Friday, November 30, 2018

Fur Trade May Have Spread the Plague through Europe Repeatedly

A new ancient DNA study shows that 14th century plague outbreaks might have resulted from repeated introductions of Yersinia pestis to Europe. Commercial trade routes, including the fur trade routes, would have contributed to the rapid spread of plague in whole Europe during the Middle Ages.

The bacteriumYersinia pestisis the causative agent of bubonic and pulmonary plague in humans. Plague is primarily a disease of wildlife and is maintained in reservoirs, which nowadays are present on all continents with the exception of Australia and Western Europe.

The fur trade from the East towards Western Europa followed two major routes during the Middle Ages. 
Illustration: Amine Namouchi

Without doubt, the Black Death, which marks the arrival of Y. pestisinto Europe in 1347, represents one of the most significant events that marked the beginning of the second plague pandemic during the medieval period. In fact, from 1347 to 1353, plague spread through whole Europe like wildfire, leading to the decline of the European population by 30 %. After this dramatic period and for more than 350 years, Europe knew a series of recurrent devastating outbreaks ofY. pestis.

Understanding the plague
During the last decades, different studies tried to understand the origin of these outbreaks. Two hypotheses emerged from these studies. According to the first hypothesis, after a first introduction during the Black Death, one or more reservoirs ofY. pestiswere established in Western Europe – which explains these recurrent outbreaks.

“The other hypothesis suggest that the plague was repeatedly introduced to Western Europe from a reservoir located in Eastern Europe/Central Asia and spread via commercial trade routes and human movement”, explains Professor Nils Chr. Stenseth. He was the leader of the Centre for Ecological and Evolutionary Synthesis (CEES) at the University of Oslo for more than 10 years, and is now a strategic advisor at the UiO’s Faculty of Mathematics and Natural Sciences.

In a new paper from the CEES, published in PNAS, these two scenarios are investigated using five newly presented ancient genomes (aDNA) of Y. pestis isolated from skeletons distributed in archaeological sites from South (Abbadia San Salvatore, Italy and Saint-Laurent-de-la-Cabrerisse, France) to North Europe (Bergen-op-Zoom in the Netherlands and Oslo, Norway). The ancient genomes from Abbadia San Salvatore and Oslo are the first ancient DNA sequences reported from Italy and Norway.

The Second Pandemic
Contrary to previous studies, the authors built an integrative approach aiming at interpreting all ancient genomes of the Second plague Pandemic with regards to their historical context. A total number of 126 Y. pestis strains and fifteen ancient genomes were analysed in this study. Five out of the eleven ancient DNA samples dated to the Second Plague Pandemic were part of the first wave of introduction of Y. pestis into Europe during the Black Death.

These ancient DNA samples were isolated from the cities of Abbadia San Salvatore (Italy), Saint-Laurent-de-la-Cabrairisse (France), Barcelona (Spain), London (United Kingdom) and Oslo (Norway). Intriguingly, all these ancient genomes were identical except the one isolated from Abbadia San Salvatore, for which the authors found two extra point mutations.

Historical data investigation of contacts and bed testaments conducted by the authors revealed the high percentage of people killed by plague within four months from late June to early September 1348 in Abbadia San Salvatore. CEES researcher Amine Namouchi and colleagues advance in their paper that these two additional point mutations were acquired through a large transmission chain in Italy, rather than having been gained within a newly established local wildlife reservoir. Regarding the aDNA found in Oslo, the authors found that it is most likely dated to 1348. This is in line with historical, archeological and radiocarbon dating data described in their paper.

A new hypothesis
While the origin of the Black Death remains unclear, in their PNAS paper, the authors advance a new hypothesis that relates the onset of the Black Death with the arrival of a considerable variety of fur in the ports of the Black Sea by 1340 from trade routes starting from Sarai.

In fact, during the same period a new mainland route connecting Sarai, Tana and Caffa had been established with the support of theGolden Horde, observes Amine Namouchi and colleagues. The Golden Horde was originally a Mongol and later Turkicized khanate established in the 13th century and originating as the northwestern sector of the Mongol Empire. The Crimean Khanate and the Kazakh Khanate, the last remnants of the Golden Horde, survived until 1783 and 1847 respectively.
Just after the Black Death period, the authors confirm the so-calledpestis secundathat occured from 1357 to 1366.

“The group of aDNA that belongs to thepestis secundaincludes samples from London, Bolgar-City (Russia) and the newly presented two aDNA from Bergen-op-Zoom. Four point mutations separate the group of aDNA of the Black Death from the group that belongs to thepestis secunda. Corroborated with historical data, we claim that thepestis secundamight also be the result of the introduction ofY. pestisalong the fur trade routes established between Novgorod (Russia) and Western Europe through the Hanseatic League”, adds Namouchi.

Multiple waves of introduction
Overall, in this new paper published in PNAS, by describing all previously and newly described aDNA ofY. pestisin their historical context, Namouchi and colleagues provided additional evidence that the recurrent plague outbreaks during the Second plague Pandemic were the result of multiple waves of introduction of Y. pestis from a reservoir located in Eastern Europe/Central Asia.
This result is in line with previous studies based on Ecological evidence. Commercial trade routes, including the fur trade route, as-well-as human movement would have contributed to the rapid spread of plague in whole Europe during the Middle Ages.

The investigation behind the new scientific paper was done in the context of the research projectMedPlag, led by the paleogenetist and CEES researcher Barbara Bramanti. In 2013, she received an Advanced Grant from the European Research Council (ERC). The grant is being used to investigate, using DNA technology, the plague and other potential human diseases caused by medieval microbes.
https://titan.uio.no/node/3133

Full bibliographic information

Amine Namouchi, Meriam Guellil, Oliver Kersten, Stephanie Hänsch, Claudio Ottoni, Boris V. Schmid, Elsa Pacciani, Luisa Quaglia, Marco Vermunt, Egil L. Bauer, Michael Derrick, Anne Ø. Jensen, Sacha Kacki, Samuel K. Cohn Jr., Nils C. Stenseth and Barbara Bramanti: Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. PNAS, November 26, 2018.
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Black Hole 'Donuts' Are Actually 'Fountains'

Based on computer simulations and new observations from the Atacama Large Millimeter/submillimeter Array (ALMA), researchers have found that the rings of gas surrounding active supermassive black holes are not simple donut shapes. Instead, gas expelled from the center interacts with infalling gas to create a dynamic circulation pattern, similar to a water fountain in a city park.

ALMA image of the gas around the supermassive black hole in the center of the Circinus Galaxy. The distributions of CO molecular gas and C atomic gas are shown in orange and cyan, respectively.


Credit: ALMA (ESO/NAOJ/NRAO), Izumi et al.

Most galaxies host a supermassive black hole, millions or billions of times as heavy as the Sun, in their centers. Some of these black holes swallow material quite actively. But astronomers have believed that rather than falling directly into the black hole, matter instead builds up around the active black hole forming a donut structure.

Takuma Izumi, a researcher at the National Astronomical Observatory of Japan (NAOJ), led a team of astronomers that used ALMA to observe the supermassive black hole in the Circinus Galaxy located 14 million light-years away from the Earth in the direction of the constellation Circinus. The team then compared their observations to a computer simulation of gas falling towards a black hole made with the Cray XC30 ATERUI supercomputer operated by NAOJ. This comparison revealed that the presumptive “donut” is not actually a rigid structure, but instead a complex collection of highly dynamic gaseous components. First, cold molecular gas falling towards the black hole forms a disk near the plane of rotation. 

As it approaches the black hole, this gas is heated until the molecules break down into the component atoms and ions. Some of these atoms are then expelled above and below the disk, rather than being absorbed by the black hole. This hot atomic gas falls back onto the disk creating a turbulent three dimensional structure. These three components circulate continuously, similar to a water fountain in a city park.

Artist’s impression of the gas motion around the supermassive black hole in the center of the Circinus Galaxy. The three gaseous components form the long-theorized “donut” structure: (1) a disk of infalling dense cold molecular gas, (2) outflowing hot atomic gas, and (3) gas returning to the disk.

Credit: NAOJ

“Previous theoretical models set a priori assumptions of rigid donuts,” explains Keiichi Wada, a theoretician at Kagoshima University in Japan, who lead the simulation study and is a member of the research team. “Rather than starting from assumptions, our simulation started from the physical equations and showed for the first time that the gas circulation naturally forms a donut. Our simulation can also explain various observational features of the system.”

Cross section of the gas around a supermassive black hole simulated with NAOJ’s supercomputer ATERUI. The different colors represent the density of the gas, and the arrows show the motion of the gas. It clearly shows the three gaseous components forming the “donut” structure.

Credit: Wada et al.

“By investigating the motion and distribution of both the cold molecular gas and warm atomic gas with ALMA, we demonstrated the origin of the so-called ‘donut’ structure around active black holes,” said Izumi. “Based on this discovery, we need to rewrite the astronomy textbooks.”

Paper and the research team
These observation results were published as T. Izumi et al. “Circumnuclear Multiphase Gas in the Circinus Galaxy. II. The Molecular and Atomic Obscuring Structures Revealed with ALMA” in the Astrophysical Journal in October 2018.

