The Great Beyond

by Heidi Ledford

So what does a swinging Nature reporter do on a Thursday night? Given yesterday’s news that there was an online protein folding game (Economist;MIT Technology Review), isn’t the answer obvious?

The game is called Foldit, and it lets users manipulate different parts of a protein (amino acid sidechains, beta sheets, and helices) to optimize its 3-D structure. A tutorial guided by a cartoon image of protein structure guru David Baker (University of Washington), complete with his trademark unruly ‘Einstein-the-early-years’ hair, teaches you a few basics: bring your sheets together to allow hydrogen bonding between them, and don’t let your amino acid sidechains bump into each other.

Wannabe structural biologists can download it here. Baker and his colleagues previously designed a program called Rosetta@home that harnesses idle computers to solve protein structures. But users who downloaded the program watched as their computers cranked away evaluating different structural possibilities and began to wonder: might a human do better? The Howard Hughes Medical Institute’s press release quotes Baker: “People were writing in, saying, `Hey! The computer is doing silly things! It would be great if we could help guide it.”

So now the skeptics get to try their hand. I gave the game a quick try, just enough to make it through the tutorial and take a stab at the first challenge puzzle: a beginner’s task based on a protein from a bacteria that can cause strep throat. (Somewhere around the sixth or seventh puzzle in the tutorial my mind started to wander and I turned on the webcast of the mock news program Colbert Report from the previous night. I finished the puzzle somewhere between when Stephen Colbert declared: “Scientists are so snooty” and when he shocked himself on a homemade electromagnet.)

Overall, I’m hooked. Not cancel-my-weekend-plans hooked, but I’ve definitely found a new way to procrastinate. I’d say you don’t necessarily learn a whole lot about protein structure, but really, did you want to? And if you did, they provide a separate tutorial that covers the details. Meanwhile, the game does give you that conceptual sense of how elegant (and frustratingly delicate) protein structure can be.

According to one press release, the high score could earn the winner a Nobel Prize for medicine. But I won’t hold my breath.

Posted by Nicola Jones on May 09, 2008
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Flowers have been found to have several tricks up their, um, sleeves when it comes to attracting pollinators, according to two reports we spied today.

First off, they wave at passing insects to attract their attention (BBC).

John Warren from the University of Aberystwyth was apparently inspired by watching flowers waving about in the wind at his daughter’s birthday, and wondering why they risked having their slender stems snapped by such movement. Not finding much in the literature, he set out to find an answer.

In a study of 300 specially grown flowers of varying stem lengths, tall wavy flowers attracted more pollinators, they found (Journal of Evolutionary Biology). Sadly the story doesn’t say by how much, nor is this mentioned in the freely available abstract… though the abstract does add that insects stayed on wobbly flowers less long than they did on stationary ones. (If only Wordsworth knew there was a reason for his host of daffodils "fluttering and dancing in the breeze" his poem might have been different).

Secondly, researchers have found just how effective orchids can be at mimicking female wasps, as a way to lure male wasps in to collect their pollen (Reuters). Not only do they attract the boys (which was already known), but they also seem to excite them enough to cause an ejaculation (releasing “copious sperm” according to the report). Obviously this is a waste of time and energy for the wasps, but apparently it helps the orchids, somehow – I guess by increasing stickiness? “Orchid species provoking such extreme pollinator behavior have the highest pollination success," they report in The American Naturalist.

Photo by Keith Weller, USDA

Posted by Nicola Jones on May 08, 2008
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Baby birds babble before they learn to speak properly, just like human babies. Intriguingly, according to a new study published this week in Science, a totally different part of the brain seems to be used in babbling than is used in proper, adult speech patterns.

When researchers at MIT disabled part of the brain used in learning called the LMAN (lateral magnocellular nucleus of the nidopallium) the young birds stopped babbling. However, young birds who had an area called the high vocal centre or HVC disabled continued to babble, despite the HVC being a key area for singing in adults

When the researchers shut down the HVC in adult birds, they stopped singing and reverted to babbling (press release).

