Mar 25, 2017

Scientists make new discovery about bird evolution

Chinese countryside (stock image). The new specimen from the rich Early Cretaceous Jehol Biota comes only from the 130.7 Ma Huajiying Formation deposits in Hebei, which preserves the second oldest known fossil birds. Birds from this layer are very rare.
In a new paper published in National Science Review, a team of scientists from the Institute of Vertebrate Paleontology and Paleoanthropology, the Shandong Tianyu Museum of Nature, and the Nanjing Institute of Geology and Paleontology (all in China) described the most exceptionally preserved fossil bird discovered to date.

The new specimen from the rich Early Cretaceous Jehol Biota (approximately 131 to 120 million years old) is referred to as Eoconfuciusornis, the oldest and most primitive member of the Confuciusornithiformes, a group of early birds characterized by the first occurrence of an avian beak. Its younger relative Confuciusornis is known from thousands of specimens but this is only the second specimen of Eoconfuciusornis found. This species comes only from the 130.7 Ma Huajiying Formation deposits in Hebei, which preserves the second oldest known fossil birds. Birds from this layer are very rare.

This new specimen of Eoconfuciusornis, housed in the Shandong Tianyu Museum of Nature, in Eastern China, is a female. The ovary reveals developing yolks that vary in size, similar to living birds. This suggests that confuciusornithiforms evolved a period of rapid yolk deposition prior to egg-laying (crocodilians, which are archosaurs like birds, deposit yolks slowly in all eggs for months with no period of rapid yolk formation), which is indicative of complex energetic profiles similar to those observed in birds.

This means Eoconfuciusornis and its kin, like living birds, was able to cope with extremely high metabolic demands during early growth and reproduction (whereas energetic demands in crocodiles are even, lacking complexity). In contrast, other Cretaceous birds including the more advanced group the Enantiornithes appear to have lower metabolic rates and have required less energy similar to crocodilians and non-avian dinosaurs (their developing yolks show little size disparity indicating no strong peak in energy associated with reproduction, and much simpler energetic profiles, limited by simpler physiologies).

Traces of skin indicate that the wing was supplemented by flaps of skin called patagia. Living birds have numerous wing patagia that help the bird to fly. This fossil helps show how bird wings evolved. The propatagium (the flap of skin that connects the shoulder and wrist) and postpatagium (the flap of skin that extends off the back of the hand and ulna) evolved before the alular patagium (the flap of skin connecting the first digit to the rest of the hand), which is absent in Eoconfuciusornis. Even more unique is the preservation of the internal structure of the propatagium which reveal a collagenous network identical to that in living birds. This internal network gives the skin flap its shape, allowing it to generate aerodynamic lift and aid the bird in flight.

The nearly complete plumage preserves remnants of the original plumage pattern, revealing the presence of spots on the wings and the earliest documentation of sexual differences in plumage within birds. This new specimen suggests that female Eoconfuciusornis were smaller than males and lacked tail feathers, similar to many sexually dimorphic living birds and the younger Confuciusornis in which the plumage of the males and females are different from each other. Samples of the feathers viewed under a microscope reveal differences in color characteristics, allowing scientists to reconstruct the plumage. Female Eoconfuciusornis had black spotted wings and gray body with a red throat patch.

Researchers have not found fossils from any other bird from the Jehol period that reveal so many types of soft tissue (feathers, skin, collagen, ovarian follicles). These remains allow researchers to create the most accurate reconstruction of a primitive early bird (or dinosaur) to date. This information provides better understanding of flight function in the primitive confuciusornithiforms and of the evolution of advanced flight features within birds.

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Ravens: Non-breeders live in highly dynamic social groups

Ravens have impressive cognitive skills when interacting with conspecifics.
Several recent studies have revealed that ravens are among the most intelligent species of birds and even species in general. But which factors caused the evolution of intelligence? According to a common hypothesis life in social groups can drive brain evolution especially when individuals benefit from remembering the identity of conspecifics and the interactions with them. With such knowledge, animals can avoid conflicts with higher ranking group members or develop alliances to gain better access to resources.

Researchers around Thomas Bugnyar in Austria and colleagues in France outfitted around 30 ravens with little "backpacks," which measured with GPS the position of the animal every hour. The devices were charged with solar power and the data were transmitted using the GSM network for mobile phones. During the last four years of data collection movements up to 160 kilometers per day were observed. In addition in Austria and Italy a total number of 332 ravens have been marked individually with colored rings and wing-tags and their presence patterns in two study sites were monitored over years.

Conclusion of the biologists: While some non-breeding ravens seem to stay only in relatively small areas, others may move thousands of kilometers per year. Still many ravens meet repeatedly in different locations usually at rich food sources (e.g. landfills, compost stations) and adjacent common night roosts. "We were surprised about the similarity to humans: Some people prefer to spend their entire life in a single city or even a small village, while others want to travel and explore the world. We find exactly the same in non-breeding ravens," says lead-author Matthias Loretto.

When ravens form groups they make friends but also fight heavily with other group members for access to resources. "Every time a raven joins a group of conspecifics at food sources, it can benefit from remembering previous interactions to decide who is friend or foe. The combination of social bonds within non-breeders and such a highly dynamic system might have driven brain evolution in ravens," ends Loretto.

From Science Daily

Mar 24, 2017

Milky Way-like galaxies in early universe embedded in 'super halos'

Artist impression of a progenitor of Milky Way-like galaxy in the early universe with a background quasar shinning through a 'super halo' of hydrogen gas surrounding the galaxy. New ALMA observations of two such galaxies reveal that these vast halos extend well beyond the galaxies' dusty, star-forming disks. The galaxies were initially found by the absorption of background quasar light passing through the galaxies. ALMA was able to image the ionized carbon in the galaxies' disks, revealing crucial details about their structures.
By harnessing the extreme sensitivity of the Atacama Large Millimeter/submillimeter Array (ALMA), astronomers have directly observed a pair of Milky Way-like galaxies seen when the universe was only eight percent of its current age. These progenitors of today's giant spiral galaxies are surrounded by "super halos" of hydrogen gas that extend many tens-of-thousands of light-years beyond their dusty, star-filled disks.

Astronomers initially detected these galaxies by studying the intense light from even-more-distant quasars. As this light travels through an intervening galaxy on its way to Earth, it can pick up the unique spectral signature from the galaxy's gas. This technique, however, normally prevents astronomers from seeing the actual light emitted by the galaxy, which is overwhelmed by the much brighter emission from the background quasar.

"Imagine a tiny firefly next to a high-power search light. That's what astronomers are up against when it comes to observing these youthful versions of our home galaxy," said Marcel Neeleman a postdoctoral fellow at the University of California, Santa Cruz, and lead author on a paper appearing in the journal Science. "We can now see the galaxies themselves, which gives us an amazing opportunity to learn about the earliest history of our own galaxy and others like it."

With ALMA, the astronomers were finally able to observe the natural millimeter-wavelength "glow" emitted by ionized carbon in the dense and dusty star-forming regions of the galaxies. This carbon signature, however, is considerably offset from the gas first detected by quasar absorption. This extreme separation indicates that the galaxies' gas content extends well beyond their star-filled disks, suggesting that each galaxy is embedded in a monstrous halo of hydrogen gas.

"We had expected we would see faint emissions right on top of the quasar, and instead we saw strong bright carbon emission from the galaxies at large separations from their background quasars," said J. Xavier Prochaska, professor of astronomy and astrophysics at UC Santa Cruz and coauthor of the paper. The separation from the quasar to the observed galaxy is about 137,000 light-years for one galaxy and about 59,000 light-years for the other.

According to the researchers, the neutral hydrogen gas revealed by its absorption of quasar light is most likely part of a large halo or perhaps an extended disk of gas around the galaxy. "It's not where the star formation is, and to see so much gas that far from the star-forming region means there is a large amount of neutral hydrogen around the galaxy," Neeleman said.

The new ALMA data show that these young galaxies are already rotating, which is one of the hallmarks of the massive spiral galaxies we see in the universe today. The ALMA observations further reveal that both galaxies are forming stars at moderately high rates: more than 100 solar masses per year in one galaxy and about 25 solar masses per year in the other.

"These galaxies appear to be massive, dusty, and rapidly star-forming systems, with large, extended layers of gas," Prochaska said.

"ALMA has solved a decades-old question on galaxy formation," said Chris Carilli, an astronomer with the National Radio Astronomy Observatory in Socorro, N.M., and co-author on the paper. "We now know that at least some very early galaxies have halos that are much more extended that previously considered, which may represent the future material for galaxy growth."

