Archive for the ‘Science’ Category

Microbes ate the oil and now plants clean up pollution

October 22, 2010

Not only do microbes eat up methane and other oil wastes faster than expected, it now seems that vegetation eats up air pollution to a much greater degree than thought. A new paper in Science finds that oxygenated volatile organic compounds (oVOCs) are taken up by deciduous plants at an unexpectedly fast rate–as much as four times more rapidly than previously thought.

T. Karl, P. Harley, L. Emmons, B. Thornton, A. Guenther, C. Basu, A. Turnipseed, K. Jardine. Efficient Atmospheric Cleansing of Oxidized Organic Trace Gases by VegetationScience, 2010; DOI: 10.1126/science.1192534

From Eurekalert:

“Plants clean our air to a greater extent than we had realized,” says NCAR scientist Thomas Karl, the lead author. “They actively consume certain types of air pollution.”

The research team focused on a class of chemicals known as oxygenated volatile organic compounds (oVOCs), which can have long-term impacts on the environment and human health. “The team has made significant progress in understanding the complex interactions between plants and the atmosphere,” says Anne-Marie Schmoltner of NSF’s Division of Atmospheric and Geospace Sciences, which funded the research. The compounds form in abundance in the atmosphere from hydrocarbons and other chemicals that are emitted from both natural sources–including plants–and sources related to human activities, including vehicles and construction materials.

The compounds help shape atmospheric chemistry and influence climate.

Eventually, some oVOCs evolve into tiny airborne particles, known as aerosols, that have important effects on both clouds and human health.

By measuring oVOC levels in a number of ecosystems in the United States and other countries, the researchers determined that deciduous plants appear to be taking up the compounds at an unexpectedly fast rate–as much as four times more rapidly than previously thought.

The uptake was especially rapid in dense forests and most evident near the tops of forest canopies, which accounted for as much as 97 percent of the oVOC uptake that was observed. Karl and his colleagues then tackled a follow-up question: How do plants absorb such large quantities of these chemicals?

The scientists moved their research into their laboratories and focused on poplar trees. The species offered a significant advantage in that its genome has been sequenced. The team found that when the study trees were under stress, either because of a physical wound or because of exposure to an irritant such as ozone pollution, they began sharply increasing their uptake of oVOCs. At the same time, changes took place in expression levels of certain genes that indicated heightened metabolic activity in the poplars.

The uptake of oVOCs, the scientists concluded, appeared to be part of a larger metabolic cycle. Plants can produce chemicals to protect themselves from irritants and repel invaders such as insects, much as a human body may increase its production of white blood cells in reaction to an infection.

But these chemicals, if produced in enough quantity, can become toxic to the plant itself.

 

Wagers paper (without Mayack) also questioned

October 21, 2010

(Thanks to Phil Score for pointing out the typos which have been fixed)

A few days ago the paper in Nature “Systemic signals regulate ageing and rejuvenation of blood stem cell niches” by Shane R. Mayack, Jennifer L. Shadrach, Francis S. Kim & Amy J. Wagers was retracted at the request of 3 of the authors. Then the Journal Blood issued a Notice of Concern regarding a second paper with Shane Mayack as the lead author and published with Amy Wagers.

In both of these cases, Shane Mayack who was the post-doctoral fellow at the Joslin Diabetes Center of Harvard Medical School was the lead author and the implication was that they could be something untoward with her work.

Now Retraction Watch reports that a  Scientist raised serious questions about 2008 Cell study by Amy Wagers. The questions were of a scientific and technical nature and in themselves carry no implications of impropriety.

Shane Mayack was not involved with this paper but since Amy Wagers led the team at the Joslin Diabetes Center, the question that arises is one of leadership and of the environment within which research is carried out. As I have posted earlier this atmosphere and the pressure of publication for the researchers may be leading to errors of judgement and misconduct. Professors and leaders of scientific teams cannot, I think, abdicate their responsibility for the environment in which their teams work especially where their names are included as co-authors of the resulting publications. The senior author on any published paper must be the first quality gate to be passed and must provide the final assurance of the integrity of the work being reported.