“The main point of our finding is that the child-like behaviour of young animals may not be just because they have an immature form of the circuitry that makes adult behaviours, but because they have special circuits in the brain that purposefully drive their exploratory and random-looking behaviours,” says author Michale Fee (Daily Telegraph).

“I suspect that there is a similar process going on in the brain of the human infant as he learns how to speak and how to convey meaning.”

That experiment could be harder to get ethical approval for.

Audio clips and more news coverage below the fold...

Continue reading "Audio special: babbling bird brains" »

Posted by Daniel Cressey on May 02, 2008
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A new genus of rather ugly parasitic plant should finally be named this year, two decades after a lone example was first examined by botanists.

The weird thing, a type of Orobanchaceae, has completely lost its chlorophyll and leaches nutrients and water out of its host tree.

In 1985 a researcher named Wayt Thomas from the New York Botanical Garden first obtained a sample of the plant in Mexico. It remained unidentified until 20 years later when George Yatskievych, of the Missouri Botanical Garden, set out to find it.

“I’ve always been interested in plants that don’t fit the preconceived notion of what
plants should be,” he says (press release pdf). “The specimen collected by Dr Thomas was so unusual that I had to see for myself what it looked like alive.”

Continue reading "Parasitic hermit plant found in Mexico" »

Posted by Daniel Cressey on May 01, 2008
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We’re one step closer to making synthetic spider silk, thanks to work by researchers in Germany.

Sebastian Rammensee and colleagues have constructed a microfluidic device which combines two spider silk proteins into fibers.

“The major breakthrough is that this is the first time one has produced fully synthetic silk threads and understood why,” says Andreas Bausch, co-author on a new paper describing the device in PNAS (quoted in the Daily Telegraph).

The Independent gets excited about all the things we could make with super-synthetic-silk: “from bullet-proof vests and lightweight material for parachutes, to extremely strong ropes and fishing nets that will decompose quickly if lost at sea” or even “biodegradable sutures for sealing up internal wounds”.

The research team believe three stages are needed for fibers to form. The proteins must condense into spherical particles; pH must drop; and then particles must be forced to slide past each other in a thin chamber.
Both New Scientist and Scientific American go into the technical details.

Image: Corbis

Posted by Daniel Cressey on April 29, 2008
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A humongous – though technically only colossal -- squid is about to be dissected live over the internet.

This rare example of a colossal squid (Mesonychoteuthis hamiltoni) was frozen when it was pulled out of the sea early in 2007. Now researchers at Te Papa museum in New Zealand are defrosting it in preparation for its autopsy.

“They’re incredibly rare - this is probably one of maybe six specimens ever brought up,” says Carol Diebel, director of natural environment at the museum (BBC).

Continue reading "Live super-size squid autopsy" »

Posted by Daniel Cressey on April 28, 2008
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Analysis of a protein from Tyrannosaurus Rex confirms that our modern chickens really are descendants the closest living relatives of the fearsome beast. The finding has divided opinion over whether it means we should have more respect for the humble chicken, or whether we should instead look down on T. Rex for its pathetic, distant offspring relation.*

Researchers from the United States this week report the first use of analysis of a protein, in this case extracted from a femur found in 2003, to place a non-avian dino in the ‘tree of life’. The team also did the same thing for the mastodon, unsurprisingly finding it grouped with modern elephants (new paper in Science).

“We determined that T. rex, in fact, grouped with birds – ostrich and chicken – better than any other organism that we studied,” says John Asara, of the Harvard Medical School (press release). “We also showed that it groups better with birds than modern reptiles, such as alligators and green anole lizards.”

Continue reading "Protein shows chicken’s dino heritage" »

Posted by Daniel Cressey on April 25, 2008
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Our brains show distinctive patterns in the moments before we make mistakes, according to new research. This could one day lead to monitoring of those doing critical jobs, to prevent mistakes before they even happen.

Using MRI scans, Tom Eichele and colleagues found certain brain regions activated 30 seconds before errors were made by study subjects performing a simple repetitive task (research paper in PNAS). A number of news outlets note that previous studies have shown similar activity, but only seconds before errors.