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Gravitational wave kicks monster black hole out of galactic core

This image, taken by NASA's Hubble Space Telescope, reveals an unusual sight: a runaway quasar fleeing from its galaxy's central hub. A quasar is the visible, energetic signature of a black hole. Black holes cannot be observed directly, but they are the energy source at the heart of quasars -- intense, compact gushers of radiation that can outshine an entire galaxy. The green dotted line marks the visible periphery of the galaxy. The quasar, named 3C 186, appears as a bright star just off-center. The quasar and its host galaxy reside 8 billion light-years from Earth. Researchers estimate that it took the equivalent energy of 100 million supernovas exploding simultaneously to jettison the black hole. The most plausible explanation for this propulsive energy is that the monster object was given a kick by gravitational waves unleashed by the merger of two hefty black holes at the center of the host galaxy. The Hubble image combines visible and near-infrared light taken by the Wide Field Camera 3.
Astronomers have uncovered a supermassive black hole that has been propelled out of the center of a distant galaxy by what could be the awesome power of gravitational waves.

Though there have been several other suspected, similarly booted black holes elsewhere, none has been confirmed so far. Astronomers think this object, detected by NASA's Hubble Space Telescope, is a very strong case. Weighing more than 1 billion suns, the rogue black hole is the most massive black hole ever detected to have been kicked out of its central home.

Researchers estimate that it took the equivalent energy of 100 million supernovas exploding simultaneously to jettison the black hole. The most plausible explanation for this propulsive energy is that the monster object was given a kick by gravitational waves unleashed by the merger of two hefty black holes at the center of the host galaxy.

First predicted by Albert Einstein, gravitational waves are ripples in space that are created when two massive objects collide. The ripples are similar to the concentric circles produced when a hefty rock is thrown into a pond. Last year, the Laser Interferometer Gravitational-Wave Observatory (LIGO) helped astronomers prove that gravitational waves exist by detecting them emanating from the union of two stellar mass black holes, which are several times more massive than the sun.

Hubble's observations of the wayward black hole surprised the research team. "When I first saw this, I thought we were seeing something very peculiar," said team leader Marco Chiaberge of the Space Telescope Science Institute (STScI) and Johns Hopkins University, in Baltimore, Maryland. "When we combined observations from Hubble, the Chandra X-ray Observatory, and the Sloan Digital Sky Survey, it all pointed towards the same scenario. The amount of data we collected, from X-rays to ultraviolet to near-infrared light, is definitely larger than for any of the other candidate rogue black holes."

Chiaberge's paper will appear in the March 30 issue of Astronomy & Astrophysics.

Hubble images taken in visible and near-infrared light provided the first clue that the galaxy was unusual. The images revealed a bright quasar, the energetic signature of a black hole, residing far from the galactic core. Black holes cannot be observed directly, but they are the energy source at the heart of quasars -- intense, compact gushers of radiation that can outshine an entire galaxy. The quasar, named 3C 186, and its host galaxy reside 8 billion light-years away in a galaxy cluster. The team discovered the galaxy's peculiar features while conducting a Hubble survey of distant galaxies unleashing powerful blasts of radiation in the throes of galaxy mergers.

"I was anticipating seeing a lot of merging galaxies, and I was expecting to see messy host galaxies around the quasars, but I wasn't really expecting to see a quasar that was clearly offset from the core of a regularly shaped galaxy," Chiaberge recalled. "Black holes reside in the center of galaxies, so it's unusual to see a quasar not in the center."

The team calculated the black hole's distance from the core by comparing the distribution of starlight in the host galaxy with that of a normal elliptical galaxy from a computer model. The black hole had traveled more than 35,000 light-years from the center, which is more than the distance between the sun and the center of the Milky Way.

Based on spectroscopic observations taken by Hubble and the Sloan survey, the researchers estimated the black hole's mass and measured the speed of gas trapped near the behemoth object. Spectroscopy divides light into its component colors, which can be used to measure velocities in space. "To our surprise, we discovered that the gas around the black hole was flying away from the galaxy's center at 4.7 million miles an hour," said team member Justin Ely of STScI. This measurement is also a gauge of the black hole's velocity, because the gas is gravitationally locked to the monster object.

The astronomers calculated that the black hole is moving so fast it would travel from Earth to the moon in three minutes. That's fast enough for the black hole to escape the galaxy in 20 million years and roam through the universe forever.

The Hubble image revealed an interesting clue that helped explain the black hole's wayward location. The host galaxy has faint arc-shaped features called tidal tails, produced by a gravitational tug between two colliding galaxies. This evidence suggests a possible union between the 3C 186 system and another galaxy, each with central, massive black holes that may have eventually merged.

Based on this visible evidence, along with theoretical work, the researchers developed a scenario to describe how the behemoth black hole could be expelled from its central home. According to their theory, two galaxies merge, and their black holes settle into the center of the newly formed elliptical galaxy. As the black holes whirl around each other, gravity waves are flung out like water from a lawn sprinkler. The hefty objects move closer to each other over time as they radiate away gravitational energy. If the two black holes do not have the same mass and rotation rate, they emit gravitational waves more strongly along one direction. When the two black holes collide, they stop producing gravitational waves. The newly merged black hole then recoils in the opposite direction of the strongest gravitational waves and shoots off like a rocket.

The researchers are lucky to have caught this unique event because not every black-hole merger produces imbalanced gravitational waves that propel a black hole in the opposite direction. "This asymmetry depends on properties such as the mass and the relative orientation of the back holes' rotation axes before the merger," said team member Colin Norman of STScI and Johns Hopkins University. "That's why these objects are so rare."

An alternative explanation for the offset quasar, although unlikely, proposes that the bright object does not reside within the galaxy. Instead, the quasar is located behind the galaxy, but the Hubble image gives the illusion that it is at the same distance as the galaxy. If this were the case, the researchers should have detected a galaxy in the background hosting the quasar.

Read more at Science Daily

Computer program developed to diagnose and locate cancer from a blood sample

DNA from tumour cells is known to end up in the bloodstream in the earliest stages of cancer so offers a unique target for early detection of the disease.
Researchers in the United States have developed a computer program that can simultaneously detect cancer and identify where in the body the cancer is located, from a patient's blood sample. The program is described in research published this week in the open access journal Genome Biology.

Professor Jasmine Zhou, co-lead author from the University of California at Los Angeles, said: "Non-invasive diagnosis of cancer is important, as it allows the early diagnosis of cancer, and the earlier the cancer is caught, the higher chance a patient has of beating the disease. We have developed a computer-driven test that can detect cancer, and also identify the type of cancer, from a single blood sample. The technology is in its infancy and requires further validation, but the potential benefits to patients are huge."

The program works by looking for specific molecular patterns in cancer DNA that is free flowing in the patients' blood and comparing the patterns against a database of tumour epigenetics, from different cancer types, collated by the authors. DNA from tumour cells is known to end up in the bloodstream in the earliest stages of cancer so offers a unique target for early detection of the disease.

Professor Zhou explained: "We built a database of epigenetic markers, specifically methylation patterns, which are common across many types of cancer and also specific to cancers originating from specific tissue, such as the lung or liver. We also compiled the same 'molecular footprint' for non-cancerous samples so we had a baseline footprint to compare the cancer samples against. These markers can be used to deconvolute the DNA found freely in the blood into tumor DNA and non-tumor DNA."

In this study, the new computer program and two other methods (called Random Forest and Support Vector Machine) were tested with blood samples from 29 liver cancer patients, 12 lung cancer patients and 5 breast cancer patients. Tests were run 10 times on each sample to validate the results. The Random Forest and Support Vector Machine methods had an overall error rate (the chance that the test produces a false positive) of 0.646 and 0.604 respectively, while the new program obtained a lower error rate of 0.265.

Twenty-five out of the 29 liver cancer patients and 5 out of 12 lung cancer patients tested in this study had early stage cancers, which the program was able to detect in 80% of cases. Although the level of tumour DNA present in the blood is much lower during the early stages of these cancers, the program was still able to make a diagnosis demonstrating the potential of this method for the early detection of cancer, according to the researchers.

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Astronomers identify purest, most massive brown dwarf

An artist's impression of the new pure and massive brown dwarf.
An international team of astronomers has identified a record breaking brown dwarf (a star too small for nuclear fusion) with the 'purest' composition and the highest mass yet known. The object, known as SDSS J0104+1535, is a member of the so-called halo -- the outermost reaches -- of our Galaxy, made up of the most ancient stars. The scientists report the discovery in Monthly Notices of the Royal Astronomical Society.

