The Great Beyond

The jumbo dumbo (Photo courtesy of Mike Vecchione)

New species of 'dumbo' (Photo courtesy of David Shale)

In total, five deep-sea projects will have undertaken 210 expeditions when the census has been completed.

“There is both a great lack of information about the ‘abyss’ and substantial misinformation,” says Robert Carney, of Louisiana State University. “Many species live there. However, the abyss has long been viewed as a desert. Worse, it was viewed as a wasteland where few to no environmental impacts could be of any concern.”

Now that they have stared into the abyss, says Carney, the census scientists are concerned. Here are some of the critters they are concerned about.

Collected between 1,000 to 3,000 meters deep, was a very large example of a finned octopod, normally called a dumbo due to its endearing habit of swimming by flapping a pair of large fins that look like ears.

This jumbo example was nearly two metres long and 6 kg heavy, the largest ever collected. In total nine species were found on the mid-Atlantic ridge, including one new to science.

Later a huge catch of corals, sea cucumbers and sea urchins was pulled up from the ridge. Researchers described it as “indescribable”. “It’s hard to believe that such exuberance of life exists a kilometre deep into the ocean,” says the census.

The team also pulled up a Neocyema, the strange orange thing pictured right, only the fifth example of this fish ever caught.

Perhaps the strangest find though was a Lamellibranchia tubeworm. When a robot arm lifted the worm clear of the sea floor, crude oil started leaking from the hole it had left behind. Apparently the worm had been feasting on the oil.

More photos below the fold...

Continue reading "Weird beasts from the abyss" »

Posted by Daniel Cressey
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A proposed resolution to restrict human embryonic stem cell research at the University of Nebraska has failed. The University's Board of Regents today split their votes 4-4, defeating a measure that would have limited research to embryonic stem cell lines approved under former President George W. Bush. The resolution needed a majority of five votes to pass.

"That probably settles the question for the time being," Thomas Rosenquist, vice chancellor for research at the University of Nebraska Medical School in Omaha, told Nature. "It's permission to go ahead and take part in 21st-century research with embryonic stem cells."

Nebraska law prohibits the destruction of embryos for research. But the state does allow scientists to follow federal standards in embryonic stem cell research. Earlier this year, President Barack Obama removed government funding restrictions on new stem-cell lines derived from embryos left over from fertility treatment, and an advisory panel is currently mulling over which of hundreds of potential new cell lines to approve.

The governing board's decision "is a big relief", says Angie Rizzino, a stem cell biologist at the University of Nebraska Medical School. "But I fear that they'll be back in a year or two trying to put a block on embryonic stem cell research again."

Posted by Elie Dolgin
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It's Friday evening, time once again for the "refresh game", where I sit on the CERN website waiting to find out what terrorism/food/drink crisis will befall the Large Hadron Collider next (TGB's Daniel Cressey is putting his money on a badger from the future quantum mechanically tunneling his way into the beamline).

At the moment, though, it's all looking pretty good! Commissioning of the machine should be completed any minute now, and the physicists and engineers in charge of the LHC could begin injecting beams of protons into the machine tonight. Optimistically, we could be about a week or two away from collisions.

Well, unless the United Nations intervenes. A cleverly-named group of LHC critics called conCERNed (get it? Because the LHC is at the European Organization for Nuclear Research, which is shortened to CERN in French? And CERN is right there in the word? Oh never mind), have filed a complaint with the UN's Human Rights Committee warning that the LHC might destroy the world. If true that would, it seem, infringe on a human right or two.

conCERNed would like to see the formation of an agency similar to the International Atomic Energy Agency (IAEA) to regulate particle accelerators. But I wouldn't necessarily expect this to stop collisions in the coming weeks. Given what I've seen of IAEA diplomacy, even if the UN decides to form such an agency, it will take most of the LHC's first physics run just to draw up an agenda for its inaugural meeting.

Stay tuned for more updates next week!