Fellow author Stefan Debener, of the University of Southampton, likens this to the person switching to autopilot.

“The brain begins to economise, by investing less effort to complete the same task,” he says (BBC). “We see a reduction in activity in the prefrontal cortex. At the same time, we see an increase in activity in an area which is more active in states of rest, known as the Default Mode Network (DMN).”

Continue reading "Seeing mistakes before they happen" »

Posted by Daniel Cressey on April 23, 2008
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A Swedish university last week announced the discovery of the ‘world’s oldest living tree’, a 9,550 year old spruce. This is far older than previous record holders, says Umeaa University, which were North American pines dated to around 4,500 years ago.

Researchers found wood from four generations of spruces in the Dalarna province and dated these to 375, 5,660, 9,000 and 9,550 years old. These remains have the same genetic makeup as the trees above them, says the university (press release, news coverage).

However the press release notes that “Since spruce trees can multiply with root penetrating braches, they can produce exact copies, or clones. ... Although summers have been colder over the past 10,000 years, these trees have survived harsh weather conditions due to their ability to push out another trunk as the other one died.”

This makes me wonder if there isn’t a classification argument here, and whether this really counts as the world’s oldest tree.

Continue reading "‘World’s oldest tree’ found in Sweden" »

Posted by Daniel Cressey on April 21, 2008
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Birds in Africa post their fellow warblers on sentry duty where they sing a song of reassurance to their foraging friends, researchers report.

One pied babbler gives a distinctive watchman’s song, which makes other birds more comfortable in their feeding, the researchers from the UK’s University of Bristol discovered.

“These exciting results point to a great example of true cooperation,” says Andy Radford (press release). “The unselfish behaviour of the sentry is probably rewarded down the line by the improved survival of group mates, which leads to a larger group size. This increases the sentinel’s chances of survival when the group is under attack from predators or having to repel rivals from their territory.”

Radford’s team found that birds who heard recordings of the watchman’s song spent less time looking for predators and spread out more widely. This meant that they caught more food, the team showed.

The pied babblers used in the study are accustomed to researchers so they could be closely observed when foraging. They are, in fact, so well trained that they fly to researchers in response to a whistle and weigh themselves on a set of scales. If only they could write research papers too….

The research has been published in Current Biology.

Press coverage
Birds smart enough to stand guard, say scientists at University of Bristol – The Times
Birds post a sentry when foraging for food – The Daily Telegraph

Image: pied babbler / Andy Radford

Posted by Daniel Cressey on April 18, 2008
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Darwin’s private papers have been placed online for the first time. You can now read why he thought a wife was better than a dog.

The Darwin Online project, which has been making his work available for years, says this is the “largest ever publication of Darwin papers and manuscripts”. In total 20,000 items have been added to the website. The new additions include Darwin’s first musing on evolution by natural selection and drafts for Descent of Man, as well as more day-to-day documents such as Emma Darwin’s recipe book*.

“His papers reveal how immensely detailed his researches were. The family has always wanted Darwin's papers and manuscripts to be available to anyone who wants to read them,” says John van Wyhe, the man running the archive (BBC). “The fact that everyone around the world can now see them on the web is simply fantastic.”

The Daily Telegraph notes that the collection now includes Darwin’s classic musing on marriage:

Reasons for not marrying: freedom to go where one liked; choice of Society & little of it. - Conversation of clever men at clubs - Not forced to visit relatives, & to bend in every trifle. - to have the expense & anxiety of children - perhaps quarrelling - Loss of time. - cannot read in the Evenings - fatness & idleness - Anxiety & responsibility - less money for books.

[Reasons for:] Children - (if it Please God) - Constant companion, (& friend in old age) who will feel interested in one, - object to be beloved & played with. - better than a dog anyhow.

You old romantic Charles.

*I will be attempting her ‘Irish Charlotte’ this weekend. Stay tuned to see how it goes...