Microbes consume methane 10 to 100 times faster than thought

October 20, 2010

 

Structure of the methane molecule: the simples...

methane: Image via Wikipedia

 

A follow up to my previous post:

https://ktwop.wordpress.com/2010/09/12/microbes-ate-the-bp-oil-plume/

From EurekAlert:

Microbes may consume far more oil-spill waste than earlier thought

Microbes living at the bottom of the Gulf of Mexico may consume far more of the gaseous waste from the Deepwater Horizon oil spill than previously thought, according to research carried out within 100 miles of the spill site.

A paper on that research, conducted before the Deepwater Horizon rig exploded six months ago today, will appear in a forthcoming issue of the journal Deep-Sea Research II. It describes the anaerobic oxidation of methane, a key component of the Gulf oil spill, by microbes living in seafloor brine pools.

“Because of the ample oil and gas reserves under the Gulf of Mexico, slow seepage is a natural part of the ecosystem,” says Peter R. Girguis, associate professor of organismic and evolutionary biology at Harvard University. “Entire communities have arisen on the seafloor that depend on these seeps. Our analysis shows that within these communities, some microbes consume methane 10 to 100 times faster than we’ve previously realized.”

Girguis is quick to note that methane is just part of what spilled from the ruptured Deepwater Horizon well for three months earlier this year, and that the rate at which methane spewed from the damaged well far exceeds the flow that microbes would ordinarily encounter in the Gulf.

Key to the work by Girguis, Harvard research scientist Scott D. Wankel, and their colleagues was the ability to use on-site mass spectrometry to obtain direct, accurate measurements of seafloor methane. It’s been difficult to make such measurements because most tools don’t work accurately 5,000 to 7,000 feet below the surface, where pressures can reach roughly 220 atmospheres.

Using this new technique, the scientists were able to ascertain methane concentrations in brine pools surrounding gas seeps at the bottom of the Gulf — which were extremely high — as well as in the water column above the pools. Combining this data with measurements of microbial activity, they were able to extrapolate just how quickly the microbes were consuming the methane.

“In fact, we observed oxidation of methane by these microbes at the highest rates ever recorded in seawater,” Girguis says.

Methane is a greenhouse gas, up to 60 times more potent than carbon dioxide. Gigatons of the volatile gas are produced in seafloor sediments, above and beyond that generated by gas seeps that pockmark the floor of the Gulf of Mexico and other bodies of water. But, Girguis says, somewhere between the seafloor and the sea’s surface, much of the methane vanishes.

“We found that concentrations of methane in brine pools are tremendously high: five to six orders of magnitude higher than in the water column above,” Girguis says. “Mass spectrometry has given us a window on both the amount of methane diffusing into the water column and how much of this methane is consumed through anaerobic oxidation by microbes within the brine pool. It appears the microbes consume much of the methane, and the rest dissipates over time into the water column.”

A study published in the journal Science in August detailed a bacterial species reportedly able to degrade oil anaerobically in the Gulf. But a subsequent Science paper contended that these microbes mainly digested gases like methane, propane, ethane, and butane, not oil. The Deep-Sea Research II paper adds to scientists’ growing understanding of these species’ ability to degrade the byproducts of the Deepwater Horizon spill.

Girguis and Wankel’s co-authors are Samantha B. Joye and Vladimir A. Samarkin of the University of Georgia, Sunita R. Shah of the U.S. Naval Research Laboratory, Gernot Friederich of the Monterey Bay Aquarium Research Institute, and John Melas-Kyriazi of Stanford University.

“Gene pool of plants and animals still expanding”

October 20, 2010

Xinhua reports today from Wuhan:

 

Shennangojia in Hubei Province

 

Twenty-three unique new plant species have been found over the past five years in the mysterious Shennongjia Nature Reserve in central China’s Hubei Province, a researcher said Wednesday. “We are pretty much sure that the new species, which have not been discovered elsewhere in the world, are new members of the plant kingdom,” said Yang Jingyuan, head of the reserve’s research institute.

