пятница, 1 февраля 2019 г.

‘Mars Buggy’ Curiosity Measures a Mountain’s Gravity

NASA – Mars Science Laboratory (MSL) patch.

Feb. 1, 2019

Apollo 17 astronauts drove a moon buggy across the lunar surface in 1972, measuring gravity with a special instrument. There are no astronauts on Mars, but a group of clever researchers realized they have just the tools for similar experiments with the Martian buggy they’re operating.

Animation above: Side-by-side images depict NASA’s Curiosity rover (illustration at left) and a moon buggy driven during the Apollo 16 mission. Animation Credits: NASA/JPL-Caltech.

In a new paper in Science, the researchers detail how they repurposed sensors used to drive the Curiosity rover and turned them into gravimeters, which measure changes in gravitational pull. That enabled them to measure the subtle tug from rock layers on lower Mount Sharp, which rises 3 miles (5 kilometers) from the base of Gale Crater and which Curiosity has been climbing since 2014. The results? It turns out the density of those rock layers is much lower than expected.

Just like a smartphone, Curiosity carries accelerometers and gyroscopes. Moving your smartphone allows these sensors to determine its location and which way it’s facing. Curiosity’s sensors do the same thing but with far more precision, playing a crucial role in navigating the Martian surface on each drive. Knowing the rover’s orientation also lets engineers accurately point its instruments and multidirectional, high-gain antenna.

Image above: A selfie taken by NASA’s Curiosity Mars rover on Sol 2291 (January 15) at the “Rock Hall” drill site, located on Vera Rubin Ridge. Image Credits: NASA/JPL-Caltech/MSSS.

By happy coincidence, the rover’s accelerometers can be used like Apollo 17’s gravimeter. The accelerometers detect the gravity of the planet whenever the rover stands still. Using engineering data from the first five years of the mission, the paper’s authors measured the gravitational tug of Mars on the rover. As Curiosity ascends Mount Sharp, the mountain adds additional gravity – but not as much as scientists expected.

“The lower levels of Mount Sharp are surprisingly porous,” said lead author Kevin Lewis of Johns Hopkins University. “We know the bottom layers of the mountain were buried over time. That compacts them, making them denser. But this finding suggests they weren’t buried by as much material as we thought.”

Science from a Mars Buggy

The Apollo 17 astronauts drove their buggy across the Moon’s Taurus-Littrow Valley, periodically stopping to capture 25 measurements. Lewis has studied Martian gravity fields using data collected by NASA’s orbiters and was familiar with Apollo 17’s gravimeter.

Apollo 17 Lunar Roving Vehicle. Image Credit: NASA

The Science paper uses over 700 measurements from Curiosity’s accelerometers, taken between October 2012 and June 2017. These data were calibrated to filter out “noise,” such as the effects of temperature and the tilt of the rover during its climb. The calculations were then compared to models of Mars’ gravity fields to ensure accuracy.

The results were also compared to mineral-density estimates from Curiosity’s Chemistry and Mineralogy instrument, which characterizes the crystalline minerals in rock samples by using an X-ray beam. That data helped inform how porous the rocks are.

Mountain of Mystery

There are many mountains within craters or canyons on Mars, but few approach the scale of Mount Sharp. Scientists still aren’t sure how the mountain grew inside of Gale Crater. One idea is that the crater was once filled with sediment. How much of it was filled remains a source of debate, but the thinking is that many millions of years of wind and erosion eventually excavated the mountain.

If the crater had been filled to the brim, all that material should have pressed down, or compacted, the many layers of fine-grained sediment beneath it. But the new paper suggests Mount Sharp’s lower layers have been compacted by only a half-mile to a mile (1 to 2 kilometers) – much less than if the crater had been completely filled.

“There are still many questions about how Mount Sharp developed, but this paper adds an important piece to the puzzle,” said study co-author Ashwin Vasavada, Curiosity’s project scientist at NASA’s Jet Propulsion Laboratory in Pasadena, California. JPL manages the Mars Science Laboratory mission that Curiosity is a part of. “I’m thrilled that creative scientists and engineers are still finding innovative ways to make new scientific discoveries with the rover,” he added.

Lewis said that Mars holds plenty of mystery beyond Mount Sharp. Its landscape is like Earth’s, but sculpted more by wind and blowing sand than by water. They’re planetary siblings, at once familiar and starkly different.