The research team members are:
Izumi Takuma (National Astronomical Observatory of Japan), Keiichi Wada (Kagoshima University / Ehime University / Hokkaido University), Ryosuke Fukushige (Kagoshima University), Sota Hamamura (Kagoshima University), and Kotaro Kohno (The University of Tokyo)

This research was supported by JSPS KAKENHI (Grant Numbers 17K14247, 16H03959, JP17H06130).




Contacts and sources:
National Astronomical Observatory of Japan


Citation:  “Circumnuclear Multiphase Gas in the Circinus Galaxy. II. The Molecular and Atomic Obscuring Structures Revealed with ALMA”
T. Izumi et al.、2018, Astrophysical Journal 867, 48. https://doi.org/10.3847/1538-4357/aae20b
https://alma-telescope.jp/en/news/press/agn-201811





Brilliant Iron Molecule Can Make Solar Energy Cheaper


For the first time, researchers have succeeded in creating an iron molecule that can function both as a photocatalyst to produce fuel and in solar cells to produce electricity. The results indicate that the iron molecule could replace the more expensive and rarer metals used today.

Some photocatalysts and solar cells are based on a technology that involves molecules containing metals, known as metal complexes. The task of the metal complexes in this context is to absorb solar rays and utilise their energy. The metals in these molecules pose a major problem, however, as they are rare and expensive metals, such as the noble metals ruthenium, osmium and iridium.

“Our results now show that by using advanced molecule design, it is possible to replace the rare metals with iron, which is common in the Earth’s crust and therefore cheap”, says Chemistry Professor Kenneth Wärnmark of Lund University in Sweden.


The new iron molecule 
Illustration: Nils Rosemann


Together with colleagues, Kenneth Wärnmark has for a long time worked to find alternatives to the expensive metals. The researchers focused on iron which, with its six per cent prevalence in the Earth’s crust, is significantly easier to source. The researchers have produced their own iron-based molecules whose potential for use in solar energy applications has been proven in previous studies.

In this new study, the researchers have moved one step further and developed a new iron-based molecule with the ability to capture and utilise the energy of solar light for a sufficiently long time for it to react with another molecule. The new iron molecule also has the ability to glow long enough to enable researchers to see iron-based light with the naked eye at room temperature for the first time.

“The good result depends on the fact that we have optimised the molecular structure around the iron atom”, explains colleague Petter Persson of Lund University.

The study is now published in the journal Science. According to the researchers, the iron molecule in question could be used in new types of photocatalysts for the production of solar fuel, either as hydrogen through water splitting or as methanol from carbon dioxide. Furthermore, the new findings open up other potential areas of application for iron molecules, e.g. as materials in light diodes (LEDs).

What surprised the Lund researchers is that they arrived at good results so quickly. In just over five years, they succeeded in making iron interesting for photochemical applications, with properties largely as good as those of the best noble metals.

“We believed it would take at least ten years”, says Kenneth Wärnmark.

Besides the researchers from Lund University, colleagues from Uppsala University and the University of Copenhagen were also involved in the collaboration.


 


Contacts and sources:
Lund University

Citation:Luminescence and reactivity of a charge-transfer excited iron complex with nanosecond lifetime 
Kasper Skov Kjær1,*, Nidhi Kaul2,*, Om Prakash3,*, Pavel Chábera1, Nils W. Rosemann1, Alireza Honarfar1, Olga Gordivska3, Lisa A. Fredin4,†, Karl-Erik Bergquist3, Lennart Häggström5, Tore Ericsson5, Linnea Lindh1, Arkady Yartsev1, Stenbjörn Styring2, Ping Huang2, Jens Uhlig1, Jesper Bendix6, Daniel Strand3, Villy Sundström1,‡, Petter Persson4,‡, Reiner Lomoth2,‡, Kenneth Wärnmark3,‡ Science 29 Nov 2018: eaau7160 
DOI: 10.1126/science.aau7160

Move Over Man, Women Sleep Better with Dogs

According to recent research conducted by Canisius College Animal Behaviorist Christy Hoffman, PhD, women report that canine companions are better bed partners than human or feline companions. The new research shows that canine companions are less disruptive and offer comfort and security 

Hoffman, associate professor of Animal Behavior, Ecology and Conservation at Canisius, explored the impacts pets have on human sleep quality. Data collected from nearly 1,000 women across the United States showed:

"Best friends" make the best bed partners

Credit: Edralis / Wikimedia Commons

- Sleep patterns of dogs more closely coincide with sleep patterns in humans than do cats’ sleep patterns, which may explain why dog moms stick to a stricter sleep schedule.

- Dogs who slept in their owners' beds were perceived to be less disruptive for sleep than human partners and cats

- Dogs as bed partners scored higher on comfort and security than human and feline bed partners

Cats and humans may be sharing space on the couch

When it comes to sharing a bed with humans and felines, the results were far less soothing:

- Cats who slept in their owners' beds were reported to be equally disruptive for sleep as human partners

- Cats were associated with weaker feelings of comfort and security than both human and canine bed partners

Contacts and sources:
Canisius College





These Wasps Are Creating Zombies



It sounds like the plot of the world's tiniest horror movie: deep in the Ecuadorian Amazon, a newly discovered species of wasp transforms a "social" spider into a zombie-like drone that abandons its colony to do the wasp's bidding.

That's the gruesome, real-life discovery by University of British Columbia researchers, who detail the first example of a manipulative relationship between a new Zatypota species wasp and a social Anelosimus eximius spider in a study published recently in Ecological Entomology.

"Wasps manipulating the behaviour of spiders has been observed before, but not at a level as complex as this," said Philippe Fernandez-Fournier, lead author of the study and former master's student at UBC's department of zoology. "Not only is this wasp targeting a social species of spider but it's making it leave its colony, which it rarely does."

This is the adult stage of the parasitoid Zatypota species wasp

Credit: Philippe Fernandez-Fournier

Fernandez-Fournier was in Ecuador studying different kinds of parasites that live in the nests of Anelosimus eximius spiders, one of only about 25 species of "social" spiders worldwide. They are notable for living together in large colonies, cooperating on prey capture, sharing parental duties and rarely straying from their basket-shaped nests.

When Fernandez-Fournier noticed that some of the spiders were infected with a parasitic larva and spotted them wandering a foot or two away from their colonies to spin enclosed webs of densely spun silk and bits of foliage, he was puzzled. "It was very odd because they don't normally do that, so I started taking notes," he said.

Intrigued, he carefully took a few of the structures, known as "cocoon webs" back to the laboratory to see what would emerge from the depths.

To his surprise, it was a wasp.

"These wasps are very elegant looking and graceful," said Samantha Straus, co-author of the study and PhD student in UBC's department of zoology. "But then they do the most brutal thing."

Using data gathered in Ecuador for different projects between 2012 and 2017, the researchers began to piece together the life cycle of the wasp and its parasitic relationship to the spider.

What they found was equal parts fascinating and horrifying: after an adult female wasp lays an egg on the abdomen of a spider, the larva hatches and attaches itself to its hapless arachnid host. It then presumably feeds on the spider's blood-like haemolymph, growing larger and slowly taking over its body. The now "zombified" spider exits the colony and spins a cocoon for the larva before patiently waiting to be killed and consumed. After feasting on the spider, the larva enters its protected cocoon, emerging fully formed nine to eleven days later.

In other similar instances of parasitism, wasps are known to target solitary species of spiders like orb weavers and manipulate them into behaviours that are within their normal repertoire.

"But this behaviour modification is so hardcore," said Straus. "The wasp completely hijacks the spider's behaviour and brain and makes it do something it would never do, like leave its nest and spinning a completely different structure. That's very dangerous for these tiny spiders."

It's not known how the wasps do this, but scientists believe it may be caused by an injection of hormones that make the spider think it's in a different life-stage or cause it to disperse from the colony.

"We think the wasps are targeting these social spiders because it provides a large, stable host colony and food source," said Straus. "We also found that the larger the spider colony, the more likely it was that these wasps would target it."

Straus, who now sports a tattoo of the wasp, will return to Ecuador to investigate whether the wasps return to the same spider colonies generation after generation and what evolutionary advantage that might present.

Meanwhile, the wasps will likely continue their starring role in the spiders' worst nightmares.





Contacts and sources:
University of British Columbia


Citation:Behavioural modification of a social spider by a parasitoid wasp
Philippe Fernandez‐FournierSamantha StrausRuth SharpeLeticia Avilés
First published: 04 November 2018 Natural History https://doi.org/10.1111/een.12698
Associate Editor: Dirk Mikolajewski


New Device Widens Light Beams by 400 Times, Broadening Science and Technology Possibilities

By using light waves instead of electric current to transmit data, photonic chips—circuits for light—have advanced fundamental research in many areas from timekeeping to telecommunications. But for many applications, the narrow beams of light that traverse these circuits must be substantially widened in order to connect with larger, off-chip systems. Wider light beams could boost the speed and sensitivity of medical imaging and diagnostic procedures, security systems that detect trace amounts of toxic or volatile chemicals and devices that depend on the analysis of large groupings of atoms.

