November in Books, 2014 On Pace for Hottest Year

With November’s temperature numbers in the books, 2014 is on track to be the hottest year ever recorded, newly released data from NASA and the National Oceanic and Atmospheric Administration show.

During the month, the patterns that have been in place for much of the year held fast: While the eastern U.S. was plunged into a deep freeze, the world as a whole continued warming, fueled by the rise of greenhouse gases in the atmosphere.

November didn’t set a global warm mark (as August, September and October did), in part because oceans cooled slightly and because of the cold that covered much of North America, said Jessica Blunden, a climate scientist with ERT, Inc., at NOAA’s National Climatic Data Center. But the month still came in 1.17°F above average, according to both NOAA and NASA records. That’s enough to keep the year on track to set the record.

The 11 months of the year to date are the hottest such period on record, according to NOAA, coming in at 1.22°F above the 20th century average of 57°F. For 2014 to set the mark, Blunden said it would need to be only around the 18th warmest December on record, which is a definite possibility.

No matter how December impacts the final tally, it will mean that 14 of the 15 hottest years on record have occurred in the 21st century (the exception was the blockbuster El Niño year of 1998). That clustering of hot years in the two most recent decades highlights the long-term warming trend. And as some climate scientists — such as Gavin Schmidt, director of NASA’s Goddard Institute of Space Studies, which keeps NASA’s temperature data — like to note, that’s far more important than any monthly or yearly temperature record.

Another indicator of that long-term warming trend is the lack of record cold years for more than a century, despite the chill across the eastern U.S. The world’s last record cold year was 1911, according to a Climate Central analysis. Meanwhile, over that same period, 18 records for hottest years were set; 2014 would make the 19th.

November was unusually chilly in the eastern U.S., ranking as the 16th coldest November in the records, which extend back to 1895, and the coldest November since 2000. The deep freeze was due to several bouts of Arctic airthat descended over a broad swath of the country to the east of the Rockies, leading to stark 24-hour temperature changes and the largest November snow coverin the 49-year satellite record.

The West, however, saw its continued pattern of warmer-than-normal temperatures, with California recording its ninth warmest November. All year, the state has been baking under a ridge of high pressure that has brought record temperatures and exacerbated the three-year-long drought. California is all but certain to see it’s warmest year on record.

Read more at Discovery News

Oldest African Penguin Treated for Skin Cancer

A 40-year-old penguin from Pueblo Zoo that hatched when "All in the Family" was the top-rated television show underwent a specialized treatment for skin cancer at Colorado State University (CSU).

Tess, the world's oldest known African penguin, had a sarcoma between her beak and right eye. Veterinarians at the university trained a tiny shaft of radiation at the growth for just shy of 22 minutes. The treatment, electronic brachytherapy, is able to focus the beam of radiation so precisely that tissues and organs surrounding the area aren't affected.

The procedure was so non-invasive, in fact, that Tess was out the door and on her way back to Pueblo Zoo the same day. After two weeks of isolation in which to recuperate, she was placed back in her habitat, where a reunion ensued with her 33-year-old mate Mongo. The video below has some terrific footage of Tess and her treatment.

The zoo's primary penguin keeper, Melanie Pococke, said it was fortunate that Tess' tumor was in a place where it could be seen readily. Otherwise, it would likely have been hidden in her dense feathers. "I have always known that Tess is spectacular and extremely special. It was fun to see the excitement everyone had for her at the CSU vet hospital," she said in a statement.

Skin cancer is rare to encounter in captive penguins, according to Pueblo Zoo. The facility reports that Tess is in otherwise excellent health, though, noting that her age is a marvel, given that African penguins don't typically live beyond 20 years in the wild.

Read more at Discovery News

Sixth-Remaining Northern White Rhino Dies

Angalifu, a northern white rhino housed at the San Diego Zoo's Safari Park, has died of old age at 44. With his death the subspecies draws closer to extinction, as only five remain.

Angalifu was housed at San Diego Zoo with another elderly northern white rhino named Nola. The pair, however, was not able to produce offspring, and the outlook for babies elsewhere looks grim.