Image: Nature

Posted by Daniel Cressey on April 17, 2008
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Elephants share a common aquatic ancestor with manatees and dugongs, according to a paper released in PNAS.

“It has often been assumed that elephants have evolved from fully terrestrial ancestors and have always had this kind of a lifestyle,” says one of the study’s authors, Erik Seiffert of the Stony Brook University, New York (BBC). “Now we can really start to think about how their lifestyle and behaviour might have been shaped by a very different kind of existence in the distant past.”

Seiffert and colleagues analysed the composition of teeth from early elephant Moeritherium and appear to have confirmed previous suspicions that it was amphibious. “We now have substantial evidence to suggest that modern elephants do have ancient relatives which lived primarily in water,” says fellow author Alexander Liu, of the University of Oxford (press release).

Continue reading "Elephants’ aquatic ancestor" »

Posted by Daniel Cressey on April 15, 2008
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Although it’s the Nature piece on use of cognitive enhancers by academics that is getting all the press, there’s another cool story from Nature this week that deserves more attention than it’s getting. By crunching a huge amount of genetic data, a research team has redrawn the tree of life.

By looking at sequence tags from 29 animals they worked out their evolutionary history. Surprisingly, the oldest animal isn’t the simple sponge; it’s something rather more complex: the comb jelly (this is covered only by LiveScience as far as I can tell).

“This was a complete shocker,” says study leader Casey Dunn, of Brown University (press release). “So shocking that we initially thought something had gone very wrong.”

There are two ways, Dunn says, that the comb jelly could have beaten the sponge to primacy. It could have evolved its complex nature independent of other animals or the sponge could have evolved from more complex animals (diagram). Other people crunching through genetics though think the evidence stacks up for sponges (see this recent article from National Geographic).

Other stuff from Nature: tell us what you want to read.

Image top: comb jelly / Casey Dunn
Image lower: Zina Deretsky, NSF

Posted by Daniel Cressey on April 11, 2008
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About 40 million years ago this arachnid went out for a walk and made the mistake of blundering into amber.

It is only the second example of Dicranopalpus ramiger, a type of harvestman rather than a true spider, to be acquired by London’s Natural History Museum (press release).

“Complete harvestmen are rare finds. It’s more common to find just the legs in amber, where a trapped leg or two were sacrificed so the harvestman could escape the sticky resin, says Andrew Ross, the museum’s fossil invertebrates expert.

“This is a particularly impressive example because all its legs are present and still attached to the body.”

The bug was noticed by Terence Collingwood, who runs a fossil shop in Rochester. “I buy bulk lots of amber to sell, and I have to search through them carefully looking for unusual items that other people may have missed,” he explains. “Finding this was pure chance, but I realised straight away that it was something special.”

More on this from the BBC.

Image: copyright NHM

Posted by Daniel Cressey on April 09, 2008
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Prompted by shenanigans involving rowdy biologists and the inability of certain creationists to identify said biologists, we set a quiz last week (full shenanigans story and quiz).

We asked you to match six pictures to six names, to see who the most recognised warrior in the Darwin Wars is. Thanks to the 6,500 or so readers who took part.

Results below the fold...

Continue reading "Results of our quiz are in..." »

Posted by Daniel Cressey on April 04, 2008
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This strange beast is a new species of fish discovered off Indonesia. It is definitely an Anglerfish, according to Ted Pietsch, a University of Washington fishery sciences expert, despite lacking the lure that gives that group their name (press release).

“As soon as I saw the photo I knew it had to be an anglerfish because of the leglike pectoral fins on its sides,” he says. “Only anglerfishes have crooked, leglike structures that they use to walk or crawl along the seafloor or other surfaces.”

Pietsch reckons the 10-cm long new species has avoided detection up to now by hiding in crevices. It was photographed by divers from the Maluku Divers company, who turned to Pietsch after being unable to ID it from guide books.

“What you usually see is variations of a fish you’ve seen before,” says the company’s co-owner Andy Shorten (Seattle PI). “We’ve never seen a fish with remotely this kind of face.”