The new discoveries showed the “gene pool” of plants and animals was still expanding, said Yang. Researchers had identified 143 previously undocumented plant species in Shennongjia since 2006, excluding the 23 new varieties that are unique to the area, he added. Scientists had also discovered 16 kinds of snakes and 270 kinds of insects that were new to Hubei Province. The number of albino animals, including bears, snakes and magpies, found in the reserve have also baffled scientists.

The area is also believed to be home to the legendary Bigfoot-like ape man. The Hubei Wild Man Research Association said earlier this month that it was considering launching a high-profile search for the elusive creature, almost 30 years after the last organized expedition to seek the legendary beast in the early 1980s.

 

Shennangojia Nature Reserve : image http://english.cnhubei.com

 

Black holes, white holes, sinks and sources

October 20, 2010

There is hope for mankind when the Universe can be modelled in your kitchen!

From New Scientist

A black hole is a dense concentration of mass surrounded by an extremely powerful gravitational field. Nothing that falls within a certain radius surrounding it, known as the event horizon, escapes. A white hole is the opposite: its event horizon allows things to escape but prevents anything from entering. However, so far white holes only exist in theory, so cannot be studied observationally.

Horizon effects with surface waves on moving water is a  new paper by Germain Rousseaux1, Philippe Maïssa1, Christian Mathis1, Pierre Coullet1, Thomas G Philbin2 and Ulf Leonhardt2 (Affiliations 1 Université de Nice-Sophia Antipolis, France, 2 School of Physics and Astronomy, University of St Andrews, UK ), 2010 New J. Phys. 12 095018

doi: 10.1088/1367-2630/12/9/095018

From Wired Science:

The ring-like ridge formed when a stream of fluid hits a flat surface behaves like a white hole event horizon (Image: Germain Rousseaux/U. Nice-Sophia Antipolis)

The ring-like ridge formed when a stream of fluid hits a flat surface behaves like a white hole event horizon (Image: Germain Rousseaux/U. Nice-Sophia Antipolis)

When a stream of tap water hits the flat surface of the sink, it spreads out into a thin disc bounded by a raised lip, called the hydraulic jump. Physicists’ puzzlement with this jump dates back to Lord Rayleigh in 1914. More recently, physicists have suggested that, if the water waves inside the disc move faster than the waves outside, the jump could serve as an analogue event horizon. Water can approach the ring from outside, but it can’t get in.

“The jump would therefore constitute a one-directional membrane or white hole,” wrote physicist Gil Jannes and Germain Rousseaux of the University of Nice Sophia Antipolis in France and colleagues in a study on ArXiv Oct. 8. “Surface waves outside the jump cannot penetrate in the inner region; they are trapped outside in precisely the same sense as light is trapped inside a black hole.”

The analogy is not just surface-deep. The math describing both situations is exactly equivalent. But so far, no one had been able to prove experimentally that what’s going on in the kitchen sink really represents a white hole.

plumber in the sky

plumber in the sky

If fluid mechanics provides the correct analogy for physics, then a black hole can be considered a “sink” and a white hole is then a “source”. In fluid mechanics flow is always out of a source and into a sink. So black holes in the universe provide the way out of the universe for matter into some great Cosmic Drain exhausting into some other universe. Then white holes must be the taps from which matter flows into our universe from the Great Unknown.

The only time that a backflow of fluids occurs through a sink is when the drains are backed up or a reverse pressure surge drives fluid back through the sink-hole.

Which begs the question: “What happens in a black hole when the Cosmic Drain gets clogged?”.

Which in turn leads to the answer “Just call the Great Plumber in the sky”!

 

Benoît Mandelbrot RIP

October 17, 2010

Benoît Mandelbrot, the father of fractals, passed away on 14th October at the age of 85. He was suffering from pancreatic cancer.

I used to spend hours generating fractals for no other reason than to see what they looked like.

Born in Poland, on 20th November 1924 he moved to France with his family when he was a child. Mandelbrot spent much of his life living and working in the United States, acquiring dual French and American citizenship.

File:Mandelbrot Set - Periodicites.png

The Mandelbrot Set: Wikipedia

 

Climategate leads to Wikipedia action (finally)

October 15, 2010
Image representing Wikipedia as depicted in Cr...

