of Britain from continental Europe, the demise of the mammoths and saber-toothed cats, and the birth of human agriculture. It is among the oldest plants in existence, first sprouting from an acorn around 13,000 years ago. According to the creationist view of history, this tree was around 7,000 years old when the universe was created.


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CATEGORIZED UNDER: Plants, Sex and reproduction
MORE ABOUT: Jurupa, oak, oldest, Palmer's, tree

One parasite to rule them all – Wolbachia protects against mosquito-borne diseases

By Ed Yong | December 24, 2009 1:32 pm

This is an updated version of the first post I wrote this year. The scientists in question were looking at ways of recruiting bacteria in the fight against mosquito-borne diseases, such as dengue fever. They’ve just published new results that expand on their earlier experiments.

Mosquitoes are incredibly successful parasites and cause millions of human deaths every year through the infections they spread. But they are no match for the most successful parasite of all – a bacterium called Wolbachia. It infects around 60% of the world’s insect species and it could be our newest recruit in the fight against malaria, dengue fever and other mosquito-borne infections.

Lolbachia1.jpgWolbachia doesn’t usually infect mosquitoes but Scott O’Neill from the University of Queensland is leading a team of researchers who are trying to enlist it. Earlier this year, they published the story of their first success. They had developed a strain that not only infects mozzies, but halves the lifespans of infected females. Now, as the year comes to an end, they’re back with another piece of good news – their life-shortening bacteria also guard the mosquitoes from other infections.

It protects them against a species of Plasmodium, related to the parasite that causes malaria in humans, as well as the viruses responsible for dengue fever and Chikungunya. Infected insects are less likely to carry parasites that cause human disease, and those that do won’t live long enough to spread them. It’s a significant double-whammy that could have a lot of potential in controlling mosquito-borne diseases.

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You're having fun when time flies

By Ed Yong | December 23, 2009 9:30 am

They say that time flies when you’re having fun but it also works the other way round. If you make people think that time is passing more quickly, you can make tasks more fun, noises less irritating and good songs even better.

   I’M NOT HAVING FUN!It’s clear that our perception of the passage of time depends on how we spend it. When we’re motivated, engaged or alert, it shoots by and when there’s nothing to occupy our minds, it slows to a crawl. This was demonstrated most evocatively by a French geologist called Michel Siffre, who spent 2 months in a cave, completely isolated from human contact, clocks or daylight. He emerged after 59 days but thought that he had spent just 25.

We’re so familiar with this effect that it can lead to faulty causal deductions. When our sense of time is distorted, we look for an explanation. And the most obvious one is that we’re doing something that’s either more or less fun.

Aaron Sackett form the University of Chicago demonstrated this through a series of clever experiments. First, he led 37 students into a room, deprived them of clocks and phones, started a stopwatch and asked them to underline specific words in a text. They were told they had 10 minutes, but Sackett told them their time was up after either 5 or 20 minutes. Alternatively, he came back after 10 minutes and said that 5 or 20 minutes had passed.

In both cases, preset stopwatches sealed the illusion. And in both studies, students who thought that time had flown by rated the test as more enjoyable, challenging, engaging and fun than those who were fooled into thinking that time had dragged.

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CATEGORIZED UNDER: Neuroscience and psychology
MORE ABOUT: fun, time flies

Ballistic penises and corkscrew vaginas – the sexual battles of ducks

By Ed Yong | December 22, 2009 7:10 pm

Patricia Brennan from Yale University is trying to encourage male Muscovy ducks to launch their ballistic penises into test tubes.

Normally, the duck keeps its penis inside-out within a sac in its body. When the time for mating arrives, the penis explodes outwards to a fully-erect 20cm, around a quarter of the animal’s total body length. The whole process takes just a third of a second and Brennan captures it all on high-speed camera. This isn’t just bizarre voyeurism. Duck penises are a wonderful example of the strange things that happen when sexual conflict shapes the evolution of animal bodies.

Childhood… violated… Innocence… lost… SCIENCE!Many ducks form bonds between males and females that last for a whole mating season. But rival males often violently force themselves onto females. To gain the edge in these conflicts, drakes have evolved large corkscrew phalluses, lined with ridges and backward-pointing spines, which allow them to deposit their sperm further into a female than their rivals. These extreme penises are even more unusual when you consider that 97% of bird species lack any penises whatsoever.

But female ducks have developed countermeasures. Their vaginas are equally long and twisting, lined with dead-end pockets and spirals that curve in the opposite direction. They are organic chastity belts, evolved to limit the effectiveness of the males’ lengthy genitals. Two years ago, Brennan showed that duck species whose males have the longest penises tend to have females with the most elaborate vaginas. Now, she has found further evidence that these complex genitals are the result of a long-lasting war of the sexes.

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