Scientists at the National Institute of Standards and Technology (NIST) have now developed a highly efficient converter that enlarges the diameter of a light beam by 400 times. NIST physicist Vladimir Aksyuk and his colleagues, including researchers from the University of Maryland NanoCenter in College Park, Maryland, and Texas Tech University in Lubbock, described their work in the journal Light: Science and Applications.





This mode expansion device is made of a linear waveguide, a slab waveguide, and a grating. Light enters the device through the linear waveguide. When the waveguide makes contact with the slab, the light expands laterally. The grating then converts the expanded light into waves through free-space. The process can also happen in reverse, bringing free-space light into the waveguide. This enables researchers to connect two mode expansion devices together. For instance, they can use two devices to prove an unknown gas. Credit: Sean Kelley/NIST

The converter widens the cross section, or area of the beam, in two consecutive stages. Initially, the light travels along an optical waveguide —a thin, transparent channel whose optical properties limit the diameter of the beam to a few hundred nanometers, less than one-thousandth the average diameter of a human hair. Because the waveguide channel is so narrow, some of the traveling light extends outward beyond the edges of the waveguide. Taking advantage of this broadening, the team placed a rectangular slab composed of the same material as the waveguide a tiny, precisely measured distance from the waveguide. The light can jump across the tiny gap between the two components and gradually leak into the slab.

The slab maintains the narrow width of the light in the vertical (top-to- bottom) dimension, but it provides no such constraints for the lateral, or sideways, dimension. As the gap between the waveguide and the slab is gradually changed, the light in the slab forms a precisely directed beam 400 times wider than the approximately 300 nm diameter of the original beam.



In the second stage of the expansion, which enlarges the vertical dimension of the light, the beam traveling through the slab encounters a diffraction grating. This optical device has periodic rulings or lines, each of which scatters light. The team designed the depth and spacing of the rulings to vary so that the light waves combine, forming a single wide beam directed at nearly a right angle to the chip’s surface.

Importantly, the light remains collimated, or precisely parallel, throughout the two-stage expansion process, so that it stays on target and does not spread out. The area of the collimated beam is now large enough to travel the long distance needed to probe the optical properties of large diffuse groupings of atoms.

Working with a team led by John Kitching of NIST in Boulder, Colorado, the researchers have already used the two-stage converter to successfully analyze the properties of some 100 million gaseous rubidium atoms as they jumped from one energy level to another. That’s an important proof-of-concept because devices based on interactions between light and atomic gasses can measure quantities such as time, length and magnetic fields and have applications in navigation, communications and medicine.

“Atoms move very quickly, and if the beam monitoring them is too small, they move in and out of the beam so fast that it becomes difficult to measure them,” said Kitching. “With large laser beams, the atoms stay in the beam for longer and allow for more precise measurement of the atomic properties,” he added. Such measurements could lead to improved wavelength and time standards.

Paper: S. Kim, D.A. Westly, B.J. Roxworthy, Q. Li, A. Yulaev, K. Srinivasan and V.A. Aksyuk. Photonic waveguide to free-space Gaussian beam extreme mode converter. Light: Science & Applications. DOI: 10.1038/s41377-018-0073-2


Contacts and sources:
Ben P. Stein
National Institute of Standards and Technology (NIST)

Citation: Photonic waveguide to free-space Gaussian beam extreme mode converter Published: October 10, 2018 Author(s) Sangsik Kim, Daron A. Westly, Brian J. Roxworthy, Qing Li, Alexander Yulaev, Kartik A. Srinivasan, Vladimir A. Aksyuk
 : Light: Science & Applications Volume: 7 Issue: 1 Pub 
Download Paper https://doi.org/10.1038/s41377-018-0073-2
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Why the Future of Water Purification May Involve Chinese Ink

A substance developed thousands of years ago could help accelerate solutions to the world's freshwater crisis.

Long used for calligraphy, Chinese ink possesses almost all of the qualities needed to help generate steam using sunlight — a critical strategy for purifying water in a resource-constrained world.

This shows a) Chinese ink and writing brush, similar to those used for writing and drawing for over 2000 years, b) digital and infrared images of the Chinese character “water” written in Chinese ink under simulated sunlight and c) a scheme of the fabrication process for ALD/Chinese‐ink‐coated materials.


Credit: Argonne National Laboratory

From California to Dubai, dry climates, development and growing populations are driving demand for new sources of clean water. Alternative desalination strategies that address energy-intensity and cost would have a large-scale impact.

At the U.S. Department of Energy’s (DOE) Argonne National Laboratory, researchers are exploring affordable photothermal materials that could absorb the sunlight necessary to evaporate water and recapture that water, leaving salt and contaminants behind. Instead of trying to heat a whole vat of water, for example, this solar steam approach aims to concentrate heat only at the surface, where evaporation occurs, by covering it with a light-absorbing material.

"Chinese ink is a very effective material at absorbing that broad range of light, which makes it fantastic for this application of solar steam generation." — Seth Darling, director of Argonne’s Institute for Molecular Engineering and Advanced Materials for Energy-Water Systems (AMEWS) Center

Wood, sponges, fabric and membranes are all good candidates for this purpose, because they can float and are porous enough to let the water seep up and evaporate. But those materials need help heating up under the sun.

"We're looking for dark liquids that we can coat onto porous materials for this application," said Seth Darling, director of Argonne’s Institute for Molecular Engineering and Advanced Materials for Energy-Water Systems (AMEWS) Center.

Ink, of course, quickly came to mind. Darling and a team of researchers including Hao-Cheng Yang, a postdoctoral researcher at Argonne's Center for Nanoscale Materials (CNM), a DOE Office of Science User Facility, experimented with regular pen ink, but found it didn't coat uniformly across the varied surfaces.

Yang thought back to his upbringing in China, where every child took a class in conventional calligraphy. He decided to explore the traditional ink from his childhood as a coating.

Unlike the ink in modern pens, Chinese ink is designed to have staying power on surfaces of all kinds, from fabric to pottery. Made with soot, glue and a preservative, the ancient ink turned out to have the perfect combination of qualities for solar steam generation. The results of the ink experiments — titled “Chinese Ink: A Powerful Photothermal Material for Solar Steam Generation” — were published recently in Advanced Materials Interfaces.

In addition to its ability to uniformly coat porous materials, Chinese ink's viscosity keeps it from penetrating too far down into the substrate. This helps focus the heating right at the surface, where it's needed. But the carbon-based paint's biggest asset may be its propensity to absorb light across the visible spectrum and into the infrared range, where most of the sun's energy lies.

"This is a very effective material at absorbing that broad range of light," Darling said, "which makes it fantastic for this application of solar steam generation."

One hitch: Chinese ink is water-soluble, so it wouldn't last long on its own in a steamy setting.

The researchers used atomic layer deposition, a technique for depositing thin films, to apply a transparent coating of titanium dioxide over the ink, sealing it in place. Tested under simulated sunlight on various substrates, including wood and sponges, the combination proved to be a stable, potent steam generator. The coating integrates materials with broad light absorption, strong coating capability, water-attracting properties and extreme durability — a challenging set of characteristics to assemble into one system.

This shows scanning electron microscopy images of nascent materials and Chinese‐ink‐coated materials before and after atomic layer deposition. It also shows energy dispersive spectroscopy mapping of the cross‐section of a Chinese‐ink‐coated membrane (e).

Credit: Argonne National Laboratory


Researchers at the Institute for Molecular Engineering and Argonne’s recently awarded AMEWS Center continue to explore materials and technologies that purify and conserve water.

"Time will tell if Chinese ink — or some other fluid with similar properties — will see practical use out in the field," Darling said. But its low cost, versatility and abundance make Chinese ink an indelible addition to the choices.

The Center for Nanoscale Materials is one of the five DOE Nanoscale Science Research Centers, premier national user facilities for interdisciplinary research at the nanoscale supported by the DOE Office of Science. Together the NSRCs comprise a suite of complementary facilities that provide researchers with state-of-the-art capabilities to fabricate, process, characterize and model nanoscale materials, and constitute the largest infrastructure investment of the National Nanotechnology Initiative. The NSRCs are located at DOE’s Argonne, Brookhaven, Lawrence Berkeley, Oak Ridge, Sandia and Los Alamos National Laboratories. For more information about the DOE NSRCs, please visit https://science.energy.gov/bes/suf/user-facilities/nanoscale-science-research-centers/

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science.

The U.S. Department of Energy’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit the Office of Science website.


Contacts and sources:
Tona Kunz
 Argonne National Laboratory




Thursday, November 29, 2018

Whales Lost Their Teeth Before Evolving Hair-like Baleen in Their Mouths

Baleen is the soft, hair-like structure on the upper mouth of whales, such as the humpback whale in this photo, which allows them to trap prey in their mouth.
Baleen Whale
Credit: Ari S. Friedlaender/University of California, Santa Cruz under NOAA permit

Rivaling the evolution of feathers in dinosaurs, one of the most extraordinary transformations in the history of life was the evolution of baleen—rows of flexible hair-like plates that blue whales, humpbacks and other marine mammals use to filter relatively tiny prey from gulps of ocean water. The unusual structure enables the world’s largest creatures to consume several tons of food each day, without ever chewing or biting. Now, Smithsonian scientists have discovered an important intermediary link in the evolution of this innovative feeding strategy: an ancient whale that had neither teeth nor baleen.