Brown dwarfs are intermediate between planets and fully-fledged stars. Their mass is too small for full nuclear fusion of hydrogen to helium (with a consequent release of energy) to take place, but they are usually significantly more massive than planets.

Located 750 light years away in the constellation of Pisces, SDSS J0104+1535 is made of gas that is around 250 times purer than the Sun, so consists of more than 99.99% hydrogen and helium. Estimated to have formed about 10 billion years ago, measurements also suggest it has a mass equivalent to 90 times that of Jupiter, making it the most massive brown dwarf found to date.

It was previously not known if brown dwarfs could form from such primordial gas, and the discovery points the way to a larger undiscovered population of extremely pure brown dwarfs from our Galaxy's ancient past.

The research team was led by Dr ZengHua Zhang of the Institute of Astrophysics in the Canary Islands. He said: "We really didn't expect to see brown dwarfs that are this pure. Having found one though often suggests a much larger hitherto undiscovered population -- I'd be very surprised if there aren't many more similar objects out there waiting to be found."

SDSS J0104+1535 has been classified as an L type ultra-subdwarf using its optical and near-infrared spectrum, measured using the European Southern Observatory's "Very Large Telescope" (VLT). This classification was based on a scheme very recently established by Dr Zhang.

From Science Daily

New portal to unveil the dark sector of the universe

Portals can allow the exploration of the dark sector with the Standard Model particles Portals mix or connect the dark sector particles with the Standard Model particles. Through the portals it is possible to explore the dark sector particles using the Standard Model particles. The portals play a basic and critical role in the study of the dark sector particles both theoretically and experimentally.
Once upon a time, the Universe was just a hot soup of particles. In those days, together with visible particles, other particles to us hidden or dark might have formed. Billions of years later scientists catalogued 17 types of visible particles, with the most recent one being the Higgs boson, creating the 'Standard Model'. However, they are still struggling to detect the hidden particles, the ones that constitute the dark sector of the Universe.

Scientists at the Center for Theoretical Physics of the Universe, within the Institute for Basic Science (IBS) have proposed a hypothetical portal that connects two possible dark sector particles; their research could open a new perspective into the murky understanding of the dark sector. Published in Physical Review Letters, this study has implications in cosmology and astroparticle physics.

Physicists have plenty of ideas about what these dark sector particles might look like. One candidate is the axion, which is a very light particle that can solve some theoretical problems of the Standard Model. Another candidate is the dark photon: A very light particle which shares some properties with one of the particles of the Standard Model, that is the photon, the constituent of visible light. However, while photons couple to the electromagnetic charge, dark photons couple to the so-called dark charge, that might be carried by other dark sector particles.

Physicists believe that the dark sector communicates with the Standard Model, via portals. For example, a vector portal would allow the mixing between photons and dark photons. And, an axion portal connects axions and photons. There are only several possible portals physicists have identified, and each portal is a major tool in theoretical and experimental studies in searching for dark sector particles. A team of IBS scientists, hypothesized the existence of a new portal they named the "dark axion portal" that connects dark photons and axions.

The central idea of the dark axion portal is based on the observation that new heavy quarks may also have a dark charge that couples to the dark photon. Through the heavy quarks, axion, photon, and dark photon can interact with each other.

Read more at Science Daily

Mar 23, 2017

Most cancer mutations are due to random DNA copying 'mistakes'

No matter how perfect the environment, random DNA copying errors occur.
Johns Hopkins Kimmel Cancer Center scientists report data from a new study providing evidence that random, unpredictable DNA copying "mistakes" account for nearly two-thirds of the mutations that cause cancer. Their research is grounded on a novel mathematical model based on DNA sequencing and epidemiologic data from around the world.

"It is well-known that we must avoid environmental factors such as smoking to decrease our risk of getting cancer. But it is not as well-known that each time a normal cell divides and copies its DNA to produce two new cells, it makes multiple mistakes," says Cristian Tomasetti, Ph.D., assistant professor of biostatistics at the Johns Hopkins Kimmel Cancer Center and the Johns Hopkins Bloomberg School of Public Health. "These copying mistakes are a potent source of cancer mutations that historically have been scientifically undervalued, and this new work provides the first estimate of the fraction of mutations caused by these mistakes."

"We need to continue to encourage people to avoid environmental agents and lifestyles that increase their risk of developing cancer mutations. However, many people will still develop cancers due to these random DNA copying errors, and better methods to detect all cancers earlier, while they are still curable, are urgently needed," says Bert Vogelstein, M.D., co-director of the Ludwig Center at the Johns Hopkins Kimmel Cancer Center.

Tomasetti and Vogelstein conducted the new study described in a report published March 24 in the journal Science.

The researchers say their conclusions are in accord with epidemiologic studies showing that approximately 40 percent of cancers can be prevented by avoiding unhealthy environments and lifestyles. But among the factors driving the new study, say the researchers, is that cancer often strikes people who follow all the rules of healthy living -- nonsmoker, healthy diet, healthy weight, little or no exposure to known carcinogens -- and have no family history of the disease, prompting the pained question "Why me?"

Tomasetti and Vogelstein believe the answer to this question rests in random DNA copying errors. Current and future efforts to reduce known environmental risk factors, they say, will have major impacts on cancer incidence in the U.S. and abroad. But they say the new study confirms that too little scientific attention is given to early detection strategies that would address the large number of cancers caused by random DNA copying errors.

"These cancers will occur no matter how perfect the environment," says Vogelstein.

In a previous study authored by Tomasetti and Vogelstein in the Jan. 2, 2015, issue of Science, the pair reported that DNA copying errors could explain why certain cancers in the U.S., such as those of the colon, occur more commonly than other cancers, such as brain cancer.

In the new study, the researchers addressed a different question: What fraction of mutations in cancer are due to these DNA copying errors?

To answer this question, the scientists took a close look at the mutations that drive abnormal cell growth among 32 cancer types (Supplemental Materials, Table S6). They developed a new mathematical model using DNA sequencing data from The Cancer Genome Atlas and epidemiologic data from the Cancer Research UK database.

According to the researchers, it generally takes two or more critical gene mutations for cancer to occur. In a person, these mutations can be due to random DNA copying errors, the environment or inherited genes. Knowing this, Tomasetti and Vogelstein used their mathematical model to show, for example, that when critical mutations in pancreatic cancers are added together, 77 percent of them are due to random DNA copying errors, 18 percent to environmental factors, such as smoking, and the remaining 5 percent to heredity.

In other cancer types, such as those of the prostate, brain or bone, more than 95 percent of the mutations are due to random copying errors.

Lung cancer, they note, presents a different picture: 65 percent of all the mutations are due to environmental factors, mostly smoking, and 35 percent are due to DNA copying errors. Inherited factors are not known to play a role in lung cancers.

Looking across all 32 cancer types studied, the researchers estimate that 66 percent of cancer mutations result from copying errors, 29 percent can be attributed to lifestyle or environmental factors, and the remaining 5 percent are inherited.

The scientists say their approach is akin to attempts to sort out why "typos" occur when typing a 20-volume book: being tired while typing, which represents environmental exposures; a stuck or missing key in the keyboard, which represent inherited factors; and other typographical errors that randomly occur, which represent DNA copying errors. "You can reduce your chance of typographical errors by making sure you're not drowsy while typing and that your keyboard isn't missing some keys," says Vogelstein. "But typos will still occur because no one can type perfectly. Similarly, mutations will occur, no matter what your environment is, but you can take steps to minimize those mutations by limiting your exposure to hazardous substances and unhealthy lifestyles."

Tomasetti and Vogelstein's 2015 study created vigorous debate from scientists who argued that their previously published analysis did not include breast or prostate cancers, and it reflected only cancer incidence in the United States.

However, Tomasetti and Vogelstein now report a similar pattern worldwide, supporting their conclusions. They reasoned that the more cells divide, the higher the potential for so-called copying mistakes in the DNA of cells in an organ. They compared total numbers of stem cell divisions with cancer incidence data collected by the International Agency for Research on Cancer on 423 registries of cancer patients from 68 countries other than the U.S., representing 4.8 billion people, or more than half of the world's population. This time, the researchers were also able to include data from breast and prostate cancers. They found a strong correlation between cancer incidence and normal cell divisions among 17 cancer types, regardless of the countries' environment or stage of economic development.

Tomasetti says these random DNA copying errors will only get more important as societies face aging populations, prolonging the opportunity for our cells to make more and more DNA copying errors. And because these errors contribute to a large fraction of cancer, Vogelstein says that people with cancer who have avoided known risk factors should be comforted by their findings. "It's not your fault," says Vogelstein. "Nothing you did or didn't do was responsible for your illness."