All hopes for offspring rest with a single male named Sudan living on a reserve in Kenya with two females. Dvur Kralove Zoo, in the Czech Republic, meanwhile, is home to one elderly female.

The northern white rhino has been brought to the brink of extinction by poachers, who kill the animals for their horns, which are sold in markets in East Asia, where rhino horn is believed to have medicinal value.

From Discovery News

Birds Evolved in 'Big Bang,' New Family Tree Reveals

A new family tree of the world's bird species may be the most complete one ever made, and reveals some surprising relationships, as well as showing how characteristics such as birdsong evolved.

More than 200 scientists at 80 institutions spent more than four years sequencing the genomes of bird species and analyzing them using supercomputers as part of a massive effort to reconstruct how birds evolved.

The new bird genealogy is the most comprehensive one to date in terms of the amount of genomic data and the scientific approaches used, said Erich Jarvis, a neurobiologist at Duke University in Durham, North Carolina, who led one of eight reports based on the findings published today (Dec. 11) in the journal Science.

In one finding, the analysis revealed that the common ancestor of a group called the core landbirds — which includes today's songbirds, parrots and woodpeckers — was a top-level predator of its time, the researchers said.

Previous studies have tried to reconstruct the relationships between bird species using just a few dozen genes, but each study gave different results. "You couldn't figure out who to believe," Jarvis said.

More than 10,000 bird species are alive today, and from the colorful birds-of-paradise of New Guinea, to the iconic blue-footed boobies of the west coast of the Americas, birds are some of the most varied and fascinating creatures around.

In the new project, the researchers analyzed the genomes of 48 bird species (including 45 that had not been sequenced before), representing all major branches of birds, including the crow, duck, falcon, parakeet, crane, ibis, woodpecker and eagle. About 95 percent of today's birds belong to a group called Neoaves, and most of the species the researchers analyzed belong to this group.

The new findings show that Neoaves underwent a "Big Bang" of evolution, with many new species appearing within just a few million years of the time that most dinosaurs went extinct about 66 million years ago. Previous work had suggested a more gradual evolutionof this group.

Neoavesinitially split into two groups, called Columbea and Passerea, Jarvis and his colleagues said.

One of the most surprising findings was that flamingoes are closely related to pigeons, much more so than they are to birds that might seem more similar, such as pelicans, the researchers said.

Another important finding was that vocal learning, which is the ability to hear sounds and reproduce them (a key feature of human speech), may have evolved independently in several groups of birds. What's more, a brain region in these birds shares similarities with human brain areas involved in speech.

To construct the family tree, the researchers used supercomputers to compare the complete genome sequences of all the birds studied. Using nine supercomputers, the analysis took 300 CPU years (a CPU year is the time it would take a single computer to complete the task on its own).

Birds have smaller genomes than most other vertebrates, but even with these powerful tools, some parts of the tree were hard to flesh out. It wasn't enough to look at the parts of the genome that encode proteins, the vital biological machinery in cells, the researchers found. They had to look at non-coding sequences between genes, too.

Read more at Discovery News

Denmark Makes Land Grab for North Pole

Denmark will lay claim to energy-rich but contested territory around the North Pole on Monday by submitting data to the UN which it says demonstrates the area is an extension of its continental shelf.

The Danish government said it would tell the UN Commission on the Limits of the Continental Shelf that data collected since 2002 supports its claim to ownership over an area of about 895,000 square kilometres (346,000 square miles) beyond the current nautical borders of Greenland, an autonomous Danish territory.

"The submission of our claim to the continental shelf north of Greenland is a historic and important milestone for the Kingdom of Denmark," Foreign Minister Martin Lidegaard said in a statement.

"The objective of this huge project is to define the outer limits of our continental shelf and thereby -- ultimately -- of the Kingdom of Denmark," he added.

Claims on a continental shelf beyond 200 nautical miles from a country's borders must be supported by scientific and technical data. However, the remote region is hotly disputed by other countries.