CERN

Posted by Geoff Brumfiel
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“Our engineers are exploring how we might contribute to this effort by developing a global forest platform that would enable anyone in the world, including tropical nations, to monitor deforestation and draw attention to it.”
Philipp Schindler, of Google UK, says his company may build a programme to allow internet users to identify illegal logging via satellite photos (Times).

“From the beginning, this case was marked by a fundamentally unfair and unconstitutional trial plan that allowed the jury to rely on findings by a prior jury.”
Murray Garnick, associate general counsel for Altria, says the company will appeal a $300 million damages award against its Philip Morris company to a former smoker in Florida who suffers from emphysema (Bloomberg).

“No new safety issue has been identified from reports issued to date.”
Marie-Paule Kieny, of the World Health Organisation, says H1N1 vaccination is not to blame for 41 deaths (Reuters).

“Dismantling this institution, which is a huge economic driver for the state, is a stupendously stupid thing to do, but that’s the path the Legislature has embarked on.”
Richard Mathies, dean of the College of Chemistry at Berkeley, takes issue with cuts to California’s education budget (LA Times).

Posted by Daniel Cressey
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More safety data is needed before an experimental flu vaccine made inside insect cells should be approved, a US federal advisory committee said yesterday.

A US Food and Drug Administration (FDA) panel voted 6-to-5 that Protein Sciences, a vaccine company based in Meriden, Connecticut, hadn’t proven that its FluBlok vaccine was safe enough to enter mass production. Nine of the 11 panellists, however, said the shot was effective in adults aged 18 to 49, although the vaccine did not appear to work as well in older patients.

The vaccine is made by inserting flu genes into an insect virus and growing it in caterpillar ovary cells. This process only takes two months, compared to the five or six needed to grow virus in chicken eggs, and so it has been touted as a way to speed up manufacturing when new vaccines against potentially pandemic flu strains are urgently needed — like now. Fewer than 50 million doses of H1N1 vaccine are currently available in the US.

Continue reading "Bug-based flu vaccine rebuffed" »

Posted by Elie Dolgin
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The disappearance of the huge herbivores that once roamed North America triggered a massive change in the environment with new trees and more fires.

Reporting in Science, researchers say lake sediments show that the decline of mammoths, mastodons, ground sloths and giant beavers allowed broadleaved trees to flourish as the beasties weren’t around to eat them. The rise of these trees then meant that more fuel for fires accumulated.

“Our work thus shows close connections among the late-glacial histories of fire, vegetation, and mammalian herbivores and suggests that the loss of a broad guild of consumers contributed to substantial restructuring of plant communities and an enhanced fire regime,” write Jacquelyn Gill, of the University of Wisconsin, Madison, and her colleagues.

To make these links Gill’s team looked at sediment from Appleman Lake in Indiana and other sediments from New York sites. They traced fungus spores that live on dung as a proxy for megafauna. As the number of spores in the sediments decreases about 13.8 thousand years ago, new types of pollen appear, showing the increasing dominance of the broadleaf trees. At the same time a big increase in charcoal is seen, showing the increasing number of fires.

The big question though is what does this tell us about why the mammoth died out…

Continue reading "Dung dating illuminates mammoth mystery" »

Posted by Daniel Cressey
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Posted for Meredith Wadman

The National Institutes of Health (NIH) is once again under fire for lax oversight of conflicts of interest among the extramural researchers it supports.

A November 18 report by the Inspector General of the Department of Health and Human Services, the NIH’s parent agency, recommends that the agency significantly tighten its policing of conflicts. NIH is the world’s largest biomedical research funder, and it channels 80% of its $31 billion budget to extramural grants.

The inspector general reached his conclusions by examining the financial conflict documentation from 41 extramural institutions for the government’s 2006 fiscal year. Current regulations require grantee institutions to “reduce, manage or eliminate” conflicts reported by their researchers that could reasonably be affected by their NIH-funded work.

The inspector found that, among the documentation for 184 conflicts involving 165 researchers, only six researchers’ conflicts were eliminated by their universities. The lion’s share, totalling 136, were “managed”. Grantee institutions “rarely” reduce or eliminate conflicts, the report concluded.