“To me, Mars is the uncanny valley of Earth,” Lewis said. “It’s similar but was shaped by different processes. It feels so unnatural to our terrestrial experience.”

For more about Curiosity, visit: https://mars.nasa.gov/msl/

For more about NASA’s Mars program, visit: https://mars.nasa.gov

Images (mentioned), Animation (mentioned), Text, Credits: NASA/JPL/Andrew Good.

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The Boscombe Bowmen

I’m thinking that the Boscombe Bowmen site in Wiltshire, Southern England, might be a valuable case study of how the Bell Beaker population, and thus also the present-day Western European gene pool, came to be.
Dated to 2500–2140 BCE, this isn’t an especially early Bell Beaker grave, but its inventory is intriguing. It includes seven All-Over-Cord (AOC) beakers and one Cord-Zoned-Maritime (CZM) beaker.
Maritime beakers are quintessential Bell Beaker gear, and they’re named as such because most of them have been recovered from sites along the Atlantic and Mediterranean coasts. However, strictly speaking, AOC beakers aren’t Bell Beaker artifacts. Rather, their origin is said to be in the Single Grave culture, which is, of course, the Northwestern European variant of the Corded Ware culture.
Genotype data for two samples from the Boscombe cemetery were analyzed in and published along with last year’s Olalde et al. Beaker paper. In tune with the archeological data, one of these individuals came out very Corded Ware-like, with a lot of steppe ancestry, and the other rather southern, with among the lowest level of steppe ancestry for a Beaker dated to later than ~2500 BCE.
To take a closer look at their genetic affinities, I put together the graph below based on a couple of D-stats of the form D(Mbuti,X)(Yamnaya_Samara)/D(Mbuti,X)(Barcin_N,WHG). Look for the labels I2416 and I2417. The relevant datasheet is available here.

Considering these results, I2416 and I2417 may have been migrants, or the descendants of migrants, from such relatively far flung places as, say, what are now Northern Germany and Western France, respectively.
Note also that almost all of the populations are basically sitting between the two bowmen. This indeed suggests to me that the cultural processes and resulting population mixtures that took place at the Boscombe site also played out across the width and breadth of the Beaker realm, giving rise to heterogeneous Beaker groups almost everywhere within it and, eventually, the present-day Western European gene pool.
Most of the Scandinavians, as well as the closely related British Anglo-Saxons, are slightly pulled above the red trend line by their excess genetic affinity to Western European Hunter-Gatherers (WHG). This phenomenon appears to date back to at least 2275-2032 BCE, because Nordic_LN:RISE98 is clearly affected by it and dated to this period.
My guess is that Single Grave populations from what is now Denmark and surrounds harbored much higher levels of WHG-related ancestry than the more easterly Corded Ware (aka Battle-Axe) Scandinavian groups, and they passed this onto present-day Scandinavians. Nordic_LN:RISE98, although from a burial site in what is now Southern Sweden, might well be of Danish Single Grave origin.
See also…
Single Grave > Bell Beakers
Dutch Beakers: like no other Beakers
Hungarian Yamnaya > Bell Beakers?


Next generation imaging

Fig. 1: Probability model of the sky and its observation by a radio telescope. The arrows represent stochastic influences that are ultimately imprinted on the data. When reconstructing the sky signal from the data using NIFTy5, these correlations must be traced backwards in order to deduce causes from the observed effects. © South African Radio Astronomy Observatory; MPA

The Information Field Theory Group at the Max Planck Institute for Astrophysics has released a new version of the NIFTy software for scientific imaging. NIFTy5 generates an optimal imaging algorithm from the complex probability model of a measured signal. Such algorithms have already proven themselves in a number of astronomical applications and can now be used in other areas as well.

Each day, a large number of astronomical telescopes scan the sky at different wavelengths, from radio to optical to gamma rays. The images generated from these observations are usually the result of a complex series of calculations developed specifically for each telescope. But all these different telescopes observe the same cosmos – possibly just different facets of it. Therefore, it makes sense to standardize the imaging of all these instruments. Not only does this save a lot of work in developing different imaging algorithms, it also makes results from different telescopes easier to compare, allows measurements from different sources to be combined into one common image, and means that advances in software development will directly benefit a larger number of instruments.