In addition to Tomasetti and Vogelstein, Lu Li, a doctoral student in Tomasetti's laboratory in the Department of Biostatistics at the Johns Hopkins Bloomberg School of Public Health, also contributed to the research. Funding for the research was provided by the John Templeton Foundation, the Lustgarten Foundation for Pancreatic Cancer Research, the Virginia and D.K. Ludwig Fund for Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, and the National Institutes of Health's National Cancer Institute (CA006973, CA43460, and CA62924).

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Tracing aromatic molecules in the early Universe

In this study, astronomers used data from the Keck and Spitzer telescopes to trace the star forming and dusty regions of galaxies at about 10 billion years ago. The picture in the background shows the GOODS field, one of the five regions in the sky that was observed for this study.
A molecule found in car engine exhaust fumes that is thought to have contributed to the origin of life on Earth has made astronomers heavily underestimate the amount of stars that were forming in the early Universe, a University of California, Riverside-led study has found.

That molecule is called polycyclic aromatic hydrocarbon (PAH). On Earth it is also found in coal and tar. In space, it is a component of dust, which along with gas, fills the space between stars within galaxies.

The study, which was just published in the Astrophysical Journal, represents the first time that astronomers have been able to measure variations of PAH emissions in distant galaxies with different properties. It has important implications for the studies of distant galaxies because absorption and emission of energy by dust particles can change astronomers' views of distant galaxies.

"Despite the ubiquity of PAHs in space, observing them in distant galaxies has been a challenging task," said Irene Shivaei, a graduate student at UC Riverside, and leader of the study. "A significant part of our knowledge of the properties and amounts of PAHs in other galaxies is limited to the nearby universe."

The research was conducted as part of the University of California-based MOSDEF survey, a study that uses the Keck telescope in Hawaii to observe the content of about 1,500 galaxies when the universe was 1.5 to 4.5 billion years old. The researchers observed the emitted visible-light spectra of a large and representative sample of galaxies during the peak-era of star formation activity in the universe.

In addition, the researchers incorporated infrared imaging data from the NASA Spitzer Space Telescope and the European Space Agency-operated Herschel Space Observatory to trace the polycyclic aromatic hydrocarbon emission in mid-infrared bands and the thermal dust emission in far-infrared wavelengths.

The researchers concluded that the emission of polycyclic aromatic hydrocarbon molecules is suppressed in low-mass galaxies, which also have a lower fraction of metals, which are atoms heavier than hydrogen and helium. These results indicate that the polycyclic aromatic hydrocarbon molecules are likely to be destroyed in the hostile environment of low-mass and metal-poor galaxies with intense radiation.

The researchers also found that the polycyclic aromatic hydrocarbon emission is relatively weaker in young galaxies compared to older ones, which may be due to the fact that polycyclic aromatic hydrocarbon molecules are not produced in large quantities in young galaxies.

They found that the star-formation activity and infrared luminosity in the universe 10 billion years ago is approximately 30 percent higher than previously measured.

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Scientists reveal hidden structures in bacterial DNA

Quick-freeze deep-etch replica TEM imaging of a M. pneumoniae cell.
DNA contains the instructions for life, encoded within genes. Within all cells, DNA is organised into very long lengths known as chromosomes. In animal and plant cells these are double-ended, like pieces of string or shoelaces, but in bacteria they are circular. Whether stringy or circular, these long chromosomes must be organised and packaged inside a cell so that the genes can be switched on or off when they are required.

Working together with colleagues in Spain, Japan and Australia, researchers led by Luis Serrano, ICREA research professor and leader of the Design of Biological Systems laboratory at the Centre for Genomic Regulation, focused their attention on the organisation of DNA within an organism with an extremely small genome -- the pneumonia pathogen Mycoplasma pneumoniae. Its circular chromosome is five times smaller than that of larger bacteria such as the gut bug E. coli.

Using a technique called Hi-C, which reveals the interactions between different pieces of DNA, the researchers created a three-dimensional 'map' of the Mycoplasma chromosome. They then used super-resolution microscopy to prove that this computer-generated map matched up with the real-life chromosome organisation inside bacterial cells.

Notably, the CRG team, which counted with the expertise in Mycoplasma from the Serrano's laboratory and the collaboration of the ICREA research professor Marc Marti-Renom at CNAG-CRG, discovered that Mycoplasma's circular chromosome is consistently organised the same way in all the cells, with a region called the Origin (where DNA copying begins) at one end of the structure and the midpoint of the chromosome located at the opposite end. This is a similar arrangement to that seen in some other larger bacterial species.

The scientists also used the Hi-C technique to study more detailed patterns of organisation within the Mycoplasma genome. In recent years, scientists all over the world have investigated the organisation of chromosomes inside cells from species ranging from larger bacteria to human. Next Generation Sequencing has allowed scientists to 'read' the DNA sequence of any genome, but this doesn't reveal how genetic information is managed and organised in the crowded and bustling biological environment inside a cell. Now, new tools have revealed complex organisational structures within the genomes of larger organisms, with certain regions of chromosomes clustered together to form domains containing genes that are switched on or off together.

However, it was thought that these domains would not be found in Mycoplasma, because its genome is so small and it only makes around 20 different DNA binding proteins responsible for organising the chromosome, compared to the hundreds made by other bacterial species.

Intriguingly, the CRG team found that even the tiny Mycoplasma chromosome is organised into distinct structural domains, each containing genes that are also turned on or off in a co-ordinated way.

Marie Trussart, the lead author on the paper, said: "Studying bacteria with such a small genome was a big technical challenge, especially because we were using super-resolution microscopy, and it took us five years to complete the project. We had suspected that the Mycoplasma genome might have a similar overall organisation to other bacteria, but we were completely surprised to find that it was also organised into domains, which can be considered as regulatory units of chromatin organisation and that we had identified a previously unknown layer of gene regulation. This research shows that the organisation and control of genes cannot be understood by just looking at the linear sequence of DNA in the genome. Indeed, to get the full picture of gene regulation we need to look at the three-dimensional organisation of the chromatin that also coordinates gene activity."

The discovery suggests that this level of organisation and genetic control is common to all living cells, from the largest to the smallest, and can be achieved with little more than a handful of DNA binding proteins and the structural properties of the DNA itself.

Read more at Science Daily

A new web of life: First full family tree of the world's spiders

Leucauge venusta suspended from its web.
For the first time biologists have made a full family tree of the world's spiders, giving us knowledge about venoms that can be useful in medicine. And we might be able to develop silk just as good as the spider's.

They may make you cringe in horror, or they may intrigue you. Some even have them as pets.

Regardless of how you judge them, spiders are a plentiful and widespread group of animals. They have been around for 400 million years, count 45,000 species, and crawl around on nearly every terrestrial habitat in in the world.

For long, researchers have tried to unlock the secrets to their evolutionary history, striking diversity and success.

First of its kind

One team, including Dimitar Dimitrov from the Natural History Museum in Oslo, has taken this task to an unrivalled level, sampling 932 spider species from across the globe, representing every but one of the world's 116 known families.

The spiders of the last family are extremely small, and involving them was too complicated. But they are not really significant in this context, Dimitrov says. They will be included in further analyses.

The spiders were sequenced for several gene markers and then compared to each other, analyses in which Dimitrov was heavily involved. Simply put, the more similar the genetic code is between two species, the more closely they are related.

The team was thereby able to order and place the different spider branches in relation to each other, reconstructing their history through a so-called phylogenetic tree (see fact box).

"It is the most comprehensive study of spiders' evolution until now," says Dimitrov.

Drivers of diversification

One of the main challenges for understanding spider evolution is the identification of the drivers that have led to spider diversity.

"Our findings are important for understanding how different characters such as webs, vision or venoms have evolved and have affected the diversification of different groups that have these characters. For example why do some families have thousands of species and others just a few? Now that we have a large-scale phylogeny we may actually address this question combining information on traits and natural history with the tree," the entomologist explains.

Far reaching applications

The newly spun web of life not only alters our understanding of spiders, but may also impact disciplines such as material science and medicine, the researchers claim. "Spiders' venoms are exceptionally diverse in terms of their components. Thus, having a large tree of spiders will help us understand how those have evolved. We can also use the tree to predict the venom type of spiders that have not been studied. This is also important for medical applications as some of the venom components are used in the pharmaceutical industry."

Another alluring prospect relates to the manufacture of artificial silk, which material scientists try to copy with the same extreme strength and elasticity as silk produced by spiders.