An example of the beastie has now been captured says the Seattle PI, and will be subject to DNA testing to see how it relates to other anglerfish.

Image: M. Snyder, starknakedfish.com/divingmaluku.com

Posted by Daniel Cressey on April 03, 2008
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Three scholars this week confessed to a repeatedly spying on in flagrante octopuses.

Biologists Christine Huffard, Roy Caldwell and Farnis Boneka snorkelled around multiple couples of Abdopus aculeatus and found they have far more complex mating behaviours that previously thought (press release, with videos).

These behaviours include “sneaker matings, mate guarding, sex-specific body patterns, frequent copulations, and male–male competition for mates” they write in Marine Biology. Or, as the press release puts it, “such sophisticated lovemaking tactics as flirting, passionate handholding and keeping rivals at arms’ length”.

I wasn’t aware that flirting and handholding counted as “sophisticated lovemaking tactics” in California, but nevermind.

Continue reading "Berkeley voyeurs spy on octopus lovin’" »

Posted by Daniel Cressey on April 02, 2008
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The British press erupted last night with news that a team at Newcastle University has produced the UK’s first animal-human hybrids: embryos made with cow eggs and inserted human DNA (the Guardian has a comprehensive report).

Human-animal hybrid embryos have been made elsewhere before, although progress in the lab has been limited. Hui Sheng of the Shanghai Institutes for Biological Sciences published a report on rabbit-human hybrid embryos in 2003 (although that was tricky to get published; see this profile in Nature Medicine; paper in Cell Research), and others have since followed (there’s a great background briefing on the topic in the Guardian, published earlier this year). Such work is done simply because animal eggs are easier to obtain than human ones. It has not as yet progressed very far; hybrids have been made, but not much done with them.

This work is creating news because it is a UK first (albeit an as-yet-unpublished and un-peer-reviewed first – it was announced by the BBC rather than in a scientific report), and because the UK, often considered a world leader in embryology, is gearing up to have a parliamentary vote on new proposed human fertilisation and embryology legislation next month. There has been much in the news in recent weeks on dithering about how this vote will be taken - whether ministers will be able to vote ‘freely’ with their personal moral values, or have to follow party lines (this ended in a compromise; Press Association) - and how the catholic church is generally against it all (Press Association). The result will impact on hybrid embryo work in the future. So announcing a ‘success’ now may have political implications. It was well known that the lab had a license to do this work, that it was actively on the case, and that it’s possible, so their progress is not necessarily surprising.

New Scientist has attacked the group for announcing the achievement through the media rather than through a scientific publication. The Independent focuses on the ethical debate. Not many organisations outside the UK gave it any coverage at all, and those that did may have been under the impression that it was a world first, not mentioning previous achievements in the field (eg. Life Scientist, Australia).

Posted by Nicola Jones on April 02, 2008
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A surprising number of quite dramatic stories today – one big round-up post will have to do for them all.

Dextre, the Canadian space agency’s new robot, is meant to be helping construct the ISS. Instead it’s making outlandish demands:
In a surprising and potentially troubling request, the new space station robot known as Dextre demanded that astronauts refer to it in the future at ‘Dextre the Magnificent.’ Brandishing power tools that would make any handyperson blush, the mobile servicing system thanked humans for creating it and promised a glorious future where humans would retain an important role in the new robot order.

Virgin and Google are going to Mars. They want YOU to join them (if you can score highly enough on their selection questionnaire that is).

Continue reading "A chemist, a physicist, and a biologist walk into a bar" »

Posted by Daniel Cressey on April 01, 2008
Categories: Biology & Biotechnology, Chemistry, Earth, environment & ecology, Health and medicine, Neat technologies, Physics & Mathematics, Policy, Space and astronomy | Permalink | Comments (0) | TrackBacks (0)

Researchers in the US have finally worked out how the aggressive and slightly-scary Humboldt squid avoids turning itself into calamari when eating.

Because it has a pretty squidgy body and a very hard beak, you might expect the squid to do just as much damage to itself as its prey when chomping down on a passing fish or scuba diver.