Among the report’s recommendations: that universities collect financial interest data in specific dollar amounts and not in ranges such as “$10,000-$50,000”. It also recommends that NIH require researchers to report to their institutions all their financial interests and not just those that they judge could reasonably be affected by their NIH-supported research.

“Full and complete disclosure ensures that the determination of whether a significant financial interest relates to the research rests with the grantee institution and not with the researcher,” the report argues.

Specific dollar amounts would certainly shed more light on the equity holdings of researchers. These were found by the inspector to be the most common financial interest, with 111 of the researchers reporting equity holdings, and six of these holding more than $100,000.

NIH is in the process of rewriting its conflict of interest reporting requirements; it is expected to issue new regulations by year’s end (see: Researcher payment reporting under scrutiny).

The report follows a similar briefing from the inspector general in January 2008 (see: NIH in the dark over conflicts of interest). Investigations by Senator Charles Grassley have pointed out several cases of underreporting of six-figure amounts by NIH-funded researchers (see: Money in biomedicine: The senator's sleuth).

Sally Rockey, acting deputy director of the office of extramural research at NIH, said in a statement that, "NIH has demonstrated its commitment to oversight activities and continues to make them an agency priority." She added that the inspector's recommendations "will be considered by the NIH along with public comments ... as it formulates a new regulation that will facilitate effective compliance."

Posted by Daniel Cressey
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Posted for David Cyranoski

The Chinese government has sent inspection teams to check on H1N1 reporting after a famed Chinese doctor accused local governments of covering up swine flu cases.

Zhong Nanshan of Guangzhou Institute of Respiratory Diseases in southern China, called into question the official number of deaths from H1N1, telling the Southern Metropolis Daily newspaper that the quoted figure of 53 was too low. “I just don’t believe that there have been 53 H1N1 deaths nationwide,” he said.

Yesterday Ministry of Health spokesman Deng Haihua, said any officials who do not carry out their H1N1 reporting duties or who delay reporting will be “held accountable”. He also said that teams had been sent to inspect pandemic control. In total nine groups have been sent to Hebei, Shanxi, Inner Mongolia, Liaoning, Jilin, Heilongjiang, Zhejiang, Hunan, Gansu, Qinghai, Ningxia, and Xinjiang (official statement).

While many have pointed out that limitations on testing capacity have led to an underreporting, Zhong suggested that some hospitals were intentionally not testing those who died from pneumonia for H1N1.

His words carry weight because he shot to fame during the Sudden Acute Respiratory Syndrome (SARS) outbreak in 2003 for quickly recognizing and reacting to the threat posed by the new virus while government officials around the country tried to cover it up.

All Nature’s pandemic flu coverage is collected on our news special page

Posted by Daniel Cressey
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Gene silencing predicted to improve drug manufacturing
Biotech firm hopes to use RNA interference to boost drug yields.

Europe puts brakes on fusion project
Firing up ITER in 2018 is not feasible, warn council delegates.

Maize genome mapped
Sequence should help corn breeders meet global demands for food and fuel.

Posted by Daniel Cressey
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“I’m here in solidarity with people across the state of California that are being subjugated to these outrageous fee increases. It’s completely unjust to put the burden on students.”
Kyle Tramberly, a junior at UC San Diego, is one of those protesting over fee increases in the UC system. Earlier today some students stormed UCLA’s Campbell Hall and blockaded themselves inside (LA Times).

“We knew about SuperCroc, the titan of all crocs, but we didn't have quite an idea of what existed in the shadows of the Cretaceous. We have crocs here [in what was once Gondwana] that ate plants and galloped and ate dinosaurs and were flat as a board.”
Paul Sereno, of the University of Chicago and National Geographic, has unearthed some terrifying prehistoric crocodiles.

“We have no time to waste here. The ecological services must be restored.”
Christian Lambrechts, a United Nations environment programme expert seconded to the Kenyan government, comments on the eviction of thousands of people who were squatting in the country’s Mau forest (Guardian).