Image via CrunchBase

There are some small encouraging signs that science may be returning to the subject of climate and man-made effects and carbon dioxide forcings and solar influences. This is one of them.

Lawrence Solomon pointed out back in December 2009 that:

The Climategate Emails describe how a small band of climatologists cooked the books to make the last century seem dangerously warm. The emails also describe how the band plotted to rewrite history as well as science, particularly by eliminating the Medieval Warm Period, a 400 year period that began around 1000 AD.

The Climategate Emails reveal something else, too: the enlistment of the most widely read source of information in the world — Wikipedia — in the wholesale rewriting of this history.

U.K. scientist and Green Party activist William Connolley took control of all things climate in the most used information source the world has ever known – Wikipedia. Starting in February 2003, just when opposition to the claims of the band members were beginning to gel, Connolley set to work on the Wikipedia site. He rewrote Wikipedia’s articles on global warming, on the greenhouse effect, on the instrumental temperature record, on the urban heat island, on climate models, on global cooling. On Feb. 14, he began to erase the Little Ice Age; on Aug.11, the Medieval Warm Period. In October, he turned his attention to the hockey stick graph. He rewrote articles on the politics of global warming and on the scientists who were skeptical of the band. Richard Lindzen and Fred Singer, two of the world’s most distinguished climate scientists, were among his early targets, followed by others that the band especially hated, such as Willie Soon and Sallie Baliunas of the Harvard-Smithsonian Center for Astrophysics, authorities on the Medieval Warm Period.

All told, Connolley created or rewrote 5,428 unique Wikipedia articles. His control over Wikipedia was greater still, however, through the role he obtained at Wikipedia as a website administrator, which allowed him to act with virtual impunity. When Connolley didn’t like the subject of a certain article, he removed it — more than 500 articles of various descriptions disappeared at his hand. When he disapproved of the arguments that others were making, he often had them barred — over 2,000 Wikipedia contributors who ran afoul of him found themselves blocked from making further contributions. Acolytes whose writing conformed to Connolley’s global warming views, in contrast, were rewarded with Wikipedia’s blessings. In these ways, Connolley turned Wikipedia into the missionary wing of the global warming movement.
The Medieval Warm Period disappeared, as did criticism of the global warming orthodoxy. With the release of the Climategate Emails, the disappearing trick has been exposed. The glorious Medieval Warm Period will remain in the history books, perhaps with an asterisk to describe how a band of zealots once tried to make it disappear.

But now over a year after the Climategate revelations, Watts Up With That reports that

in a vote of 7-0, the most prolific climate revisionist editor ever at Wikipedia, with over 5400 article revisions has been banned from making any edits about climate related articles for six months. Here’s the details at Wikipedia.

Tenacious life – a new species of snail fish found at depth of 7000m

October 14, 2010

 

The new type of snailfish was found living at a depth of 22,966ft (7,000m) in the Peru-Chile trench of the South East Pacific Ocean.

Snailfish found living at a depth of 22,966ft Peru-Chile trench of the South East Pacific Ocean. Photo: Oceanlab, University of Aberdeen

 

Hot on the heels of discovering a biological oasis of life in hot, inky-black waters at the bottom of Yellowstone Lake in the midst of hundreds of geothermal vents comes news of  a new type of snailfish found living at a depth of 22,966ft (7,000m) in the Peru-Chile trench of the South East Pacific Ocean.

The Telegraph reports:

The 10 inch long tadpole-shaped creature with a large head, tiny eyes and pelvic fins has adapted to living in an icy cold, pitch black environment under constant, crushing pressure. Mass groupings of cusk-eels and large crustacean scavengers were also found living in the narrow abyss despite the inhospitable conditions.

The findings, in one of the deepest places on the planet, were made by a team of marine biologists from the University of Aberdeen and experts from Japan and New Zealand. The team took part in a three-week expedition, during which they used deep-sea imaging technology to take 6,000 pictures at depths between 14,764ft (4,500m) and 26,247ft (8,000m) within the trench.