The research group on information field theory at the Max Planck Institute for Astrophysics has taken a big step towards achieving this goal of a uniform imaging algorithm by developing and publishing the NIFTy5 software. The research topic of this group, information field theory, is the mathematical theory on which imaging processes are based. Information field theory uses methods from quantum field theory for the optimal reconstruction of images. The latest version, NIFTy5, now automates a large part of the necessary mathematical operations.

To begin with, the user needs to program probability models of the image signal (see Fig. 1) as well as the measurement. For this, (s)he can rely on a number of prefabricated building blocks, which often simply need to be combined or only slightly modified. These modules include models for typical signals, such as point or diffuse radiation sources, or for typical measurement situations, which may differ in terms of noise statistics or instrument response. From such a ‘forward’ model of the measurement, NIFTy5 creates an algorithm to ‘backwards’ calculate the original signal, which results in computed image. However, since the source signal can never be determined uniquely, the algorithm also provides a quantification of the remaining uncertainties. This is implemented by providing a set of possible images: the greater uncertainties the greater the differences in each area.

Fig. 2: Galactic dust distribution around the Sun reconstructed with NIFTy5 from data of the Gaia satellite. With the highest spatial resolution reached so far, the figure shows (in logarithmic colour scale) the amount of dust in the galactic plane in an square with two thousand light years on a side. The dark region is the local ‘super bubble’, an area around the Sun cleared of dust by stellar explosions. © MPA

NIFTy5 has already been used for a number of imaging problems, the results of which are published simultaneously. These include the three-dimensional reconstruction of galactic dust clouds in the vicinity of the solar system (see Fig. 2, an animation can be found here), as well as a method to determine the dynamics of fields based only on their observation (see Fig. 3).

Fig.3: Reconstruction of dynamic fields and their unknown dynamic laws using NIFTy5.

Top: Space-time diagram of a field in which waves propagate after random excitations. Time runs from left to right and space is plotted vertically. The excitations are visible as triangular structures, where the excitation is located at the top of the triangle and the wave propagates from there. Centre: Measured values for the field in the top panel at a few discrete locations. Below: Reconstruction of the field from these measured data only, without prior knowledge of its dynamics. This was also reconstructed from the data. All main structures are found, details may vary due to noise in the data. © MPA

On the strength of past experience, NIFTy5 not only allows new, complex imaging methods to be generated much more conveniently, this software package also includes a number of algorithmic innovations. For example, the “Metric Gaussian Variational Inference” (MGVI) was developed specifically for NIFTy5, but can also be used for other machine learning methods. In contrast to conventional methods of probability theory, the implementation of this algorithm in NIFTy5 does not require the explicit storage of so-called covariance matrices. As a result, the memory requirement increases only linearly not quadratically with problem size, so that also gigapixel images can be calculated without problems.

 NIFTy Download

NIFTY stands for Numerical Information Field Theory. The eponymous information field theory was originally developed for the analysis of cosmological data sets. Thanks to NIFTy5, it can now be used in other scientific and technical fields as well, such as medical imaging.


Enßlin, Torsten
Scientific Staff
Phone: 2243
Email: tensslin@mpa-garching.mpg.de
Room: 010

personal homepage (the institute is not responsible for the contents of personal homepages)

Original publications

1. Enßlin, Torsten A.

Information theory for fields

Annalen der Physik 2019, 1800127


2. Knollmüller, Jakob; Enßlin, Torsten A.

Encoding prior knowledge in the structure of the likelihood

submitted to Journal of Machine Learning Research


3. Knollmüller, Jakob; Enßlin, Torsten

Metric Gaussian Variational Inference
submitted to Journal of Machine Learning Research


4. Leike, Reimar H.; Enßlin, Torsten A.

Charting nearby dust clouds using Gaia data only
submitted to Astronomy & Astrophysics


5. Frank, Philipp; Leike, Reimar H.; Enßlin, Torsten A.

Field dynamics inference for local and causal interactions

submitted to Physical Review E

Archive link

2019 February 1 Twin Galaxies in Virgo Image Credit &…

2019 February 1

Twin Galaxies in Virgo
Image Credit & Copyright: CHART32 Team, Processing – Johannes Schedler

Explanation: Spiral galaxy pair NGC 4567 and NGC 4568 share this sharp cosmic vista with lonely elliptical galaxy NGC 4564. All are members of the large Virgo Galaxy Cluster. With their classic spiral arms, dust lanes, and star clusters, the eye-catching spiral pair is also known as the Butterfly Galaxies or the Siamese Twins. Very close together, the galaxy twins don’t seem to be too distorted by gravitational tides. Their giant molecular clouds are known to be colliding though and are likely fueling the formation of massive star clusters. The galaxy twins are about 52 million light-years distant, while their bright cores appear separated by about 20,000 light-years. Of course, the spiky foreground stars lie within our own Milky Way.