In the Nov. 29 issue of the journal Current Biology, scientists at the Smithsonian’s National Museum of Natural History and colleagues describe for the first time Maiabalaena nesbittae, a whale that lived about 33 million years ago. Using new methods to analyze long-ago discovered fossils housed in the Smithsonian’s national collection, the team, which includes scientists at George Mason University, Texas A&M University and the Burke Museum of Natural History and Culture in Seattle, has determined that this toothless, 15-foot whale likely had no baleen, showing a surprising intermediary step between the baleen whales that live today and their toothed ancestors.

An artistic reconstruction of a mother and calf of Maiabalaena nesbittae nursing offshore of Oregon during the Oligocene, about 33 million years ago.
Mother and calf whale
Credit: Alex Boersma

“When we talk about whale evolution, textbooks tend to focus on the early stages, when whales went from land to sea,” said Nicholas Pyenson, the National Museum of Natural History’s curator of fossil marine mammals. “Maiabalaena shows that the second phase of whale evolution is just as important for evolution over big scales. For the first time, we can now pin down the origin of filter-feeding, which is one of the major innovations in whale history.”

When whales first evolved, they used teeth to chew their food, just like their land-dwelling ancestors. As time went on, many descendants of these early whales continued to chew their food, inheriting this trait from their predecessors. But as the oceans around them changed and animals evolved, entirely new feeding strategies arose, including baleen filter feeding, says National Museum of Natural History predoctoral fellow Carlos Mauricio Peredo, the lead author of the study who analyzed the Maiabalaena fossils.

Whales were the first mammals to evolve baleen, and no other mammal uses any anatomical structure even remotely similar to it to consume its prey. But frustratingly, baleen, whose chemical composition is more like that of hair or fingernails than bone, does not preserve well. It is rarely found in the fossil record, leaving paleontologists without direct evidence of its past or origins. Instead, scientists have had to rely on inferences from fossils and studies of fetal-whale development in the womb to piece together clues about how baleen evolved.

As a result, it has not been clear whether, as they evolved, early baleen whales retained the teeth of their ancestors until a filter-feeding system had been established. An early initial assumption, Peredo said, was that ocean-dwelling mammals must have needed teeth or baleen to eat—but several living whales contradict that idea. Sperm whales have teeth in their bottom jaw, but none on the top, so they cannot bite or chew. Narwhals’ only teeth are their long tusks, which they do not use for feeding. And some species of beaked whales, despite being classified as toothed whales, have no teeth at all.

Because of its age, Peredo said, paleontologists suspected Maiabalaena might hold important clues about baleen’s evolution. The fossil comes from a period of massive geological change during the second major phase of whale evolution, around the time the Eocene epoch was transitioning to the Oligocene. With continents shifting and separating, ocean currents were swirling around Antarctica for the first time, cooling the waters significantly. The fossil record indicates that whales’ feeding styles diverged rapidly during this timeframe, with one group leading to today’s filter-feeding whales and the other leading to echolocating ones.

Consequently, Maiabalaena had received plenty of scrutiny since its discovery in Oregon in the 1970s, but the rock matrix and material that the fossil was collected in still obscured many of its features. It was not until Peredo finally cleaned the fossil and then examined it with state-of-the-art CT scanning technology that its most striking features became clear. Maiabalaena’s lack of teeth was readily apparent from the preserved bone, but the CT scans, which revealed the fossil’s internal anatomy, told the scientists something new: Maiabalaena’s upper jaw was thin and narrow, making it an inadequate surface from which to suspend baleen.

“A living baleen whale has a big, broad roof in its mouth, and it’s also thickened to create attachment sites for the baleen,” Peredo said. “Maiabalaena does not. We can pretty conclusively tell you this fossil species didn’t have teeth, and it is more likely than not that it didn’t have baleen either.”

While Maiabalaena would not have been able to chew or to filter feed, muscle attachments on the bones of its throat indicate it likely had strong cheeks and a retractable tongue. These traits would have enabled it to suck water into its mouth, taking up fish and small squid in the process. The ability to suction feed would have rendered teeth, whose development requires a lot of energy to grow, unnecessary. The loss of teeth, then, appears to have set the evolutionary stage for the baleen, which the scientists estimate arose about 5 to 7 million years later.

Peredo and Pyenson see studying whale evolution as key to understanding their survival in today’s rapidly changing oceans. Like the emergence of baleen, tooth loss in whales is evidence of adaptability, suggesting that whales might be able to adapt to challenges posed in the ocean today. Still, Peredo cautions, evolutionary change may be slow for the largest whales, which have long life spans and take a long time to reproduce.

“Given the scale and rate of changes in the ocean today, we don’t exactly know what that will mean for all of the different species of filter-feeding whales,” he said. “We know that they’ve changed in the past. It’s just a matter of whether they can keep up with whatever the oceans are doing—and we’re changing the oceans pretty quickly right now.”


Contacts and sources:
 Smithsonian

Citation: Tooth Loss Precedes the Origin of Baleen in Whales
Carlos Mauricio Peredo, Nicholas D. Pyenson, Christopher D. Marshall, Mark D. Uhen. . Current Biology, 2018; DOI: 10.1016/j.cub.2018.10.047


Revolutionary Insulator-Like Material Also Conducts Electricity



University of Wisconsin–Madison researchers have made a material that can transition from an electricity-transmitting metal to a nonconducting insulating material without changing its atomic structure.

“This is quite an exciting discovery,” says Chang-Beom Eom, professor of materials science and engineering. “We’ve found a new method of electronic switching.”

The new material could lay the groundwork for ultrafast electronic devices. Eom and his international team of collaborators published details of their advance today (Nov. 30, 2018) in the journal Science.

Metals like copper or silver conduct electricity, whereas insulators like rubber or glass do not allow current to flow. Some materials, however, can transition from insulating to conducting.

Chang-Beom Eom, right, and Mark Rzchowski inspect a materials growth chamber. The researchers have made a new material that can be switched from electrical conductor to insulator.

Credit: UW–Madison photo by Sam Million-Weaver

This transition usually means that the arrangement of a material’s atoms and its conducting electrons must change in a coordinated way, but the atomic transition typically proceeds much more slowly than the smaller, lighter electrons that conduct electricity.

A material that can switch to conducting electricity like a metal without moving its atoms could dramatically advance switching speeds of advanced devices, says Eom.

“The metal-to-insulator transition is very important for switches and for logic devices with a one or a zero state,” he says. “We have the potential to use this concept to make very fast switches.”

In their research, Eom and his collaborators answered a fundamental question that has bothered scientists for years: Can the electronic and structural transition be decoupled — essentially, can the quickly changing electrons break out on their own and leave the atoms behind?

They used a material called vanadium dioxide, which is a metal when it’s heated and an insulator when it’s at room temperature. At high temperatures, the atoms that make up vanadium dioxide are arranged in a regularly repeating pattern that scientists refer to as the rutile phase. When vanadium dioxide cools down to become an insulator, its atoms adopt a different pattern, called monoclinic.

No naturally occurring substances conduct electricity when their atoms are in the monoclinic conformation. And it takes time for the atoms to rearrange when a material reaches the insulator-to-metal transition temperature.

Crucially, vanadium dioxide transitions between a metal and an insulator at different temperatures depending upon the amount of oxygen present in the material. The researchers leveraged that fact to create two thin layers of vanadium dioxide — one with a slightly lower transition temperature than the other — sandwiched on top of each other, with a sharp interface between.

When they heated the thin vanadium dioxide sandwich, one layer made the structural switch to become a metal. Atoms in the other layer remained locked into the insulating monoclinic phase. Surprisingly, however, that part of the material conducted electricity.

Most importantly, the material remained stable and retained its unique characteristics.

Although other research groups have attempted to create electrically conductive insulators, those materials lost their properties almost instantly — persisting for mere femtoseconds, or a few thousandths of one trillionth of a second.

The Eom team's material, however, is here to stay.

“We were able to stabilize it, making it useful for real devices,” says Eom.

Key to their approach was the dual-layer, sandwich structure. Each layer was so thin that the interface between the two materials dominated how the entire stack behaved. It’s a notion that Eom and colleagues plan to pursue further.

“Designing interfaces could open up new materials,” says Eom.

The Wisconsin Alumni Research Foundation is assisting the researchers with patent filing.

This research was supported by grants from the National Science Foundation (DMR-1629270, DMR-1420620 and DMR-1420645), Air Force Office of Scientific Research (FA9550-15-1-0334), Office of Naval Research (N00014-13-1-0183) and Department of Energy (DE-FG02-06ER46327, DE-AC02-06CH11357 and FG02-07ER46417).



Contacts and sources:
Sam Million-Weaver
University of Wisconsin–Madison




First Ancient DNA Analyzed from Mainland Finland Reveals Origin of Siberian Ancestry in Saami and Finnish Populations


A new study shows that the genetic makeup of northern Europe traces back to migrations from Siberia that began at least 3,500 years ago and that, as recently as the Iron Age, ancestors of the Saami lived in a larger area of Finland than today.