Norway already lays claim to an area overlapping the one outlined in the Danish submission to the UN, and there is "potential overlap with Canada, the Russian Federation and the US," the Ministry of Foreign Affairs said in a statement.

"It will be up to the parties themselves to negotiate bilateral delimitation agreements," it said.

Moscow has increased its military presence in the pristine but energy-rich Arctic region, while Canadian Prime Minister Stephen Harper's government has made asserting sovereignty over an expansive Arctic archipelago and surrounding waters a key policy.

When Russia planted a flag on the Arctic sea bed directly under the North Pole in 2007, Canada raised its voice to highlight that both countries claim sovereignty over the area.

Read more at Discovery News

LHC Revs-Up for Most Powerful Particle Collisions Ever

The Large Hadron Collider (LHC) is on the verge of restarting for its second 3-year run that will see it double its collisional energy and dramatically step-up the search for new physics, hopefully solving some of the most perplexing mysteries in modern physics along the way.

When starting up the world’s largest particle accelerator, it’s not just a simple case of flicking the “on” switch, however. As the most complex machine ever constructed by humankind, the LHC, which is managed by the European Organization for Nuclear Research (CERN) and located near Geneva, Switzerland, takes months to power up each component of the complex chain of superconducting magnets and massive detectors.

Announced by CERN on Friday, the LHC’s main 17 mile (27 kilometer) long ring of superconducting magnets have been cooled close to “its nominal operating temperature of 1.9 degrees above absolute zero.” 1.9 degrees Kelvin is -271.25 degrees Celsius or -456.25 degrees Fahrenheit.

After a 2 year pause in collisions in the LHC for maintenance and upgrades, the accelerator is on track to be powered up again in March 2015 to begin a new era of ultra-high energy particle collisions by the following May. The goal for 2015 is to push for proton-proton collision energies of up to 13 TeV — nearly double the energy of the first LHC run.

“With this new energy level, the LHC will open new horizons for physics and for future discoveries,” said CERN Director-General Rolf Heuer. “I’m looking forward to seeing what nature has in store for us.”

“After the huge amount of work done over the last two years, the LHC is almost like a new machine,” said CERN’s Director for Accelerators and Technology Frédérick Bordry. “Restarting this extraordinary accelerator is far from routine. Nevertheless, I’m confident that we will be on schedule to provide collisions to the LHC experiments by May 2015.”

Read more at Discovery News

How bird eggs get their bling

Splashy blue and green hues pop from under the glassy finish of the Tinamou species' (bird relatives of ostriches, rheas and emus) eggs.

Pigments covered by a thin, smooth cuticle reveal the mystery behind these curious shells, University of Akron researchers discovered.

The finding could lead to the development of glossy new coatings for ceramics and floors, potentially enhancing their aesthetic qualities and durability.

After removing the outer layer of the eggshells and examining their chemistry and nanostructure, the researchers discovered the presence of a weak iridescence in the Tinamou's eggshells, creating superficial colors and color changes depending on the angle at which they are viewed and the light cast upon them. The researchers' investigation of how non-pigmentary nanometer-scale structures influence light reflection and produce iridescence that impact eggshell coloration has never before been documented.

"The perceived color changes in relationship with the angles of observation and illumination. This effect can only be produced by nanostructures that influence how light is reflected," says UA post-doctoral researcher Brani Igic. He used experimental manipulations in conjunction with angle-resolved spectrophotometry, scanning electron and atomic-force microscopy, optical calculations and chemical analyses to examine the mechanical construction behind the eggshell gloss and coloration.

Sheen covering

Igic and UA research team members Matthew Shawkey, associate professor of biology, and graduate students Daphne Fechyr-Lippens and Ming Xiao, Andrew Chan and Geoffrey I. N. Waterhouse from the University of Auckland in New Zealand, Daniel Hanley and Tomas Grim from Palacký University in the Czech Republic, Patricia R. L. Brennan from the University of Massachusetts, and Mark E. Hauber from Hunter College also found Tinamou eggs' sheen results from an ultra-smooth coating, or cuticle, distinct from typically bumpy eggshells.