∞ Source: apod.nasa.gov/apod/ap190201.html

Roman Bathhouse Photoset 2, Chesters Roman Fort, Hadrian’s Wall, Northumberland,...

Roman Bathhouse Photoset 2, Chesters Roman Fort, Hadrian’s Wall, Northumberland, 27.1.19.

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Folding Under Pressure When an embryo starts to form organs,…

Folding Under Pressure

When an embryo starts to form organs, groups of cells gather and fold into shape. This process is steered by a vast array of factors, from chemical signals to physical pressures, many of which we don’t fully understand. To bend into detailed forms, neighbouring cells must apply, and be subject to, forces in varied directions. Two types of asymmetry, or polarity, guide these interactions. To investigate just how significant these polarities are in relation to other factors, researchers developed computer simulations of cellular development when driven by this alone. Virtual cells with different characteristics produced different shapes, such as the organs pictured growing from 200 to 16,000 cells when cells rapidly divide under no pressure (left) or with external pressure applied (right). Peculiarities in cell polarity can lead to cancer, and this mathematical evidence that polarity alone can produce complex shapes may help decipher how and why that happens.

Written by Anthony Lewis

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Roman Bathhouse Photoset 1, Chesters Roman Fort, Hadrian’s Wall, Northumberland,...

Roman Bathhouse Photoset 1, Chesters Roman Fort, Hadrian’s Wall, Northumberland, 27.1.19.

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Polar Vortex spills Arctic weather into North America



in the world is a polar

? On Earth, it’s a large area of low pressure and extremely cold

air that usually swirls over the Arctic, with strong counter-clockwise winds

that trap the cold around the Pole. But disturbances in the jet stream and the

intrusion of warmer mid-latitude air masses can disturb this polar vortex and

make it unstable, sending Arctic air south into middle latitudes.


has been the case in late January 2019 as frigid weather moves across the

Midwest and Northern Plains of the United States, as well as interior Canada. Forecasters

are predicting that air temperatures in parts of the continental United States

will drop to their lowest levels since at least 1994, with the potential to

break all-time record lows for January 30 and 31. With clear skies, steady

winds, and snow cover on the ground, as many as 90 million Americans could

experience temperatures at or below 0 degrees Fahrenheit (-18° Celsius),

according to the National Weather Service (NWS).

The Goddard

Earth Observing System Model
above shows this air temperature

movement at 2 meters (around 6.5 feet above the ground) from January 23-29. You

can see some portions of the Arctic are close to the freezing

point—significantly warmer than usual for the dark of mid-winter—while masses

of cooler air plunge toward the interior of North America.


Science Behind the Polar

Vortex / Credit: NOAA

Meteorologists predicted that steady northwest winds (10 to 20 miles per hour)

were likely to add to the misery, causing dangerous wind chills below -40°F

(-40°C) in portions of 12 states. A wind chill of -20°F can cause frostbite in

as little as 30 minutes, according to the weather service.

Not sure how cold

that is? Check out the low temperatures on January 30, 2019 in some of the

coldest places on Earth—and

a planetary neighbor:

 -46°F (-43°C) – Chesterfield,


-36°F (-33°C) – Yukon

Territory, Canada

-33°F (-27°C) – Fargo,

North Dakota (Within the Polar Vortex)

-28°F (-18°C) –

Minneapolis, Minnesota (Within the Polar


-27°F (-33°C) – Amundsen-Scott

South Pole Station, Antarctica

-24°F (-31°C) – Chicago,

Illinois (Within the Polar Vortex)

-15°F (5°C) – Barrow,


-99°F (-73°C) – Mars

Learn more about the science behind the polar

vortex and how NASA is modeling it here:


Make sure to follow us on Tumblr for your regular dose of space: http://nasa.tumblr.com

NASA’s AIRS Captures Polar Vortex Moving in Over US

NASA & JPL – AIRS Mission patch.