"As of now there is no artificial fiber that can match the spider silk properties. In the future," Dimitrov explains, "the research team may supply the current tree with even more species and genomic data, which may further resolve uncertain parts of the tree."

Big picture science

"What I like most about this type of studies is that they provide you with the "big picture," a perspective that is hard to gain otherwise. Yet it is necessary to put more specific studies into a general evolutionary context," Dimitrov explains.

"For example, it is really hard to gain a deep understanding on the evolution of traits if one is looking at a specific trait in just a few species."

Envision two separate species. Both of them only thrive in a harsh and arid environment and happen to look alike. Did they adapt to the arid habitat independently or did they inherit this ability through a common ancestor?

"The two options would imply rather radical differences in our understanding of adaptations to arid environments. If it happened independently, one would suggest that this might be common, while the other would suggest it is as a rate event. If we lack a phylogenetic perspective we cannot really tell which one would be the case."

Read more at Science Daily

Under the Dead Sea, warnings of dire drought

Deep below the seabed, drilling revealed thick layers of salt, precipitated out during past warm, dry periods. In this specimen, transparent crystals (left) formed on what was then the bottom during winter; finer white ones (right) formed on the water surface in summer and later sank.
Nearly 1,000 feet below the bed of the Dead Sea, scientists have found evidence that during past warm periods, the Mideast has suffered drought on scales never recorded by humans -- a possible warning for current times. Thick layers of crystalline salt show that rainfall plummeted to as little as a fifth of modern levels some 120,000 years ago, and again about 10,000 years ago. Today, the region is drying again as climate warms, and scientists say it will get worse. The new findings may cause them to rethink how much worse, in this already thirsty and volatile part of the world.

"All the observations show this region is one of those most affected by modern climate change, and it's predicted to get dryer. What we showed is that even under natural conditions, it can become much drier than predicted by any of our models," said lead author Yael Kiro, a geochemist at Columbia University's Lamont-Doherty Earth Observatory. The findings were just published in an early online edition of the journal Earth and Planetary Science Letters.

The landlocked Dead Sea, straddling Israel, Jordan and Palestinian lands, is earth's lowest spot on land. Its current shoreline lies about 1,300 feet below sea level, and its floor extends down another 900 feet. Fed mainly by the Jordan River drainage, which extends also into Syria and Lebanon, it is a dead end for water, and so is extremely salty; its Biblical name in Hebrew is Y?m ha-Melah, the sea of salt. In recent years, its level has dropped about four feet a year. But hot, dry weather is not the main cause yet; rather, booming populations in the region need more water than ever, and people are sucking so much from the watershed, very little reaches the Dead Sea, where evaporation is outweighing input.

The U.N. Food and Agriculture Organization estimates that much of the region already has per capita water availability only a tenth of the world average. Rainfall has declined about 10 percent since 1950, and existing climate models say it could sink another 20 percent this century, even as population continues to grow. Israel is meeting demand by desalinating Mediterranean seawater, but poorer, landlocked Jordan and the Palestinian territories are desperate for more. In adjoining Syria, a record 1998-2012 drought likely stoked by climate change is believed to have helped spark the ongoing civil war, which has now claimed more than 500,000 lives and infected neighboring nations.

In 2010, scientists from a half-dozen nations drilled 1,500 feet into the deepest part of the seabed, bringing up a cross section of deposits recording 200,000 years of regional climate history -- the longest such archive in the Mideast. (Around-the-clock drilling went for 40 days and 40 nights -- perhaps a respectful bow to the rainfall of the Biblical Flood.) The cores revealed alternating layers of mud washed in with runoff during wet times, and crystallized salt, precipitated out during dry times when the water receded. This instantly made it clear that the region has suffered epic dry periods, but the core was not analyzed in great detail until now.

The new study shows that the salt accumulated rapidly?an estimated half-inch per year in many cases. The researchers spotted two striking periods. About halfway down they found salty layers some 300 feet thick, indicating a long-term drop below the sea's current level. This came in a period between ice ages, 115,000 to 130,000 years ago, when variations in Earth's orbit brought temperatures about 4 degrees hotter those of the 20th century?equivalent to what is projected for the end of the 21st century. The lake refilled when glaciers readvanced in sub-polar regions and the Mideast climate cooled and became moister. The cores show a similar drop in lake level just 6,000 to 10,000 years ago, following the most recent ice age, when temperatures were probably a bit cooler than now.

The chemistry of tiny fluid bubbles within the salt allowed the researchers to extrapolate rainfall and runoff patterns of these periods. They calculated that runoff to the Dead Sea generally declined 50 to 70 percent compared to today, dwarfing current projections for this century. In the most extreme periods, it went down 80 percent, and this lasted for decades to centuries at a time. The declines are probably linked to broader shifts in atmospheric flow patterns. Storms coming in from the Mediterranean could have slackened, as they appear to be doing today; and then as now, higher temperatures increase evaporation of moisture from the land.

To alleviate growing water shortages, Jordan plans to break ground next year on a canal to bring in water from the Red Sea for desalination; leftover brine would be dumped into the Dead Sea, possibly stabilizing its level. But the project is controversial, because it could cause drastic environmental changes in both seas, and could still leave much of the rest of the region with inadequate water.

Read more at Science Daily

Mar 22, 2017

First mutations in human life discovered

Artist's depiction of four-cell embryo
The earliest mutations of human life have been observed by researchers at the Wellcome Trust Sanger Institute and their collaborators. Analysing genomes from adult cells, the scientists could look back in time to reveal how each embryo developed.

Published in Nature, the study shows that from the two-cell stage of the human embryo, one of these cells becomes more dominant than the other and leads to a higher proportion of the adult body.

A longstanding question for researchers has been what happens in the very early human development as this has proved impossible to study directly. Now, researchers have analysed the whole genome sequences of blood samples (collected from 279 individuals with breast cancer) and discovered 163 mutations that occurred very early in the embryonic development of those people.

Once identified, the researchers used mutations from the first, second and third divisions of the fertilised egg to calculate which proportion of adult cells resulted from each of the first two cells in the embryo. They found that these first two cells contribute differently to the whole body. One cell gives rise to about 70 percent of the adult body tissues, whereas the other cell has a more minor contribution, leading to about 30 percent of the tissues. This skewed contribution continues for some cells in the second and third generation too.

Originally pinpointed in normal blood cells from cancer patients, the researchers then looked for these mutations in cancer samples that had been surgically removed from the patients during treatment. Unlike normal tissues composed of multiple somatic cell clones, a cancer develops from one mutant cell. Therefore, each proposed embryonic mutation should either be present in all of the cancer cells in a tumour, or none of them. This proved to be the case, and by using these cancer samples, the researchers were able to validate that the mutations had originated during early development.

Dr Young Seok Ju, first author from the Wellcome Trust Sanger Institute and the Korea Advanced Institute of Science and Technology (KAIST), said: "This is the first time that anyone has seen where mutations arise in the very early human development. It is like finding a needle in a haystack. There are just a handful of these mutations, compared with millions of inherited genetic variations, and finding them allowed us to track what happened during embryogenesis."

Dr Inigo Martincorena, from the Sanger Institute, said: "Having identified the mutations, we were able to use statistical analysis to better understand cell dynamics during embryo development. We determined the relative contribution of the first embryonic cells to the adult blood cell pool and found one dominant cell -- that led to 70 percent of the blood cells -- and one minor cell. We also sequenced normal lymph and breast cells, and the results suggested that the dominant cell also contributes to these other tissues at a similar level. This opens an unprecedented window into the earliest stages of human development."

During this study, the researchers were also able to measure the rate of mutation in early human development for the first time, up to three generations of cell division. Previous researchers had estimated one mutation per cell division, but this study measured three mutations for each cell doubling, in every daughter cell.

Mutations during the development of the embryo occur by two processes -- known as mutational signatures 1 and 5. These mutations are fairly randomly distributed through the genome, and the vast majority of them will not affect the developing embryo. However, a mutation that occurs in an important gene can lead to disease such as developmental disorders.

Read more at Science Daily

New study shakes the roots of the dinosaur family tree

The new family tree structure is shown.
More than a century of theory about the evolutionary history of dinosaurs has been turned on its head following the publication of new research from scientists at the University of Cambridge and Natural History Museum in London. Their work suggests that the family groupings need to be rearranged, re-defined and re-named and also that dinosaurs may have originated in the northern hemisphere rather than the southern, as current thinking goes.

For 130 years palaeontologists have been working with a classification system in which dinosaur species have been placed in to two distinct categories: Ornithischia and Saurischia. But now, after careful analysis of dozens of fossil skeletons and tens of thousands of anatomical characters, the researchers have concluded that these long-accepted familial groupings may, in fact, be wrong and that the traditional names need to be completely altered.