Read more at Science Daily

Genes tell story of birdsong and human speech

His office is filled with all sorts of bird books, but Duke neuroscientist Erich Jarvis didn't become an expert on the avian family tree because of any particular interest in our feathered friends. Rather, it was his fascination with how the human brain understands and reproduces speech that brought him to the birds.

"We've known for many years that the singing behavior of birds is similar to speech in humans -- not identical, but similar -- and that the brain circuitry is similar, too," said Jarvis, an associate professor of neurobiology at the Duke University Medical School and an investigator at the Howard Hughes Medical Institute. "But we didn't know whether or not those features were the same because the genes were also the same."

Now scientists do know, and the answer is yes -- birds and humans use essentially the same genes to speak.

After a massive international effort to sequence and compare the entire genomes of 48 species of birds representing every major order of the bird family tree, Jarvis and his colleagues found that vocal learning evolved twice or maybe three times among songbirds, parrots and hummingbirds.

Even more striking is that the set of genes involved in each of those song innovations is remarkably similar to the genes involved in human speaking ability.

The findings are part of a package of eight scientific papers in a Dec. 12 special issue of Science and 21 additional papers appearing nearly simultaneously in Genome Biology, GigaScience and other journals. Jarvis' name appears on 20 papers and he is a corresponding author for 8 of them.

Jarvis co-led the Avian Phylogenomics Consortium with Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen and M. Thomas P. Gilbert of the Natural History Museum of Denmark. His Duke lab contributed to preparing samples, sequencing and annotating the genomes, performing the analyses and coordinating the overall project.

The Jarvis lab in the Bryan Research Building prepared DNA of many of the species, pulling it from little chunks of frozen, pink bird flesh collected over the past 30 years by museums and other institutions around the world. To ensure the DNA being sequenced really belonged to the Golden-collared manakin and not an undergraduate lab assistant, the lab has been kept spotlessly clean and many of its tools are used only once, to avoid the possibility of subsequent contamination.

"We change gloves a lot," said Carole Parent, the lab research analyst who set up a DNA isolation pipeline for the next stage of the project to sequence still more birds and supervised sample prep with a team of Duke undergrads and a student from East Chapel Hill High School.

All of this meticulous and somewhat tedious work has given Jarvis and hundreds of colleagues around the world a crack at an unprecedented amount of genomic data generated by BGI in China. The whole-genome comparison of the 48 bird species required new algorithms written at the University of Illinois and University of Texas that ran for 400 years of CPU time on three supercomputers in the U.S.

Of the 29 papers covering everything from penguin evolution to color vision, eight are devoted to bird song.

One of the Dec. 12 papers in Science found there is a consistent set of just over 50 genes that show higher or lower activity in the brains of vocal learning birds and humans. These changes were not found in the brains of birds that do not have vocal learning and of non-human primates that do not speak, according to this Duke team, which was led by Jarvis; Andreas Pfenning, a graduate of the Ph.D. program in computational biology and bioinformatics (CBB); and Alexander Hartemink, professor of computer science, statistical science and biology.

"This means that vocal learning birds and humans are more similar to each other for these genes in song and speech brain areas than other birds and primates are to them," Jarvis said.

These genes are involved in forming new connections between neurons of the motor cortex and neurons that control the muscles that produce sound.

A companion study by another CBB doctorate, Rui Wang, looked at the specialized activity of a pair of genes involved in the regions of the brain that control song and speech. This study, appearing in the Journal of Comparative Neurology, found that these genes are down- and up-regulated in one brain region of song-learning birds during the juvenile period of their vocal learning , changes that last into adulthood. This study, and that of Pfenning, hypothesize that changes in these genes could be critical for the evolution of song in birds and speech in humans.

"You can find those same genes in the genomes of all species, but they're active at much higher or lower levels in the specialized song or speech brain regions of vocal learning birds and humans," Jarvis said. "What this suggests to me is that when vocal learning evolves, there may be a limited way in which the brain circuits can evolve."