Researchers from the Max Planck Institute for the Science of Human History and the University of Helsinki have analyzed the first ancient DNA from mainland Finland. As described in Nature Communications, ancient DNA was extracted from bones and teeth from a 3,500 year–old burial on the Kola Peninsula, Russia, and a 1,500 year-old water burial in Finland. The results reveal the possible path along which ancient people from Siberia spread to Finland and Northwestern Russia.

Artistic impression of an ancient fisherman from Bolshoy Oleni Ostrov.

Illustration: Kerttu Majander

Researchers found the earliest evidence of Siberian ancestry in Fennoscandia in a population inhabiting the Kola Peninsula, in Northwestern Russia, dating to around 4,000 years ago. This genetic ancestry then later spread to populations living in Finland. The study also found that people genetically similar to present-day Saami people inhabited areas in much more southern parts of Finland than the Saami today.

For the present study, genome-wide genetic data from 11 individuals were retrieved. Eight individuals came from the Kola Peninsula, six from a burial dated to 3,500 years ago, and two from an 18th to 19th century Saami cemetery. “We were surprised to find that the oldest samples studied here had the highest proportion of Siberian ancestry,” says Stephan Schiffels, co-senior author of the study, of the Max Planck Institute for the Science of Human History.

The other three individuals analyzed for the study came from a water burial in Levänluhta, Finland. Levänluhta is one of the oldest known burials in Finland in which human bones have been preserved. The bodies were buried in what used to be a small lake or a pond, and this seems to have contributed to exceptionally good preservation of the remains.
  
Location of archaeological sites with material used in this study

Image: Michelle O’Reilly; Lamnidis, Majander et al. 2018. Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe. Nature Communications, DOI: 10.1038/s41467-018-07483-5.

Siberian ancestry persists today

The study compared the ancient individuals not only to each other, but also to modern populations, including Saami, Finnish and other Uralic language speakers. Among modern European populations, the Saami have the largest proportion of this ancient Siberian ancestry. Worldwide, the Nganasan people, from north Siberia, have the largest proportion of ancient Siberian ancestry.

“Our results show that there was a strong genetic connection between ancient Finnish and ancient Siberian populations,” says Thiseas Lamnidis, co-first author of the study, “suggesting that ancient populations from Siberia may have also shared a subsistence strategy, languages and/or cultural behaviours with Bronze Age and Iron Age Finns, despite the large geographical distance.” Ancient Finnish populations possibly lived a mobile, nomadic life, trading and moving over a large range, with far-reaching contacts to other populations.

People found in Levänluhta, Finland, most resemble modern-day Saami

The researchers found that the population in Levänluhta was more closely related to modern-day Saami people than to the non-Saami Finnish population today.

Artistic impression of the Levänluhta water burial site.

Illustration: Kerttu Majander

“People closely related to the Saami inhabited much more southern regions of Finland than the Saami do today,” explains Kerttu Majander, co-first author, of the University of Helsinki and the Max Planck Institute for the Science of Human History. Interestingly, a recent linguistic study suggested that the place names around Levänluhta trace back to Saami languages.

“This is the first exploration of ancient DNA from Finland and the results are very interesting,” states Schiffels. “However more ancient DNA studies from the area will be necessary to better understand whether the patterns we’ve seen are representative of Finland as a whole.”

The study was conducted as a collaboration between the SUGRIGE-project (Universities of Helsinki and Turku), and the Max Planck Institute for the Science of Human History. The archaeological materials and expertise were provided by the Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) and the Levänluhta-project with the Finnish Heritage Agency.


Contacts and sources:
Anne Gibson
Max Planck Institute For The Science Of Human History


Citation: Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in EuropeThiseas C. Lamnidis, Kerttu Majander, Choongwon Jeong, Elina Salmela, Anna Wessman, Vyacheslav Moiseyev, Valery Khartanovich, Oleg Balanovsky, Matthias Ongyerth, Antje Weihmann, Antti Sajantila, Janet Kelso, Svante Pääbo, Päivi Onkamo, Wolfgang Haak, Johannes Krause, Stephan Schiffels. Nature Communications



Stone Tools Linked To Ancient Human Ancestors Found In Arabia With A Surprisingly Recent Date

Stone handaxes, similar to those made by early humans as much as 1.5 million years ago, have been dated for the first time in the Arabian Peninsula, to less than 190,000 years old, where their production may have endured until the arrival of Homo sapiens.

Beginning more than 1.5 million years ago, early humans made stone handaxes in a style known as the Acheulean – the longest lasting tool-making tradition in prehistory. New research led by the Max Planck Institute for the Science of Human History and the Saudi Commission for Tourism and National Heritage has documented an Acheulean presence in the Arabian Peninsula dating to less than 190,000 years ago, revealing that the Arabian Acheulean ended just before or at the same time as the earliest Homo sapiens dispersals into the region.

Archaeologists excavating the site of Saffaqah, Saudi Arabia.

Credit: Paleodeserts

Much attention has been given to understanding the spread of our own species, Homo sapiens, first within Africa and then beyond. However, less attention has been given to where diverse groups of close evolutionary cousins lived in Eurasia immediately prior to the arrival of Homo sapiens. Understanding this is critical because the spatial and temporal characteristics of such groups reveal the human and cultural landscape first encountered by our species on leaving Africa.


The youngest Acheulean site in Southwest Asia

In a paper published in Scientific Reports, an international team of researchers led by the Max Planck Institute for the Science of Human History and the Saudi Commission for Tourism and National Heritage reports the first ever dates obtained from an Acheulean site in Arabia, the site of Saffaqah, situated in Central Saudi Arabia. Saffaqah is the first stratified Acheulean site to be reported in the Arabian Peninsula and the dates reveal that early humans occupied the site until at least 190,000 years ago. These dates are surprisingly recent for a region known to feature among the oldest examples of such technology outside Africa. For example, dates from the Levant document an ancient Acheulean presence from 1.5 million years ago. Conversely the site of Saffaqah features the youngest Acheulean tools yet found in southwest Asia.

Handaxes from the site of Saffaqah, Saudi Arabia.
Credit: Palaeodeserts (Ian R. Cartwright)

Over 500 stone tools, including handaxes and other artefacts known as cleavers, were recovered from the occupation levels. Some of the stone flakes used to make handaxes were in such fresh condition that they were recovered still resting on the stone nodules from which they had been detached. These and other artefacts show that the early humans responsible for making them were manufacturing stone tools at this site.

“It is not surprising that early humans came here to make stone tools,” says Dr. Eleanor Scerri of the Max Planck Institute for the Science of Human History, the lead author of the study. “The site is located on a prominent andesite dyke that rises above the surrounding plain. The spot was both a source of raw material as well as a prime location to survey a landscape that, back then, sat between two major river systems.” This choice location also seems to have continued to be attractive to early humans at an even later date than those recorded by the researchers in this study. Layers containing identical stone handaxes are also found above the dense occupation layers that were dated, raising the possibility that Saffaqah is among the youngest Acheulean sites documented anywhere.

Hominins living at the edge

The new dating results both record the late persistence of the Acheulean in the Peninsula and also show that as yet unidentified hominin populations were using networks of now extinct rivers to disperse into the heart of Arabia during a time of increased rainfall in the region. This suggests that these hominins were able to live on the margins of habitable zones and take advantage of relatively brief “greening” episodes in a generally arid area. The dispersal of these hominins into the heart of Arabia may also help to explain the surprisingly late persistence of the Acheulean, as it suggests a degree of isolation.
 e
Researcher Eleanor Scerri with giant Acheulean core from which flakes were struck to create the handaxes.

Credit: Paleodeserts

“These hominins were resourceful and intelligent,” adds Dr. Scerri, “They dispersed across a challenging landscape using technology commonly seen as reflecting a lack of inventiveness and creativity. Instead of perceiving the Acheulean this way, we should really be struck by how flexible, versatile and successful this technology was.”

Cutting edge science

To date the sediments from the site of Saffaqah, the researchers used a combination of dating techniques known as luminescence methods, including a newly developed infrared-radiofluorescence (IR-RF) dating protocol for potassium rich feldspars. The method relies on the ability of such minerals to store energy induced by natural radioactivity and to release this energy in the form of light. “The application of IR-RF dating allowed us to obtain age estimates from sediments that were previously difficult to reliably date,” explains Marine Frouin of the University of Oxford, one of the researchers involved in the dating program.

These discoveries and methods are already leading to new research. “One of the biggest questions we have is whether any of our evolutionary ancestors and close cousins met up with Homo sapiens, and if this could have happened somewhere in Saudi Arabia. Future field work will be dedicated to understanding possible cultural and biological exchanges at this critical time period,” says Professor Michael Petraglia of the Max Planck Institute for the Science of Human History, the director of the project which led to the discoveries at Saffaqah.

The international consortium of researchers involved in this project is headed by the Max Planck Institute for the Science of Human History, in partnership with HRH Prince Sultan bin Salman and the Saudi Commission for Tourism and National Heritage. Additional partners include King Saud University and other key institutions in the United Kingdom and Australia.