Jan. 31, 2019

Animation above: NASA’s Atmospheric Infrared Sounder (AIRS) instrument captures a polar vortex moving from Central Canada into the U.S. Midwest from January 20 through January 29. Animation Credits: NASA/JPL-Caltech AIRS Project.

The U.S. Midwest has been gripped by the lowest temperatures it has seen in years. An unusually cold Arctic air mass, called a polar vortex, is responsible for the severe temperatures, which in many areas have plunged well below 0 degrees Fahrenheit (-18 degrees Celsius).

NASA’s Atmospheric Infrared Sounder (AIRS) instrument aboard the Aqua satellite captured the polar vortex as it moved southward from central Canada into the U.S. Midwest from Jan. 20 through Jan. 29. The lowest temperatures are shown in purple and blue and range from -40 degrees Fahrenheit (also -40 degrees Celsius) to -10 degrees Fahrenheit (-23 degrees Celsius). As the data series progresses, you can see how the coldest purple areas of the air mass scoop down into the U.S.

Aqua satellite. Image Credit: NASA

The polar vortex is responsible for a number of deaths, disruptions to services, and energy outages in the affected areas.

AIRS, in conjunction with the Advanced Microwave Sounding Unit (AMSU), senses emitted infrared and microwave radiation from Earth to provide a three-dimensional look at Earth’s weather and climate. Working in tandem, the two instruments make simultaneous observations down to Earth’s surface. With more than 2,000 channels sensing different regions of the atmosphere, the system creates a global, three-dimensional map of atmospheric temperature and humidity, cloud amounts and heights, greenhouse gas concentrations and many other atmospheric phenomena.

Video above: The Advanced Microwave Sounding Unit (AMSU-A), a 15-channel microwave sounder designed primarily to obtain temperature profiles in the upper atmosphere (especially the stratosphere) and to provide a cloud-filtering capability for tropospheric temperature observations. The first AMSU was launched in May 1998 on board the National Oceanic and Atmospheric Administration’s (NOAA’s) NOAA 15 satellite. The EOS AMSU-A is part of a closely coupled triplet of instruments that include the AIRS and HSB.

Launched into Earth orbit in 2002, the AIRS and AMSU instruments are managed by NASA’s Jet Propulsion Laboratory in Pasadena, California, under contract to NASA. JPL is a division of the Caltech in Pasadena.

Related article:

Warming Seas May Increase Frequency of Extreme Storms

More information about AIRS can be found at: https://airs.jpl.nasa.gov

Atmospheric Infrared Sounder (AIRS): https://www.jpl.nasa.gov/missions/atmospheric-infrared-sounder-airs/

AMSU-A: https://aqua.nasa.gov/content/amsu

NASA Aqua satellite: https://aqua.nasa.gov/

Animation (mentioned), Image (mentioned), Video, Text, Credits: NASA/Tony Greicius/JPL/Esprit Smith.

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Kerala floods reveal site filled with ancient terracotta figures

On a sunny day last August, a few men were fishing in the river Pamba in Kozhippalam near Aranmula town in Kerala’s Pathanamthitta district. Like most villages in the area, Kozhippalam was devastated last year in the biggest floods to hit Kerala in living memory. Most houses in the village were empty, as people were scared to move back into homes that had been subsumed by the Pamba so recently.

Kerala floods reveal site filled with ancient terracotta figures
Terracotta figurines of the Sapta Kanyas (7 virgins), men and nagas (serpents) have been
unearthed along with votive sculptures [Credit: Krishnaraj K/Facebook]

But that day, the Pamba was calm, and the floods seemed to belong to a bad dream, except for the trees lying uprooted on the river bank. Suddenly, one of the fishermen saw some terracotta figures peeking at him through the filaments of the roots. Wondering if the floods had unearthed a piece of ancient history, the fishermen informed C.N. Sukumaran, a fellow villager. And the rest, as they say, is history — quite literally in this case.
Sukumaran, academics, historians and enthusiasts soon got together and approached the government. Things moved fast. Kerala’s Department of Archaeology swung into action within a matter of weeks. What till then had been just a ‘riverfront plot’ owned by ‘someone settled in Mumbai’ suddenly became a hotbed of activity.