The classification of dinosaurs dates back to Victorian times. Dinosaurs were first recognised as a unique group of fossil reptiles in 1842 as a result of the work of the anatomist, Professor Richard Owen (who later went on to found the Natural History Museum in London). Over subsequent decades, various species were named as more and more fossils were found and identified. During the latter half of the 19th century it was realised that dinosaurs were anatomically diverse and attempts were made to classify them into groups that shared particular features.

It was Harry Govier Seeley, a palaeontologist trained in Cambridge under the renowned geologist Adam Sedgwick, who determined that dinosaurs fell quite neatly into two distinct groupings, or clades; Saurischia or Ornithischia. This classification was based on the arrangement of the creatures' hip bones and in particular whether they displayed a lizard-like pattern (Saurischia) or a bird-like one (Ornithischia).

As more dinosaurs were described it became clear that they belonged to three distinct lineages; Ornithischia, Sauropodomorpha and Theropoda. In 1887 Seeley placed the sauropodomorphs (which included the huge 'classic' dinosaurs such as Diplodocus and Brontosaurus) together with the theropods (which included T. rex), in the Saurischia. The ornithischians and saurischians were at first thought to be unrelated, each having a different set of ancestors, but later study showed that they all evolved from a single common ancestor.

This new analysis of dinosaurs and their near relatives, published today in the journal Nature, concludes that the ornithischians need to be grouped with the theropods, to the exclusion of the sauropodomorphs. It has long been known that birds (with their obviously 'bird-like' hips) evolved from theropod dinosaurs (with their lizard-like hips). However, the re-grouping of dinosaurs proposed in this study shows that both ornithischians AND theropods had the potential to evolve a bird-like hip arrangement- they just did so at different times in their history.

Lead author, Matthew Baron, says: "When we started our analysis, we puzzled as to why some ancient ornithischians appeared anatomically similar to theropods. Our fresh study suggested that these two groups were indeed part of the same clade. This conclusion came as quite a shock since it ran counter to everything we'd learned."

"The carnivorous theropods were more closely related to the herbivorous ornithischians and, what's more, some animals, such as Diplodocus, would fall outside the traditional grouping that we called dinosaurs. This meant we would have to change the definition of the 'dinosaur' to make sure that, in the future, Diplodocus and its near relatives could still be classed as dinosaurs."

The revised grouping of Ornithischia and Theropoda has been named the Ornithoscelida which revives a name originally coined by the evolutionary biologist, Thomas Henry Huxley in 1870.

Co-author, Dr David Norman, of the University of Cambridge, says: "The repercussions of this research are both surprising and profound. The bird-hipped dinosaurs, so often considered paradoxically named because they appeared to have nothing to do with bird origins, are now firmly attached to the ancestry of living birds."

For 130 years palaeontologists have considered the phylogeny of the dinosaurs in a certain way. Our research indicates they need to look again at the creatures' evolutionary history. This is simply science in action. You draw conclusions from one body of evidence and then new data or theories present themselves and you have to suddenly reconsider and adapt your thinking. All the major textbooks covering the topic of the evolution of the vertebrates will need to be re-written if our suggestion survives academic scrutiny."

While analysing the dinosaur family trees the team arrived at another unexpected conclusion. For many years, it was thought that dinosaurs originated in the southern hemisphere on the ancient continent known as Gondwana. The oldest dinosaur fossils have been recovered from South America suggesting the earliest dinosaurs originated there. But as a result of a re-examination of key taxa it's now thought they could just as easily have originated on the northern landmass known as Laurasia, though it must be remembered that the continents were much closer together at this time.

Read more at Science Daily

Brain 'rewires' itself to enhance other senses in blind people

This is a photo of a participant in a Magnetic Resonance Imaging (MRI) scanner used in this study.
The brains of those who are born blind make new connections in the absence of visual information, resulting in enhanced, compensatory abilities such as a heightened sense of hearing, smell and touch, as well as cognitive functions (such as memory and language) according to a new study led by Massachusetts Eye and Ear researchers. The report, published online today in PLOS One, describes for the first time the combined structural, functional and anatomical changes in the brain evident in those born with blindness that are not present in normally sighted people.

"Our results demonstrate that the structural and functional neuroplastic brain changes occurring as a result of early ocular blindness may be more widespread than initially thought," said lead author Corinna M. Bauer, Ph.D., a scientist at Schepens Eye Research Institute of Mass. Eye and Ear and an instructor of ophthalmology at Harvard Medical School. "We observed significant changes not only in the occipital cortex (where vision is processed), but also areas implicated in memory, language processing, and sensory motor functions."

The researchers used MRI multimodal brain imaging techniques (specifically, diffusion-based and resting state imaging) to reveal these changes in a group of 12 subjects with early blindness (those born with or who have acquired profound blindness prior to the age of three), and they compared the scans to a group of 16 normally sighted subjects (all subjects were of the same age range). On the scans of those with early blindness, the team observed structural and functional connectivity changes, including evidence of enhanced connections, sending information back and forth between areas of the brain that they did not observe in the normally sighted group.

These connections that appear to be unique in those with profound blindness suggest that the brain "rewires" itself in the absence of visual information to boost other senses. This is possible through the process of neuroplasticity, or the ability of our brains to naturally adapt to our experiences.

The researchers hope that increased understanding of these connections will lead to more effective rehabilitation efforts that will enable blind individuals to better compensate for the absence of visual information.

Read more at Science Daily

Upper part of Earth’s magnetic field reveals details of a dramatic past

Magetic field model/Magnetic anomaly.
Satellites have been mapping the upper part of the Earth magnetic field by collecting data for three years and found some amazing features about the Earth's crust. The result is the release of highest resolution map of this field seen from space to date. This 'lithospheric magnetic field' is very weak and therefore difficult to detect and map from space. But with the Swarm satellites it has been possible.

"By combining Swarm measurements with historical data from the German CHAMP satellite, and using a new modelling technique, it was possible to extract the tiny magnetic signals of crustal magnetization with unprecedented accuracy," said professor Nils Olsen from the Technical University of Denmark (DTU), one of the team of scientists behind the new map that has just been released at a Swarm Science Meeting in Banff, Canada.

Most of the Earth magnetic field is generated at depths greater than 3000 km by the movement of molten iron in the outer core. The remaining 6 percent -- including the 'lithospheric magnetic field' -- is partly due to electrical currents in space surrounding Earth, and partly due to magnetised rocks in the upper lithosphere -- the rigid outer part of Earth, consisting of the crust and upper mantle.

Swarm is a constellation of three identical satellites launched by the European Space Agency (ESA) to track and study the Earth's magnetic field.

Possible meteorite impact

The new map shows detailed variations in this field caused by geological structures in Earth's crust. One of these anomalies occurs in Central African Republic, centred around the city of Bangui, where the magnetic field is significantly sharper and stronger. The cause for this anomaly is still unknown, but scientists speculate that it may be the result of a meteorite impact there some 540 million years ago.

Evidence of flipping poles

The new map also reveals more details about the Earth's magnetic field that has flipped its polarity many times over the millennia. The magnetic field is in a permanent state of flux. Magnetic north wanders, and every few hundred thousand years the polarity flips so that a compass would point south instead of north.

When new crust is generated through volcanic activity, mainly along the ocean floor, iron-rich minerals in the solidifying magma are oriented towards magnetic north, thus capturing a 'snapshot' of the magnetic field in the state it was in when the rocks cooled.

Since magnetic poles flip back and forth over time, the solidified minerals form 'stripes' on the seafloor and provide a record of Earth's magnetic history.

"These magnetic stripes are evidence of pole reversals and analysing the magnetic imprints of the ocean floor allows the reconstruction of past core field changes. They also help to investigate tectonic plate motions," said Dhananjay Ravat from the University of Kentucky in the USA.

"The new map defines magnetic field features down to about 250 km and will help investigate geology and temperatures in Earth's lithosphere."

ESA's Swarm mission manager, Rune Floberghagen, added:

"Understanding the crust of our home planet is no easy feat. Measurements from space have great value as they offer a sharp global view on the magnetic structure of our planet's rigid outer shell."

Read more at Science Daily

Tiller the Hun? Farmers in Roman Empire converted to Hun lifestyle -- and vice versa

Marauding hordes of barbarian Huns, under their ferocious leader Attila, are often credited with triggering the fall of one of history's greatest empires: Rome.