Contacts and sources:
Anne Gibson, Dr. Eleanor Scerri
Max Planck Institute For The Science Of Human History

Citation: The expansion of Late Acheulean hominins into the Arabian Peninsula
Eleanor M.L. Scerri, Ceri Shipton, Laine Clark-Balzan, Marine Frouin, Jean-Luc Schwenninger, Huw S. Groucutt, Paul S. Breeze, Ash Parton, James Blinkhorn, Nick A. Drake, Richard Jennings, Patrick Cuthbertson, Abdulaziz Al Omari, Abdullah M. Alsharekh, Michael D. Petraglia
Scientific Reports, DOI: 10.1038/s41598-018-35242-5


The Potentially Deadly Bacterium That’s on Your Skin

Forget MRSA and E.coli, there’s another bacterium that is becoming increasingly dangerous due to antibiotic resistance – and it’s present on the skin of every person on the planet.

A close relative of MRSA, Staphylococcus epidermidis, is a major cause of life-threatening infections after surgery, but it is often overlooked by clinicians and scientists because it is so abundant.

Researchers from the Milner Centre for Evolution at the University of Bath warn that the threat posed by this organism should be taken more seriously and use extra precautions for those at higher risk of infection who are due to undergo surgery.

Professor Sam Sheppard led the research team at the Milner Centre for Evolution
Professor Sam Sheppard looking at a petri dish containing S. epidermidis
Credit: University of Bath

They have identified a set of 61 genes that allow this normally harmless skin bacterium to cause life-threatening illness.

They hope that by understanding why some strains of S. epidermidis cause disease in certain circumstances, they could in the future identify which patients are most at risk of infection before undergoing surgery.

They took samples from patients who suffered infections following hip or knee joint replacement and fracture fixation operations and compared them with swab samples from the skin of healthy volunteers.

They compared the genetic variation in the whole genomes of bacteria found in samples from diseased and healthy individuals. From this they identified 61 genes in the disease-causing bacteria that weren’t present in most of the healthy samples.

Surprisingly however, there was a small number of healthy individuals who were found to be carrying the more deadly form of the bacteria without knowing it.

The disease-causing genes were found to help the bacterium grow in the bloodstream, avoid the host’s immune response, make the cell surface sticky so that the organisms can form biofilms and make the bug resistant to antibiotics.

The team published their study in Nature Communications this week.

Professor Sam Sheppard, Director of Bioinformatics at the Milner Centre for Evolution at the University of Bath, led the research. He said: “Staphlococcus epidermidis is a deadly pathogen in plain sight.

“It’s always been ignored clinically because it’s frequently been assumed that it was a contaminant in lab samples or it was simply accepted as a known risk of surgery.

“Post-surgical infections can be incredibly serious and can be fatal. Infection accounts for almost a third of deaths in the UK so I believe we should be doing more to reduce the risk if we possibly can.

“If we can identify who is most at risk of infection, we can target those patients with extra hygiene precautions before they undergo surgery.”

He added: “Because the bug is so abundant, they can evolve very fast by swapping genes with each other.



“If we do nothing to control this, there’s a risk that these disease-causing genes could spread more widely, meaning post-operative infections that are resistant to antibiotics could become even more common.”

Professor Dietrich Mack, from the Bioscientia Institute for Medical Diagnostics GmbH, Germany, said: “Prosthetic joint replacement surgery helps many patients to live independent and painfree lives, but can take a catastrophic course through S. epidermidis infection.

“These infections are difficult to diagnose and there is hope that disease-associated genes may help to separate harmless skin isolates from disease-causing S. epidermidisstrains in the clinical laboratory. This needs to be addressed in future studies.”


Contacts and sources:
Vicky Just
University of Bath

Citation: Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.
Guillaume Méric, Leonardos Mageiros, Johan Pensar, Maisem Laabei, Koji Yahara, Ben Pascoe, Nattinee Kittiwan, Phacharaporn Tadee, Virginia Post, Sarah Lamble, Rory Bowden, James E. Bray, Mario Morgenstern, Keith A. Jolley, Martin C. J. Maiden, Edward J. Feil, Xavier Didelot, Maria Miragaia, Herminia de Lencastre, T. Fintan Moriarty, Holger Rohde, Ruth Massey, Dietrich Mack, Jukka Corander, Samuel K. Sheppard. Nature Communications, 2018; 9 (1) DOI: 10.1038/s41467-018-07368-7



Stop—Hey, What’s That Sound? How Noise Becomes Words Going Through the Brain

You’re walking along a busy city street. All around you are the sounds of subway trains, traffic, and music coming from storefronts. Suddenly, you realize one of the sounds you’re hearing is someone speaking, and that you are listening in a different way as you pay attention to what they are saying.

How does the brain do this? And how quickly does it happen? Researchers at the University of Maryland are learning more about the automatic process the brain goes through when it picks up on spoken language.

A) Illustration of the main properties of speech processing that were used to model brain responses: detection of word onsets (green), prediction of the next phoneme based on the preceding phoneme sequence (purple) and competition of different word representations for recognition (cyan). B) Timing of brain responses associated with these stages, displayed as amplitude of the neural response over time relative to the events that are processed. C) Average brain location of the responses shown in B. D) The effect of listening to two speakers talking at the same time: the earlier acoustic stages process the sounds from both speakers, whereas the later, lexical stages track only the attended speech. 

Credit: University of Maryland

Neuroscientists have understood for some time that when we hear sounds of understandable language our brains react differently than they do when we hear non-speech sounds or people talking in languages we do not know. When we hear someone talking in a familiar language, our brain quickly shifts to pay attention, process the speech sounds by turning them into words, and understand what is being said.

In a new paper published in the Cell Press/Elsevier journal Current Biology, “Rapid transformation from auditory to linguistic representations of continuous speech,” Maryland researchers were able to see where in the brain, and how quickly—in milliseconds—the brain’s neurons transition from processing the sound of speech to processing the language-based words of the speech.

The paper was written by Institute for Systems Research (ISR) Postdoctoral Researcher Christian Brodbeck, L. Elliot Hong of the University of Maryland School of Medicine, and Professor Jonathan Z. Simon, who has a triple appointment in the Departments of Biology and Electrical and Computer Engineering as well as ISR.

“When we listen to someone talking, the change in our brain’s processing from not caring what kind of sound it is to recognizing it as a word happens surprisingly early,” said Simon. “In fact, this happens pretty much as soon as the linguistic information becomes available.”

When it is engaging in speech perception, the brain’s auditory cortex analyzes complex acoustic patterns to detect words that carry a linguistic message. It seems to do this so efficiently, at least in part, by anticipating what it is likely to hear: by learning what sounds signal language most frequently, the brain can predict what may come next. It is generally thought that this process—localized bilaterally in the brain’s superior temporal lobes—involves recognizing an intermediate, phonetic level of sound.

When we listen to someone talking, the change in our brain’s processing from not caring what kind of sound it is to recognizing it as a word happens surprisingly early. In fact, this happens pretty much as soon as the linguistic information becomes available.

Jonathan Simon

In the Maryland study, the researchers mapped and analyzed participants’ neural brain activity while listening to a single talker telling a story. They used magnetoencephalography (MEG), a common non-invasive neuroimaging method that employs very sensitive magnetometers to record the naturally occurring magnetic fields produced by electrical currents inside the brain. The subject typically sits under or lies down inside the MEG scanner, which resembles a whole-head hair drier, but contains an array of magnetic sensors.

The study showed that the brain quickly recognizes the phonetic sounds that make up syllables and transitions from processing merely acoustic to linguistic information in a highly specialized and automated way. The brain has to keep up with people speaking at a rate of about three words a second. It achieves this, in part, by distinguishing speech from other kinds of sound in about a tenth of a second after the sound enters the ears.

“We usually think that what the brain processes this early must be only at the level of sound, without regard for language,” Simon notes. “But if the brain can take knowledge of language into account right away, it would actually process sound more accurately. In our study we see that the brain takes advantage of language processing at the very earliest stage it can.”

In another part of the study, the researchers found that people selectively process speech sounds in noisy environments.

Here, participants heard a mixture of two speakers in a “cocktail party” scenario, and were told to listen to one and ignore the other. The participants’ brains only consistently processed language for the conversation to which they were told to pay attention, not the one they were told to ignore. Their brains stopped processing unattended speech at the level of detecting word forms.

“This may reveal a ‘bottleneck’ in our brains’ speech perception,” Brodbeck says. “We think that during speech perception, our brain considers the match between the incoming speech signal and many different words at the same time. Put a different way, the words compete for being recognized. It could be that this mechanism involves mental resources that can only process one speech signal at a time, making it impossible to attend simultaneously to more than one speaker.”

This study lays the foundation for additional research into how our brains interpret sounds as words. For example, how and when does the brain decide which word is being said? There is evidence that the brain actually sifts through possibilities, but it is currently unknown how the brain successfully narrows down the choices to a single word and connects it with the meaning of the ongoing discourse. Also, since it is possible to measure what fraction of the speech sounds are clear enough to be processed as being components of words, the researchers may be able to test listening comprehension when subjects can’t, or don’t understand how to, report it properly.