Down history lane

The narrow lane at Anjilimoottil Kadavu — just wide enough for our SUV to pass through — ends at a plot with a rusted gate, half open, reluctantly allowing in history enthusiasts interested in a glimpse of the excavations in the adjacent compound. The floods that had wreaked havoc a couple of months ago had pulled down the compound wall that separated these two plots, and thus made the excavation site accessible by road.

Kerala floods reveal site filled with ancient terracotta figures
Sapta Matrikas unearthed from Aranmula [Credit: Krishnaraj K/Facebook]

Inside, the trenches baked in the heat of the sun, and the coconut palms and banana plants shone an even brighter green in contrast. The artefacts in the trenches were partially visible from the outside, but were still held tightly by the soil that had protected them for centuries.

Under the sun

Unearthing these figurines under the hot Kerala sun is just the beginning. They also need to be cleaned of the mud they have been covered with for centuries. The fallen compound wall has now become a platform to dry the hundreds of terracotta faces, limbs, and torsos dug out so far. They will now need to slowly be joined together and brought to life, a task that could put a Ravensburger jigsaw puzzle to shame. Once put together, the pieces will hopefully become characters in a historical epic of the area.

Among the artefacts discovered were idols of mother goddesses (Sapta Matrika), naga (serpent) idols, and many figures of men. Each one tells a story. In the coming months, experts will examine these and the pottery shards to understand their origin and the period they belong to. Some of them, , like the stylized naga caressing the upper half of its face with its tongue, have never before been discovered anywhere in Kerala, says K. Krishnaraj, lead archaeologist, as he gently brushes mud off the eyes of one of the faces. The site, with its trenches waiting to be excavated and its discoveries drying in the sun, is a surreal sight. A bygone era returning to life.

Kerala floods reveal site filled with ancient terracotta figures
Naga idol found in Aranmula [Credit: Krishnaraj K/Facebook]

Iconographic studies and thermoluminescence dating (TL) of the pieces are expected to tell us more about their age and the lives of people who lived here and worshipped these gods. Who were they? Were they natives or settlers? When did they live? What did they eat? Was this a holy place of worship of a lost civilisation along the Pamba? What has been discovered so far appears to be only the tip of the proverbial iceberg.
Serendipity is not alien to archaeological discoveries. While the team was busy excavating these figurines from a couple of hundred years ago, another story was waiting to be told across the Pamba, in Vellangoor. Rajeev Puliyoor, a Malayalam teacher in the College of Teacher Education in nearby Elanthoor, brought some of his students to the Anjilimoottil Kadavu site. One student called Gopika saw the idols and said, “This is nothing. There are bigger such buried in my house.” Puliyoor, who is working closely with the excavations, immediately informed the archaeology team and they went to the student’s house.

Mysterious stones

Mathesseril Gopalakrishnan Nair, Gopika’s father, runs a palm leaf plate and bowl manufacturing unit. Very matter-of-factly, he took the experts around his land and showed them the various pieces lying around. There have been long cuboidal stones, obviously manually shaped, lying about his land for as long as he can remember. His family had never bothered to discover what they were. As a teenager, Nair had tried using the stones to build the house he now lives in. Fortunately for the world, the stones were too fragile for construction.

Kerala floods reveal site filled with ancient terracotta figures
Cist burial site discovered on the opposite banks of the Pamba during excavations
[Credit: Krishnaraj K/Facebook]

When the team revealed that the stones were part of cist burials from the Megalithic age, Nair was hugely surprised. The slabs he had treated so casually were part of 2,500-year-old graves, shaped by people adept at stone-cutting. The archaeologists believe more slabs lie under the earth.

Meanwhile, Nair has more practical concerns. “I am going to wait for the compensation the government will offer before I move out,” he says.

As for Aranmula, the cultural capital of what’s often called the Pamba Valley Civilisation and famous for the metal mirror and the annual boat race, it has just added one more feather to its cap.

Author: Nikhil Narayanan | Source: The Hindu [January 26, 2019]



Birds-of-paradise genomes target sexual selection

A new study published in the open access journal GigaScience explores the genomes of a fascinating group of birds, birds-of-paradise, with work providing genome sequences from 5 birds-of-paradise species: 3 that did not have available genome sequences.