The Peru-Chile Trench

The Peru-Chile Trench: Image via Wikipedia

The mission was the seventh to take place as part of HADEEP, a collaborative research project between the University of Aberdeen’s Oceanlab and the University of Tokyo’s Ocean Research Institute, supported by New Zealand’s National Institute of Water and Atmospheric research (NIWA).

Oceanlab’s Dr Alan Jamieson, who led the expedition said these latest discoveries helped shed new light on life in the depths of the Earth. “Our findings, which revealed diverse and abundant species at depths previously thought to be void of fish, will prompt a rethink into marine populations at extreme depths,” he said.

“This expedition was prompted by our findings in 2008 and 2009 off Japan and New Zealand where we discovered new species of snailfish known as Liparids inhabiting trenches … at depths of approximately 7,000 metres – with each trench hosting its own unique species of the fish.

“To test whether these species would be found in all trenches, we repeated our experiments on the other side of the Pacific Ocean off Peru and Chile, some 6,000 miles (9,656km) from our last observations.

“What we found was that indeed there was another unique species of snailfish living at 7,000 metres – entirely new to science – which had never been caught or seen before.”

The new snailfish will not be named until it is officially confirmed as a new species.

The estimates of the number of unknown marine species may be at the top end of the range estimated between 1 million and 10 million species. However, plant and animal diversity looks insignificant compared to the sea’s micro-organisms, which may number 1 billion. Their diversity is “spectacular”.

A second Mayack paper gives cause for concern

October 14, 2010

Earlier today I posted about the retraction of a Nature paper due to doubts about the work done by the lead author Shane R. Mayack.

The Journal “Blood” has now posted a Notice of concern for: Mayack and Wagers:
Blood, 1 August 2008, Vol. 112, No. 3, pp. 519-531. Prepublished online as a Blood First Edition Paper on May 2, 2008; DOI 10.1182/blood-2008-01-133710.

Based on information provided by the corresponding author, Amy J. Wagers, Blood wishes to post a Notice of Concern for this August 1, 2008 article.

As a result of an internal review by the corresponding author, serious concerns with some of the reported data were raised, specifically regarding the osteolineage differentiation of small numbers of sorted osteopontin+ niche cells. This matter is currently under further review. Blood will inform the readers of the outcomes.

It seems that Mayack’s employment at  the Joslin Diabetes Center of Harvard Medical School which started on 1st March 2005 ended on 1st October 2010.

Pachauri stays at IPCC: Ultimately it’s a question of cowardice

October 14, 2010

 

Pachauri's racy thesis

 

The IPCC has just completed its 3 day meeting in Busan. The absence of any courage by any of the delegates or by their Chairman is apparent. Rather than implement all the recommendations of the IAC review they have just accepted all the easy bits and shuffled off the more painful corrections to be studied in committee. The Chairman himself has not had the courage to swallow his overweening pride and return quietly to Almora.  (A psychiatrist might be able to explain the connections between his public utterances and his steamy novel).

The BBC reports:

(The IPCC) meeting in South Korea closed with many other reforms proposed in a recent review being passed to committees for further consideration. Chairman Rajendra Pachauri confirmed his intention to stay in post until the next assessment is published in 2014. In its recent review of the IPCC, the InterAcademy Council (IAC) – an umbrella group for the world’s science academies – highlighted a case in the 2007 assessment where studies projecting rapidly declining crop yields in Africa were given more weight than they merited, in the absence of supporting evidence.

The revised guidance emphasises that in future, authors must assess both the quality of research available and uncertainties within that research.

t urges authors to be careful of “group-think”, but maintains that it “may be appropriate to describe findings for which the evidence and understanding are overwhelming as statements of fact without using uncertainty qualifiers”.

Enhanced guidance on the use of “grey literature” – material not published in peer-reviewed scientific journals – has also been drawn up, and will be finalised by chairs of the IPCC’s working groups in the coming months.

Procedures for correcting errors should they arise were also approved – which means that the most serious error in the 2007 report, on the projected melting date for Himalayan glaciers, can be formally repaired.