“You can imagine the problems you’d encounter if you attached a knife blade to a block of Jell-o and tried to use that blade for cutting,” says Frank Zok, author of a new paper on squid beaks in Science (press release, paper). “The blade would cut through the Jell-o at least as much as the targeted object.”

Obviously this doesn’t happen with the Humboldt, or the animals wouldn’t be swarming like roaches across our seas. In fact the squids have a neat trick – a graduated tissue where the base of the beak is 100 times softer than the tip.

Continue reading "A peak at a squid-gy beak" »

Posted by Daniel Cressey on March 31, 2008
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Last week US biologist and blogger PZ Myers was unceremoniously evicted from the cinema where he was about to view the film Expelled, dismissed by many scientists as creationist propaganda (see last year’s post for more on Expelled). However the film’s producer, who had Myers kicked out, failed to expel his fellow cinema-goer, one Richard Dawkins.

Cue a mass blogosphere feeding frenzy (see here, here, here, and here).

But would you have spotted Dawkins? Or even Myers? Now you can test your knowledge of key figures in the new Great Beyond Super-Scientist-Spotting Quiz!

CLICK HERE TO TAKE THE QUIZ

Posted by Daniel Cressey on March 27, 2008
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A bizarre geek-fight has erupted in the blogosphere over which types of invertebrates are coolest, Echinoderms or Molluscs.

Back on the 20th of March The Intersection blog mused on sea cucumbers and squid, concluding, “No contest! Cukes would eat squid for breakfast...”

This drew a scathing response from some quarters, with Craig McClain on Deep Sea News delivering this cutting put down to the sea cucumber fans:

It’s just hard to get excited about a sea cucumber that either feeds on sediment muck or filters muck out of the water column and not much else. Or an organism whose idea of fun is spewing its organs all over you or creating poop trails.

However the echinoderm faction fought back. Even comics were enlisted and the Snail’s Eye View blog tried to settle the matter with reference to the ultimate arbiter: a google fight. Mollusca comfortably won.

Currently both sides appear to be licking their wounds. A summary of the war to date is here.

Having spent the weekend playing with octopus in the Med, the Great Beyond is committing the full weight of Nature’s reputation behind the mollusca cause. (This may be career jeopardising, by the way, as I have not the slightest right to claim the Nature name in this way.)

Images: Punchstock / NOAA

Posted by Daniel Cressey on March 25, 2008
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A South Korean professor is withdrawing two research papers after apparently admitting he forged data on anti-aging techniques.

Kim Tae-kook, who is called Tae Kook Kim in some coverage, has been suspended from the Korea Advanced Institute of Science and Technology since February. He has said he will retract papers in Science and Nature Chemical Biology which early this year raised suspicions of fraud (BBC, AP, Yonhap).

However, in an email to a reporter from Science he stated that a “certain party has twisted this current situation to take an advantage of it”, implying he has not entirely admitted culpability (Science; subscription required).

Continue reading "Research at centre of fraud claims to be withdrawn" »

Posted by Daniel Cressey on March 17, 2008
Categories: Biology & Biotechnology, Policy | Permalink | Comments (0) | TrackBacks (0)

A light has been shone on a gene that controls the shape of tomatoes.

In this week’s Science, a team of US researchers report that duplicating the SUN gene - named for the Sun 1642 tomato variety in which it was found – causes these fruit to have an elongated shape.

“We are trying to understand what kind of genes caused the enormous increase in fruit size and variation in fruit shape as tomatoes were domesticated,” says Esther van der Knaap, crop science expert at Ohio State University (press release). “Once we know all the genes that were selected during that process, we will be able to piece together how domestication shaped the tomato fruit — and gain a better understanding of what controls the shape of other very diverse crops, such as peppers, cucumbers and gourds.”

Most of the coverage of this focuses on the fact that scientists have found a gene for wonky tomatoes. Actually van der Knaap’s team have produced something more interesting.

Continue reading "Too much sun makes tomatoes wonky" »

Posted by Daniel Cressey on March 14, 2008
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