Posted by Daniel Cressey
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For the past 22 hours, 35 radio telescopes from around the world have been holding hands and working toward a common goal: creating the most powerful grid that's ever spanned the skies (NRAO press release).

2 hours from now, the telescopes will again go their separate ways, having measured the positions of 243 quasars — distant, blazing-bright galaxies with supermassive black holes at their cores. Quasars are ideal reference points in the sky because they're both visible and stable (due to their distance) to Earthlings. Because large groups of telescopes — whichever subset is facing the quasars of interest — are measuring the positions in unison, they are able to cover most of the sky and avoid problems of combining data from different observing sessions.

The telescope teams are measuring 1 to 3 quasars at a time for anywhere from 30 to 500 seconds each. As they crunch along, their activities and measurements are visible in real time at the Bordeaux Observatory's website.

The 24-hour, 7-continent effort demolishes the previous world record for telescope collaborations, which included 23 scopes. If all continues to go according to plan, the result will be a new, stronger reference grid for the sky, allowing more precise measurements of everything from gravity to movements of the tectonic plates.

Image: jpl.NASA.gov

Posted by Lizzie Buchen
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An endangered fish is actually two even more endangered fish, according to new research.

Although it is already listed as ‘critically endangered’ the poor old European common skate may be in an even worse state than we thought. A new paper published in Aquatic Conservation says what we thought was the skate Dipturus batis is actually two different animals.

“Morphology, genetics, and life history reveal that two distinct species have been erroneously confused since the 1920s under the single scientific name D. batis,” write Samuel Iglésias, of the French National Museum of Natural History, and colleagues.

Iglésias says the ‘common skate’ species should be split into the blue skate (provisionally D. cf. flossada) and the flapper skate (D. cf. intermedia). This is not just of academic importance.

“Revisions of incorrect synonymizations - called species resurrections - are common works for systematists, but in the present case the resurrection of D. cf. intermedia is of great conservation significance,” the authors note.

The problem is that the not-quite-so-bad state of blue skate populations has been masking the really, really bad state of the flapper. And the old ‘common skate’ is already noted as the first fish brought to the brink of extinction by commercial fishing and this confusion of blue and flapper has hamstrung those trying to conserve the species – both of which deserve independent ‘critically endangered status’ says the paper.

“The risk of extinction of these depleted species is higher than previously assessed and appears unavoidable without immediate and incisive conservation action,” Iglésias concludes.

Posted by Daniel Cressey
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Human embryonic stem cells could be one step closer to the clinic. Santa Monica, California-based Advanced Cell Technology (ACT) announced today that it has applied to US regulators to launch a new clinical trial aimed at reversing vision loss with retinal cells recreated from embryonic stem (ES) cells.

The company plans to test the stem cell-derived retinal cells in 12 patients suffering from Stargardt's disease, a form of inherited juvenile macular degeneration that affects around one in 10,000 children.

ACT researchers previously showed that ES cells could give rise to retinal pigment epithelium cells, the photoreceptors that go awry in the disease. They then demonstrated that the cells could restore vision in a rat model of retinal disease. And in September, the researchers reported that the cells were long-lasting and safe in a mouse model of Stargardt's.

"Our research clearly shows that stem cell-derived retinal cells can rescue visual function in animals that otherwise would have gone blind," said Robert Lanza, ACT's chief scientific officer, in a statement. "We are hopeful that the cells will be similarly efficacious in patients."

ACT's investigational new drug (IND) application is only the second filing with the US Food and Drug Administration for a therapy involving human ES cells. The first company out of the gate, Menlo Park, California-based Geron Corp., had its stem-cell derived therapy to treat spinal cord injury patients approved last January. But the FDA put a hold on the trial before a single patient had been injected with the cells, citing safety concerns. Geron now says it plans to restart the trial in the second half of next year.

For more on why stem cell-derived transplants could work to delay or prevent blindness, see the June 2009 news feature from the sadly now-defunct Nature Reports Stem Cells.

Image: The left eye of a Stargardt's patient from Özdek et al., Eye 19, 1222–1225 (2005).

Posted by Elie Dolgin
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