Citation
Rapid transformation from auditory to linguistic representations of continuous speech,” by Christian Brodbeck, L. Elliot Hong and Jonathan Z. Simon. Current Biology. https://doi.org/10.1016/j.cub.2018.10.042


Contacts and sources:
University of Maryland

Citation: Rapid Transformation from Auditory to Linguistic Representations of Continuous Speech.
Christian Brodbeck, L. Elliot Hong, Jonathan Z. Simon. Current Biology, 2018; DOI: 10.1016/j.cub.2018.10.042



Oldest-Known Ancestor of Modern Primates May Have Come from North America, Not Asia

About 56 million years ago, on an Earth so warm that palm trees graced the Arctic Circle, a mouse-sized primate known as Teilhardina first curled its fingers around a branch.

The earliest-known ancestor of modern primates, Teilhardina’s close relatives would eventually give rise to today’s monkeys, apes and humans. But one of the persistent mysteries about this distant cousin of ours is where it originated.

Teilhardina (ty-hahr-DEE’-nuh) species quickly spread across the forests of Asia, Europe and North America, a range unparalleled by all other primates except humans. But where did its journey begin?
Photo credit: Florida Museum of Natural History

New research shows that Teilhardina brandti, a species found in Wyoming, is as old or older than its Asian and European relatives, upending the prevailing hypothesis that Teilhardina first appeared in China.

Teilhardina’s origins, however, remain a riddle.

“The scientific conclusion is ‘We just don’t know,’” said Paul Morse, the study’s lead author and a recent University of Florida doctoral graduate. “While the fossils we’ve found potentially overturn past hypotheses of where Teilhardina came from and where it migrated, they definitely don’t offer a clearer scenario.”


Credit:   Florida Museum of Natural History


What is clear, Morse said, is that T. brandti had a wide variety of features, some of which are as primitive as those found in Teilhardina asiatica, its Asian cousin, previously thought to be the oldest species in the genus.

To make this determination, Morse studied 163 teeth and jaws in the most comprehensive analysis of T. brandti to date.

Teeth contain a treasure-trove of information and often preserve better than bone, thanks to their tough enamel. They can reveal clues about an animal’s evolutionary past, its size, diet and age as an individual and in geological time.

Primate teeth have particularly distinct structures that are immediately recognizable to the trained eye, said Jonathan Bloch, study co-author and curator of vertebrate paleontology at the Florida Museum of Natural History.

“Identifying differences between primate teeth is not so different from a biker recognizing that a Harley is different from a scooter or an art critic evaluating whether an image was created by Picasso or Banksy,” he said. “In detail, they are very different from each other in specific, predictable ways.”

While Teilhardina bones are very rare in the fossil record, its teeth are more plentiful – if you know how to find them. Bloch’s team of paleontologists, Morse included, have spent years combing the surface of Wyoming’s Bighorn Basin on hands and knees and then packing out 50-pound bags of soil to a river to screen wash. The remaining bits of bones and teeth – which can be smaller than a flea – are examined under a microscope back at the museum.

This painstaking search has built up the dental record of T. brandti from a single molar – used to first describe the species in 1993 – to hundreds of teeth, providing a broad look at the primate’s population-level variation.






Photos credit: Florida Museum of Natural History


Still, Morse and Bloch were unprepared for the peculiar variation exhibited by specimen UF 333700, a jagged piece of jaw with T. brandti teeth.

“Jon and I started arguing about the alveoli” – empty tooth sockets – “and how they didn’t look right at all,” said Morse, now a postdoctoral researcher at Duke University. “By the end of the day, we realized that specimen completely overturned both the species definition of T. asiatica and part of the rationale for why it is the oldest Teilhardina species.”

Studies based on a small number of teeth simply missed the diversity in Teilhardina’s physical characteristics, Morse said.

“There’s likely a tremendous amount of variation in the fossil record, but it’s extremely difficult to capture and measure when you have a small sample size,” he said. “That’s one of the reasons collecting additional fossils is so important.”

The analysis also reshuffled the Teilhardina family tree, reducing the number of described species from nine to six and reclassifying two species as members of a new genus, Bownomomys, named for prominent vertebrate paleontologist Thomas Bown.



Photos credit: Florida Museum of Natural History

But the precise ages of Teilhardina species are still impossible to pinpoint and may remain that way.

Teilhardina appeared during the geological equivalent of a flash in the pan, a brief 200,000-year period known as the Paleocene-Eocene Thermal Maximum, or PETM. This era was characterized by a massive injection of carbon into the Earth’s atmosphere, which sent global temperatures soaring. Sea levels surged by 220 feet, ecosystems were overhauled and the waters at the North Pole warmed to 74 degrees.

Scientists can use the distinct carbon signature of the PETM to locate this period in the rock record, and carbon isotopes in teeth can also be used to identify fossil animals from the era.

But among Teilhardina fossil sites across the globe, only Wyoming has the uninterrupted, neatly demarcated layers of rock that allow paleontologists to hone in on more precise dates.

“The humblest statement would be to say that these species are essentially equivalent in age,” Bloch said. “Determining which came earlier in the PETM probably surpasses the level of resolution we have in the rock record. But what we can say is that the only place where you can really establish where Teilhardina appears in this climate event with confidence is in the Bighorn Basin.”

“Wyoming is the richest place on Earth for finding mammal fossils from the PETM, but they’re still rare,” Bloch said. Many fossils are so small that they’re stored in empty pill capsules.

Florida Museum photo by Natalie van Hoose

As the Earth warmed, plants and animals expanded their ranges northward, returning south as temperatures cooled at the end of the PETM.

“This dance of plants and animals with climate change happened over vast landscapes, with forests moving from the Gulf Coast to the Rocky Mountains in just a few thousand years,” Bloch said.

Teilhardina likely tracked the shifts in its forest habitats across the land bridges that then connected North America, Greenland and Eurasia, he said.

“Teilhardina is not throwing its bag over its shoulder and walking,” he said. “Its range is shifting from one generation to the next. Over 1,000 years, you get a lot of movement, and over 2,000-3,000 years, you could easily cover continental distances.”

While it was well-suited to Earth’s hothouse environment, Teilhardina disappeared with the PETM, replaced by new and physically distinct primates. It’s a sobering reminder of what can happen to species – including humans – during periods of swift climatic changes, Bloch said.

“A changing planet has dramatic effects on biology, ecosystems and evolution. It’s part of the process that has produced the diversity of life we see today and mass extinctions of life that have happened periodically in Earth’s history,” Bloch said. “One of the unexpected results of global warming 56 million years ago is that it marks the origin of the group that ultimately led to us. How we will fare under future warming scenarios is less certain.”

The findings were published in the Journal of Human Evolution.

Other co-authors are Stephen Chester of Brooklyn College, City University of New York, Doug Boyer of Duke University, Thierry Smith and Richard Smith of the Royal Belgian Institute of Natural Sciences and Paul Gigase.

The National Science Foundation provided funding for the research. Additional support for the project came from a Professional Staff Congress-City University of New York Award and the Belgian Federal Science Policy Office.

3D models of the fossils are available on Morphosource, an open-access repository of data directed by Boyer.



Contacts and sources:
Natalie van Hoose, Paul Morse, Jonathan Bloch Florida Museum of Natural History


Citation: New fossils, systematics, and biogeography of the oldest known crown primate Teilhardina from the earliest Eocene of Asia, Europe, and North America
Paul E.Morse, Stephen G.B.Chester, Doug M.Boy, Thierry Smith, Richard Smith, Paul Gigaseh, Jonathan I .Bloch  Journal of Human Evolution Available online 27 November 2018
http://dx.doi.org/10.1016/j.jhevol.2018.08.005


The 'Chinese Pyramids' and the Pole Star


The funerary complex of the first Chinese emperor of the Qin dynasty (3th century BC) is one of the most famous archaeological sites in the world. This is of course due to the discovery of the statues of the terracotta army, intended to accompany the emperor in the afterlife. Much less known than the statues is the fact that tomb proper (still not excavated) lies beneath a gigantic, artificial hill of rammed earth. This hill has a square shape, a base side of more than 350 meters and is over 40 meters high, so that it can easily be called a pyramid.

Even less known is the fact that also all the emperors of the subsequent dynasty, the Western Han, chose to be buried under similar pyramids. These mausoleums are visible still today within the rapidly developing landscape of the northwestern surroundings of Xian along the Wei River. Including also the tombs of the queens and other members of royal families, there are over 40 of such "Chinese pyramids". Of these, only two have been (partly) excavated.

This is the huge mole of the Maoling Mausoleum of Emperor Wu of Han.

Credit: Giulio Magli

The new study is part of an extensive program of research on the role of astronomy and of the traditional doctrine of "feng shui" in the Chinese imperial necropolises and has just been published in the academic journal Archaeological Research in Asia. In the work simple techniques based on satellite images are used, together with field surveys, to collect a large number of new data and, in particular, to study the orientation of the pyramid bases. It is in fact well known that, for example, the Egyptian pyramids are oriented with great precision to the cardinal points, by virtue of the very strong bonds of the funerary religion of the Egyptian pharaohs with the sky and in particular with the circumpolar stars.