Historians believe Hunnic incursions into Roman provinces bordering the Danube during the 5th century AD opened the floodgates for nomadic tribes to encroach on the empire. This caused a destabilisation that contributed to collapse of Roman power in the West.

According to Roman accounts, the Huns brought only terror and destruction. However, research from the University of Cambridge on gravesite remains in the Roman frontier region of Pannonia (now Hungary) has revealed for the first time how ordinary people may have dealt with the arrival of the Huns.

Biochemical analyses of teeth and bone to test for diet and mobility suggest that, over the course of a lifetime, some farmers on the edge of empire left their homesteads to become Hun-like roaming herdsmen, and consequently, perhaps, took up arms with the tribes.

Other remains from the same gravesites show a dietary shift indicating some Hun discovered a settled way of life and the joys of agriculture -- leaving their wanderlust, and possibly their bloodlust, behind.

Lead researcher Dr Susanne Hakenbeck, from Cambridge's Department of Archaeology, says the Huns may have brought ways of life that appealed to some farmers in the area, as well learning from and settling among the locals. She says this could be evidence of the steady infiltration that shook an empire.

"We know from contemporary accounts that this was a time when treaties between tribes and Romans were forged and fractured, loyalties sworn and broken. The lifestyle shifts we see in the skeletons may reflect that turmoil," says Hakenbeck.

"However, while written accounts of the last century of the Roman Empire focus on convulsions of violence, our new data appear to show some degree of cooperation and coexistence of people living in the frontier zone. Far from being a clash of cultures, alternating between lifestyles may have been an insurance policy in unstable political times."

For the study, published today in the journal PLOS ONE, Hakenbeck and colleagues tested skeletal remains at five 5th-century sites around Pannonia, including one in a former civic centre as well as rural homesteads.

The team analysed the isotope ratios of carbon, nitrogen, strontium and oxygen in bones and teeth. They compared this data to sites in central Germany, where typical farmers of the time lived, and locations in Siberia and Mongolia, home to nomadic herders up to the Mongol period and beyond.

The results allowed researchers to distinguish between settled agricultural populations and nomadic animal herders in the former Roman border area through isotopic traces of diet and mobility in the skeletons.

All the Pannonian gravesites not only held examples of both lifestyles, but also many individuals that shifted between lifestyles in both directions over the course of a lifetime. "The exchange of subsistence strategies is evidence for a way of life we don't see anywhere else in Europe at this time," says Hakenbeck.

She says there are no clear lifestyle patterns based on sex or accompanying grave goods, or even 'skull modification' -- the binding of the head as a baby to create a pointed skull -- commonly associated with the Hun.

"Nomadic animal herding and skull modification may be practices imported by Hun tribes into the bounds of empire and adopted by some of the agriculturalist inhabitants."

The diet of farmers was relatively boring, says Hakenbeck, consisting primarily of plants such as wheat, vegetables and pulses, with a modicum of meat and almost no fish.

The herders' diet on the other hand was high in animal protein and augmented with fish. They also ate large quantities of millet, which has a distinctive carbon isotope ratio that can be identified in human bones. Millet is a hardy plant that was hugely popular with nomadic populations of central Asia because it grows in a few short weeks.

Roman sources of the time were dismissive of this lifestyle. Ammianus Marcellinus, a Roman official, wrote of the Hun that they "care nothing for using the ploughshare, but they live upon flesh and an abundance of milk."

"While Roman authors considered them incomprehensibly uncivilised and barely human, it seems many of citizens at the edge of Rome's empire were drawn to the Hun lifestyle, just as some nomads took to a more settled way of life," says Hakenbeck.

Read more at Science Daily

Mar 21, 2017

When helium behaves like a black hole

Scientists have discovered that a sphere of cold helium atoms (in green) -- interacting with a surrounding larger container of the same kind of atoms (in blue) -- follows a bizarre rule of physics, called an entanglement area law, also observed in black holes. This discovery points to a "deeper reality," says University of Vermont physicist Adrian Del Maestro and may be a step toward using superfluid helium as the fuel of a new generation of ultra-fast quantum computers.
A team of scientists has discovered that a law controlling the bizarre behavior of black holes out in space -- is also true for cold helium atoms that can be studied in laboratories.

"It's called an entanglement area law," says Adrian Del Maestro, a physicist at the University of Vermont who co-led the research. That this law appears at both the vast scale of outer space and at the tiny scale of atoms, "is weird," Del Maestro says, "and it points to a deeper understanding of reality."

The new study was published March 13 in the journal Nature Physics -- and it may be a step toward a long-sought quantum theory of gravity and new advances in quantum computing.

At the surface

In the 1970s, famed physicists Stephen Hawking and Jacob Bekenstein discovered something strange about black holes. They calculated that when matter falls into one of these bottomless holes in space, the amount of information it gobbles up -- what scientists call its entropy -- increases only as fast as its surface area increases, not its volume. This would be like measuring how many files there are in a filing cabinet based on the surface area of the drawer rather than how deep the drawer is. As with many aspects of modern physics, check your common sense at the door.

"We have found the same type of law is obeyed for quantum information in superfluid helium," says Del Maestro. To make their discovery, UVM's Del Maestro and three colleagues from the University of Waterloo in Canada first created an exact simulation of the physics of extremely cold helium after it transforms from a gas into a form of matter called a superfluid: below about two degrees Kelvin, helium atoms -- exhibiting the dual wave/particle nature that Max Planck and others discovered -- become glopped together such that the individual atoms cannot be described independent from each other. Instead, they form a cooperative dance that the scientists call quantum entangled.

Using two supercomputers, the scientists explored the interactions of sixty-four helium atoms in a superfluid. They found that the amount of entangled quantum information shared between two regions of a container -- a sphere of the helium partitioned off from the larger container -- was determined by the surface area of the sphere and not its volume. Like a holograph, it seems that a three-dimensional volume of space is entirely encoded on its two-dimensional surface. Just like a black hole.

This idea had been guessed at from a principle in physics called "locality" but had never been observed before in an experiment. By using a complete numerical simulation of all the attributes of helium, the scientists were, for the first time ever, able to demonstrate the existence of the entanglement area law in a real quantum liquid.

"Superfluid helium could become an important resource -- the fuel -- for a new generation of quantum computers," says Del Maestro, whose work is supported by the National Science Foundation. But to make use of its huge information processing potential, he says, "we have to understand more deeply how it works."

Spooky Neighborhood

In the 1920s, Albert Einstein famously -- and skeptically -- referred to entanglement as "spooky action at a distance." Since that time, entanglement has been demonstrated as real by numerous laboratory and theoretical experiments. Instead of defying the universe's maximum speed limit -- the speed of light -- what entanglement increasingly seems to show is that our human macro-scale understanding of distance, and time itself, may be illusory. A pair of entangled particles may have a quantum communication, seeming to "know" each others' state instantly across miles. But this intuition mixes up our classical view of reality with a deeper quantum reality in which a form of information -- entanglement entropy -- is "delocalized," spread out in a system, with millions of possible states, or "superpositions," that only become fixed by the action of measuring. (Consider Schrödinger's cat -- both dead and alive.)

"Entanglement is non-classical information shared between parts of a quantum state," notes Del Maestro. It's "the characteristic trait of quantum mechanics that is most foreign to our classical reality."

Being able to understand, let alone control, quantum entanglement in complex systems with many particles has proven difficult. The observation of an entanglement area law in this new experiment points toward quantum liquids, like superfluid helium, as a possible medium for starting to master entanglement. For example, the new study reveals that the density of the superfluid helium regulates the amount of entanglement. That suggests that laboratory experiments and, eventually, quantum computers could manipulate the density of a quantum liquid as a "possible knob," Del Maestro says, for regulating entanglement.

Read more at Science Daily

Dead zones may threaten coral reefs worldwide

Low oxygen conditions were most severe below a certain depth, evident in this photo of dying sponges.
Dead zones affect dozens of coral reefs around the world and threaten hundreds more according to a new study by Smithsonian scientists published in Proceedings of the National Academy of Sciences. Watching a massive coral reef die-off on the Caribbean coast of Panama, they suspected it was caused by a dead zone -- a low-oxygen area that snuffs out marine life -- rather than by ocean warming or acidification.

"Ocean warming and acidification are recognized global threats to reefs and require large-scale solutions, whereas the newly recognized threats to coral reefs caused by dead zones are more localized, said Andrew Altieri, staff scientist at the Smithsonian Tropical Research Institute and first author of the study. Fortunately dead zones can be reduced by controlling sewage and agricultural runoff into the ocean."