Another paper in Science from Duke, led by post-doc Osceola Whitney, Pfenning, Hartemink and Anne West, an associate professor of neurobiology, looked at gene activation in different areas of the brain during singing. This team found activation of 10 percent of the expressed genome during singing, with diverse activation patterns in different song-learning regions of the brain. The diverse gene patterns are best explained by epigenetic differences in the genomes of the different brain regions, meaning that individual cells in different brain regions can regulate genes at a moment's notice when the birds sing.

Among the three main groups of vocal learning birds, parrots are clearly different in their ability to mimic human speech. Mukta Chakraborty, a postdoc in the Jarvis lab, led a project that used the activity of some of the specialized genes to discover that the parrot's speech center is organized somewhat differently. It has what the researchers call a "song-system-within-a-song-system" in which the area of the brain with different gene activity for producing song has an outer ring of still more differences in gene expression.

Parrots are very social animals, Chakraborty said, and having the ability to quickly pick up "dialects" of parrot speech may account for their super-charged speech center. The "shell" or outer regions were found to be proportionally larger in the parrot species, which are believed to have the highest vocal, cognitive and social abilities. These species include Amazon parrots, the African Grey and the Blue and Gold Macaw.

Jarvis was also part of a team with Claudio Mello and his Ph.D. student Morgan Wirthlin at Oregon Health & Science University that found ten more genes that are unique to song-control regions of songbirds. This paper appears in BMC Genomics.

A paper in Science led by Zhang, Gilbert and Jarvis found the genomes of vocal learners are more rapidly evolving and have more chromosomal rearrangements compared to other bird species. This genomic comparison also found similar changes occurred independently in in the song-learning area of different birds' brains.

Jarvis said knowing more of this history of how speech evolved in birds makes vocal learning birds even more valuable model organisms for helping to answer the questions he and other researchers are addressing about human speech.

"Speech is difficult to study in human brains," he said. "Whales and elephants learn speech and songs, but they're too big to house in the lab. Now that we have a deeper understanding of how similar birdsong brain regions are to human speech regions at the genetic level, I think they'll be a better model than ever."

Jarvis' general exploration of the bird brain over his 16 years at Duke has also led to several unexpected discoveries unrelated to song.

In 2005, he and colleagues found a center of the brain in migratory birds that apparently enables sensing of magnetic fields through "night vision." That year he also led a revision of the understanding of bird brain organization and vertebrate brain evolution. Last year, he led a re-drawing of the geography of the bird brain based on analysis of 52 genes that are active in 23 areas of the brains of eight species of birds. This new map shows neuron groupings in the birds' brains to be organized in columns like the brains of humans and other mammals.

Read more at Science Daily

Oil-dwelling bacteria are social creatures in Earth's deep biosphere

Oil reservoirs are scattered deep inside Earth like far-flung islands in the ocean, so their inhabitants might be expected to be very different, but a new study led by Dartmouth College and University of Oslo researchers shows these underground microbes are social creatures that have exchanged genes for eons.

The study, which was led by researchers at Dartmouth College and the University of Oslo, appears in the ISME Journal.

The findings shed new light on the "deep biosphere," or the vast subterranean realm whose single-celled residents are estimated to be roughly equal in number and diversity to all the microbes inhabiting the surface's land, water and air. Deep microbial research may also help scientists to better understand life's early evolution on Earth and aid the search for life on Mars and other planets.

Some scientists support a "burial and isolation" scenario in which bacteria living in oil reservoirs are descendants of isolated bacterial communities buried with sediments that over time became oil reservoirs. "Instead, our analysis supports a more complex 'colonization' view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition since ancient times," says co-author Olga Zhaxybayeva, an assistant professor at Dartmouth.

Since the 1980s, a growing number of microbial life forms have been discovered deep underground, but many questions remain, including when and how these microorganisms came to inhabit places where temperatures and pressure are extreme and nutrients and energy can be scarce. Microorganisms are the oldest form of life on Earth and continue to play a crucial role in the planet's ecosystem. Those bacteria dwelling underground live not off sunlight energy but Earth's inner heat, chemicals and nutrients.