Although - of course - there is no connection with the Egyptian pyramids, also the Chinese emperors credited their power as a direct mandate of the heaven, identifying the circumpolar region as a celestial image of the imperial palace and its inhabitants. It was therefore natural to expect the Chinese pyramids, tombs of the emperors, to be oriented to the cardinal points. In this connection, the results of the new study are in part surprising.

These are the Terracotta Warriors protecting the Qin Mausoleum's east front.

Credit: Giulio Magli

It turns out that these monuments can be classified according to two "families". One such families comprises monuments oriented with good precision to the cardinal points, as expected. In the other family there are significant deviations from the true north, all of comparable and all on the same "hand "(to the west of the north looking towards the monument).

It is out of the question that this second family may have been due to errors of the Chinese astronomers and architects. One could think of the use of the compass, which was invented in China in a somewhat rudimentary form at that time, but there is no correspondence with the paleomagnetic data. The explanation proposed in the article is thus astronomical: the emperors who built the pyramids of the "family 2" did not want to point to the north celestial pole, which at the time did not correspond to any star, but to the star to which the pole would be approached in the future: Polaris.

All this discourse may look strange at first sight, but it must be remembered that there is a phenomenon, the precession of the earth's axis, which slowly but constantly moves the position in the sky in which the earth's axis points, and therefore the celestial pole. The Chinese astronomers were almost certainly aware of this. Nowadays we are used to identify the north celestial pole with Polaris (although in reality the correspondence is not perfect) but at the time of the Han emperors the pole was still far from Polaris, and with a distance in degrees approximately equal to the deviation of the Chines pyramids from the geographic north.



Contacts and sources:
Giulio Magli
Politecnico Di Milano



Citation: Royal mausoleums of the western Han and of the Song Chinese dynasties: A satellite imagery analysis. Giulio Magli. Archaeological Research in Asia Volume 15, September 2018, Pages 45-54 http://dx.doi.org/10.1016/j.ara.2017.10.003



All of The Starlight Ever Produced by The Observable Universe Measured

From their laboratories on a rocky planet dwarfed by the vastness of space, Clemson University scientists have managed to measure all of the starlight ever produced throughout the history of the observable universe.

Astrophysicists believe that our universe, which is about 13.7 billion years old, began forming the first stars when it was a few hundred million years old. Since then, the universe has become a star-making tour de force. There are now about two trillion galaxies and a trillion-trillion stars. Using new methods of starlight measurement, Clemson College of Science astrophysicist Marco Ajello and his team analyzed data from NASA’s Fermi Gamma-ray Space Telescope to determine the history of star formation over most of the universe’s lifetime.

Clemson astrophysicist Marco Ajello and his team have measured all of the starlight ever emitted in the history of the observable universe.
Clemson astrophysicist Marco Ajello and his team have measured all of the starlight ever emitted in the history of the observable universe.
Image Credit: Pete Martin / College of Science

A collaborative paper titled “A gamma-ray determination of the Universe’s star-formation history” was published Nov. 30 in the journal Science and describes the results and ramifications of the team’s new measurement process.

“From data collected by the Fermi telescope, we were able to measure the entire amount of starlight ever emitted. This has never been done before,” said Ajello, who is lead author of the paper. “Most of this light is emitted by stars that live in galaxies. And, so, this has allowed us to better understand the stellar-evolution process and gain captivating insights into how the universe produced its luminous content.”

Putting a number on the amount of starlight ever produced has several variables that make it difficult to quantify in simple terms. But according to the new measurement, the number of photons (particles of visible light) that escaped into space after being emitted by stars translates to 4×10^84.

Or put another way: 4,000,000,000,000,000,000,000,000,000,000,000,000,000,000, 000,000,000,000,000,000,000,
000,000,000,000,000,000,000 photons.



Despite this stupendously large number, it is interesting to note that with the exception of the light that comes from our own sun and galaxy, the rest of the starlight that reaches Earth is exceedingly dim – equivalent to a 60-watt light bulb viewed in complete darkness from about 2.5 miles away. This is because the universe is almost incomprehensibly huge. This is also why the sky is dark at night, other than light from the moon, visible stars and the faint glow of the Milky Way.

The Fermi Gamma-ray Space Telescope was launched into low orbit on June 11, 2008, and recently marked its 10-year anniversary. It is a powerful observatory that has provided enormous amounts of data on gamma rays (the most energetic form of light) and their interaction with the extragalactic background light (EBL), which is a cosmic fog composed of all the ultraviolet, visible and infrared light emitted by stars or from dust in their vicinity. Ajello and postdoctoral fellow Vaidehi Paliya analyzed almost nine years of data pertaining to gamma-ray signals from 739 blazars.

Blazars are galaxies containing supermassive black holes that are able to release narrowly collimated jets of energetic particles that leap out of their galaxies and streak across the cosmos at nearly the speed of light. When one of these jets happens to be pointed directly at Earth, it is detectable even when originating from extremely far away. Gamma ray photons produced within the jets eventually collide with the cosmic fog, leaving an observable imprint. This enabled Ajello’s team to measure the density of the fog not just at a given place but also at a given time in the history of the universe.

“Gamma-ray photons traveling through a fog of starlight have a large probability of being absorbed,” said Ajello, an assistant professor in the department of physics and astronomy. “By measuring how many photons have been absorbed, we were able to measure how thick the fog was and also measure, as a function of time, how much light there was in the entire range of wavelengths.”


Using galaxy surveys, the star-formation history of the universe has been studied for decades. But one obstacle faced by previous research was that some galaxies were too far away, or too faint, for any present-day telescopes to detect. This forced scientists to estimate the starlight produced by these distant galaxies rather than directly record it.

Ajello’s team was able to circumvent this by using Fermi’s Large Area Telescope data to analyze the extragalactic background light. Starlight that escapes galaxies, including the most distant ones, eventually becomes part of the EBL. Therefore, accurate measurements of this cosmic fog, which have only recently become possible, eliminated the need to estimate light emissions from ultra-distant galaxies.

Paliya performed the gamma ray analysis of all 739 blazars, whose black holes are millions to billions of times more massive than our sun.

“By using blazars at different distances from us, we measured the total starlight at different time periods,” said Paliya of the department of physics and astronomy. “We measured the total starlight of each epoch – one billion years ago, two billion years ago, six billion years ago, etc. – all the way back to when stars were first formed. This allowed us to reconstruct the EBL and determine the star-formation history of the universe in a more effective manner than had been achieved before.”

When high-energy gamma rays collide with low-energy visible light, they transform into pairs of electrons and positrons. According to NASA, Fermi’s ability to detect gamma rays across a wide range of energies makes it uniquely suited for mapping the cosmic fog. These particle interactions occur over immense cosmic distances, which enabled Ajello’s group to probe deeper than ever into the universe’s star-forming productivity.

“Scientists have tried to measure the EBL for a long time. However, very bright foregrounds like the zodiacal light (which is light scattered by dust in the solar system) rendered this measurement very challenging,” said co-author Abhishek Desai, a graduate research assistant in the department of physics and astronomy. “Our technique is insensitive to any foreground and thus overcame these difficulties all at once.”

Constructed using nine years of observations by Fermi’s Large Area Telescope, this map shows how the gamma-ray sky appears at energies above 10 billion electron volts. The plane of our Milky Way galaxy runs along the middle of the plot. Brighter colors indicate brighter gamma-ray sources.


Image Credit: NASA/DOE/Fermi LAT Collaboration

Star formation, which occurs when dense regions of molecular clouds collapse and form stars, peaked around 11 billion years ago. But though the birthing of new stars has since slowed down, it has never stopped. For instance, about seven new stars are created in our Milky Way galaxy every year.

Establishing not only the present-day EBL, but revealing its evolution in cosmic history is a major breakthrough in this field, according to team member Dieter Hartmann, a professor in the department of physics and astronomy.

“Star formation is a great cosmic cycling and recycling of energy, matter and metals. It’s the motor of the universe,” Hartmann said. “Without the evolution of stars, we wouldn’t have the fundamental elements necessary for the existence of life.”

Understanding star formation also has ramifications for other areas of astronomical study, including research regarding cosmic dust, galaxy evolution and dark matter. The team’s analysis will provide future missions with a guideline to explore the earliest days of stellar evolution – such as the upcoming James Webb Space Telescope, which will be launched in 2021 and will enable scientists to hunt for the formation of primordial galaxies.

“The first billion years of our universe’s history are a very interesting epoch that has not yet been probed by current satellites,” Ajello concluded. “Our measurement allows us to peek inside it. Perhaps one day we will find a way to look all the way back to the Big Bang. This is our ultimate goal.”

Other contributing authors on the paper include Kari Helgason of the University of Iceland; Justin Finke of the Naval Research Laboratory in Washington, D.C.; and Alberto Dominguez, a former postdoctoral researcher in Ajello’s group who is now at the Complutense University of Madrid.

  Information provided by NASA’s Goddard Space Flight Center was used in this report.




Contacts and sources:
Jim Melvin / Marco Ajello
Clemson University

Citation: A gamma-ray determination of the Universe’s star formation history.
The Fermi-LAT Collaboration. Science, 2018 DOI: 10.1126/science.aat8123