In September, 2010, coral reefs in Almirante Bay, Bocas del Toro Province, showed severe signs of stress. In addition to corals turning white and dying, which is typical during coral bleaching associated with warming events, there were other clues suggesting that more was involved than high temperatures. Many unusual observations pointed to something else as the culprit. There were thick mats of bacterial slime, and the dead bodies of crabs, sea urchins and sponges lay scattered on the ocean floor. Even more odd, there was a clear depth line above which the reefs looked OK, and below which, something had gone terribly wrong. Even single colonies of corals that straddled the line were fine above and dying below.

Scientists went to work, measuring several aspects of water quality. One set of measurements came back as a shock. Extremely low oxygen levels in deeper waters contrasted with high oxygen levels in shallow waters where corals were still healthy. This is the hallmark of a dead zone.

The team thinks that such dead zones may be common in the tropics but have gone largely unreported, simply because scientists never looked. "The number of dead zones currently on our map of the world is 10 times higher in temperate areas than it is in the tropics, but many marine biologists work out of universities in Europe and North America and are more likely to find dead zones close to home," Altieri said.

"We were lucky that there was already a reef monitoring program in place at STRI's Bocas del Toro Research Station as part of the Smithsonian's Marine Global Earth Observatory Network," said Rachel Collin, station director.

"Based on our analyses, we think dead zones may be underreported by an order of magnitude." said Nancy Knowlton, coauthor and Sant Chair for Marine Science at the Smithsonian's National Museum of Natural History. "For every one dead zone in the tropics, there are probably 10 -- nine of which have yet to be identified."

The researchers found 20 instances when dead zones were implicated in the mass mortality of coral reefs worldwide. "Hypoxia (low oxygen) isn't even mentioned in several of the most important academic reviews of threats to coral reefs and is rarely discussed at scientific meetings," Altieri said, "Even worse, many coral-reef monitoring efforts do not include measurement of oxygen levels, making it nearly impossible to identify low oxygen as the cause of mass coral mortality after the fact." For example, the cause of a 2016 mass mortality at the Flower Garden Reefs in the Gulf of Mexico remains unclear, but some of the photographs look strikingly similar to what was observed in Panama.

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Amazon River no younger than 9 million years, new study shows

Amazon river mouth.
Researchers from the University of Amsterdam (UvA) and the University of Brasilia (Brazil) have determined the age of the formation of the Amazon River at 9.4 to 9 million years ago (Ma) with data that convincingly refutes substantial younger estimates. Their results are published as early view in the journal Global and Planetary Change.

The study comprised geochemical and palynological analyses of sediments from a hydrocarbon exploration borehole, situated offshore of Brazil, that reached more than 4.5 kilometers below sea level.

The results show a distinct change in sediment composition and plant residual matter during the late Miocene (9.4 to 9 Ma). This represents a switch in river source area from the tropical lowlands to the high Andes, which is diagnostic of the onset of the transcontinental Amazon River. The new data contradict younger estimates (c. 2.6 Ma) that have been proposed in recent literature and postdates estimates from an earlier study of this borehole by about 1 to 1.5 million years.

Sediments record evolutionary history

'We were able to narrow down the age of onset of the Amazon River because we sampled the transition interval in a classical section of the Amazon submarine fan, where the sediments transported by this river are deposited and as a result accurately record its evolutionary history. We applied high resolution analytical techniques not previously performed in the region', says professor Farid Chemale, senior author from the University of Brasilia (now at Universidade do Vale do Rio dos Sinos, São Leopoldo).

The study also gives novel insights into overall changes in plant composition in the Amazon drainage basin. Particularly, the rise in grass remains suggests that mountain uplift and Quaternary climatic changes strongly affected the landscape and probably opened up new habitats for grass colonization.

Dramatic changes

'The changes detected in the sediment record lead to the tantalizing question of whether the Amazon region might have changed dramatically during Plio-Pleistocene global cooling', says Dr Carina Hoorn, lead author and researcher at the UvA's Institute for Biodiversity and Ecosystem Dynamics. 'Our new data confirm an old age for the Amazon River and also point at an expansion of grasslands during the Pleistocene that was not known before. Further research on land and at sea may give further answers but will require investment in both continental and marine drilling.'

Largest drainage basin of all rivers

The Amazon River contributes a fifth of the total fresh water supply to the global oceans and has the largest drainage basin of all rivers around the world. The onset of the river is a defining moment in the reorganization of the paleogeography of South America, forming both a bridge and a divider for biota in the Amazon landscape.

The history of the Amazon River and its drainage basin are hard to unravel, as the continental record is scarce and fragmented. The marine record is more complete, yet is equally difficult to access. Sediment aprons in the proximity of major rivers often hold continuous records of terrestrial material accumulated by the river over time. These records provide a unique insight into the historic climate, geography and biome evolution of the land.

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Last remnant of North American ice sheet on track to vanish

CU Boulder Professor Gifford Miller, shown here, is part of a team that has found the Barnes Ice Cap on Baffin Island, the last remnant of the Laurentide Ice Sheet, will vanish in several hundred years because of rising temperatures caused by human activity.
The last piece of the ice sheet that once blanketed much of North America is doomed to disappear in the next several centuries, says a new study by researchers at Simon Fraser University in British Columbia and the University of Colorado Boulder.

The Barnes Ice Cap, a Delaware-sized feature on Baffin Island in the Canadian Arctic, is melting at a rapid pace, driven by increased greenhouse gases in the atmosphere that have elevated Arctic temperatures. The ice cap, while still 500 meters thick, is slated to melt in about 300 years under business-as-usual greenhouse gas emissions.

The results provide compelling evidence that the current level of warming is almost unheard of in the past 2.5 million years, according to the authors. Only three times at most in that time period has the Barnes Ice Cap been so small, a study of isotopes created by cosmic rays that were trapped in rocks around the Barnes Ice Cap indicated.

"This is the disappearance of a feature from the last glacial age, which would have probably survived without anthropogenic greenhouse gas emissions," said Adrien Gilbert, a glaciologist at Simon Fraser University in British Columbia in Canada and lead author of the new study published online today in Geophysical Research Letters, a journal of the American Geophysical Union.

While the melting of the Barnes Ice Cap will likely have negligible effects on sea level rise, its end could herald the eventual dissolution of the larger ice sheets like Greenland and Antarctica, said CU-Boulder Professor Gifford Miller, a study co-author.

"I think the disappearance of the Barnes Ice Cap would be just a scientific curiosity if it were not so unusual," said Miller, the associate director of CU Boulder's Institute of Arctic and Alpine Research who has conducted research on Baffin Island annually for the past five decades. "One implication derived from our results is that significant parts of the southern Greenland Ice Sheet also may be at risk of melting as the Arctic continues to warm."

Elevated sea rise created by a melting Greenland would automatically cause the Antarctic Ice Sheet, whose dimensions are controlled by sea level, to also shrink in size, Miller said.

The Barnes Ice Cap is part of the Laurentide Ice Sheet that has covered millions of square miles of North America episodically since the start of Quaternary Period roughly 2.5 million years ago. The ice sheet grew and shrank over time as Earth went through various climate cycles, and the ice was a mile thick at present-day Chicago about 20,000 years ago. It started receding substantially around 14,000 years ago when Earth slipped out of its last ice age.

The ice cap stabilized about 2,000 years ago until the effects of the recent warming caught up with it. Miller was conducting research on Baffin Island in 2009 when he realized the ice cap had shrunk noticeably as compared to images from a few decades earlier. He recruited Gilbert and Gwenn Flowers from Simon Fraser to develop a model of how the ice cap might behave in the future.

In the new study, the researchers used their model to estimate when the ice cap would disappear under different greenhouse gas emissions scenarios. They project that under all future emission scenarios the ice cap will be gone within 200 to 500 years. For a moderate emissions scenario that assumes Earth's greenhouse gas emissions will peak around the year 2040, they project the ice cap to be gone in 300 years.

"The geological data is pretty clear that the Barnes Ice Cap almost never disappears in the interglacial times," Miller said. "The fact that it's disappearing now says we're really outside of what we've experienced in 2.5 million-year interval. We are entering a new climate state."

The Barnes Ice Cap is like a canary in a coal mine, said Miller, who also is a professor in CU Boulder's Department of Geological Sciences. Even if humans stopped emitting greenhouse gases today, the ice cap would still disappear in the next few centuries.

In 2010, the project received a boost from Waleed Abdalati, current director of the Cooperative Institute for Research in Environmental Sciences (a joint venture of CUBoulder and NOAA), who was NASA's chief scientist at the time. Abdalati supported the flight of a NASA plane monitoring ice loss in the Arctic to revisit the Barnes Ice Cap.

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