In their new paper, researchers asked a number of questions, including: do buried bacteria adapt to living in oil reservoirs as they form from sediments? Do bacteria evolve in isolation, or do they migrate to oil reservoirs and exchange genes with surrounding bacteria, including surface ones introduced through drilling fluids used in oil production? The researchers analyzed 11 genomes of Thermotoga, an ancient lineage of heat-loving bacteria, taken from oil reservoirs in the North Sea and Japan and from hot water vents on the ocean floor near the Kuril Islands north of Japan, Italy and the Azores, an island chain west of Portugal. They also analyzed Thermotoga community DNA from the environment (so-called metagenomes) from North America and Australia that are available in public databases.

Read more at Science Daily

Earth's most abundant mineral finally has a name

An ancient meteorite and high-energy X-rays have helped scientists conclude a half century of effort to find, identify and characterize a mineral that makes up 38 percent of the Earth.

And in doing so, a team of scientists led by Oliver Tschauner, a mineralogist at the University of Las Vegas, clarified the definition of the Earth's most abundant mineral -- a high-density form of magnesium iron silicate, now called Bridgmanite -- and defined estimated constraint ranges for its formation. Their research was performed at the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility located at DOE's Argonne National Laboratory.

The mineral was named after 1964 Nobel laureate and pioneer of high-pressure research Percy Bridgman. The naming does more than fix a vexing gap in scientific lingo; it also will aid our understanding of the deep Earth.

To determine the makeup of the inner layers of the Earth, scientists need to test materials under extreme pressure and temperatures. For decades, scientists have believed a dense perovskite structure makes up 38 percent of the Earth's volume, and that the chemical and physical properties of Bridgmanite have a large influence on how elements and heat flow through the Earth's mantle. But since the mineral failed to survive the trip to the surface, no one has been able to test and prove its existence -- a requirement for getting a name by the International Mineralogical Association.

Shock-compression that occurs in collisions of asteroid bodies in the solar system create the same hostile conditions of the deep Earth -- roughly 2,100 degrees Celsius (3,800 degrees Farenheit) and pressures of about 240,000 times greater than sea-level air pressure. The shock occurs fast enough to inhibit the Bridgmanite breakdown that takes place when it comes under lower pressure, such as the Earth's surface. Part of the debris from these collisions falls on Earth as meteorites, with the Bridgmanite "frozen" within a shock-melt vein. Previous tests on meteorites using transmission electron microscopy caused radiation damage to the samples and incomplete results.

So the team decided to try a new tactic: non-destructive micro-focused X-rays for diffraction analysis and novel fast-readout area-detector techniques. Tschauner and his colleagues from Caltech and the GeoSoilEnviroCARS, a University of Chicago-operated X-ray beamline at the APS at Argonne National Laboratory, took advantage of the X-rays' high energy, which gives them the ability to penetrate the meteorite, and their intense brilliance, which leaves little of the radiation behind to cause damage.

The team examined a section of the highly shocked L-chondrite meteorite Tenham, which crashed in Australia in 1879. The GSECARS beamline was optimal for the study because it is one of the nation's leading locations for conducting high-pressure research.

Bridgmanite grains are rare in the Tenhma meteorite, and they are smaller than 1 micrometer in diameter. Thus the team had to use a strongly focused beam and conduct highly spatially resolved diffraction mapping until an aggregate of Bridgmanite was identified and characterized by structural and compositional analysis.

This first natural specimen of Bridgmanite came with some surprises: It contains an unexpectedly high amount of ferric iron, beyond that of synthetic samples. Natural Bridgmanite also contains much more sodium than most synthetic samples. Thus the crystal chemistry of natural Bridgmanite provides novel crystal chemical insights. This natural sample of Bridgmanite may serve as a complement to experimental studies of deep mantle rocks in the future.

Read more at Science Daily