Birds-of-paradise genomes target sexual selection
Drawing by Ellis Rowan of the male and female Huan astrapia (Astrapia rothschildi), also
known as Rothschild’s Bird of Paradise. Huan astrapia is local to Papua New Guinea
[Credit: Ellis Rowan (c1847-1922), via WikiCommons]

Birds-of-paradise, with their elaborate and colorful feathers as well as complex courtship displays, have a special place in natural history. They serve as a school-book example of sexual selection, which is the outcome of generations of female mate choice of males that have “attractive” features.

The result is an unparalleled radiation of species where males exhibit extreme morphological features and behaviors with no other evolutionary meaning than to attract females for mating. However, very little is known about the genetic variants that distinguish the lavishly colored birds-of-paradise from their less conspicuous relatives, such as the collared flycatcher.

Whole genome availability of multiple species provides a rich resource for molecular evolutionary to identify genes that came under the influence of sexual selection, and a way to assess how these genes transformed the males’ plumage into a colorful asset for mating purposes.

The famous evolutionary biologist Ernst Mayr (1904-2005) once said about the birds-of-paradise: “Every ornithologist and birdwatcher has his favourite group of birds. Frankly, my own are the birds of paradise and bowerbirds. If they do not rank as high in world-wide popularity as they deserve it is only because so little is known about them.”

Taking on the task of addressing the limited amount of information available for these exotic birds were researchers from the Swedish Museum of Natural History, American scientists, and first author Stefan Prost from the Senckenberg Museum in Frankfurt.

They selected three species that did not yet have available genomes sequences: the paradise crow (Lycocorax pyrrhopterus) from Obi Island in Indonesia; the paradise riflebird (Ptiloris paradiseus) from New South Wales, Australia; and the huon astrapia (Astrapia rothschildi) from Papua New Guinea.

They further provided new genome sequence data to improve currently available genomic information for two other birds-of-paradise species from Papua New Guinea: the King of Saxony bird-of-paradise (Pteridophora alberti) and the red bird-of-paradise (Paradisaea rubra).

Martin Irestedt, senior curator at the Swedish Museum of Natural History, said that “Birds-of-paradise constitute one of the most famous examples on how sexual selection has driven the evolution of male plumage ornamentation and mating behaviors to its extreme. It is thus extremely exciting that we are able to present genomic data that provide the first glimpse to how genomic evolution is linked to the extraordinary phenotypic variation found in this fascinating group of birds.”

Using these five bird-of-paradise datasets, Prost and colleagues identified genes that show signs of past influence of selection and evolution, some of which appear to be important for coloration, morphology, and feather and eye development. For example, they identified a gene called ADAMTS20 that is potentially involved in producing the exquisite birds-of-paradise colorful feathers. ADAMTS20 is known to influence the development of melanocytes, specialized cells for the production of pigmentation patterns.

Thanks to modern genomics and the availability of these new datasets in the GigaScience DataBase, GigaDB, we are about to learn much more about these fascinating animals.

Source: GigaScience [January 28, 2019]



MaNGA data release includes detailed maps of thousands of nearby galaxies

The latest data release from the Sloan Digital Sky Survey (SDSS) includes observations revealing the internal structure and composition of nearly 5,000 nearby galaxies observed during the first three years of a program called Mapping Nearby Galaxies at Apache Point Observatory (MaNGA).

MaNGA data release includes detailed maps of thousands of nearby galaxies
The MaNGA data set will eventually include more than 10,000 nearby galaxies, and the survey is already
more than half way toward that goal [Credit: SDSS/MaNGA collaboration]

MaNGA uses a technique called resolved spectroscopy to study galaxies in much greater detail than previous surveys. Spectroscopy is a powerful tool for astronomers, yielding a wealth of information by measuring how much light an object emits at different wavelengths. In the past, astronomers typically acquired just one spectrum for each galaxy, but resolved spectroscopy (also called integral field spectroscopy) obtains hundreds of separate spectra covering every location within the galaxy.

“Resolved spectroscopy allows us to dissect a galaxy and study its internal composition and the motions of its stars and gas,” explained MaNGA principal investigator Kevin Bundy, an associate researcher at UC Observatories and adjunct professor of astronomy and astrophysics at UC Santa Cruz.

“People have been doing resolved spectroscopy for individual galaxies, but we’ve never had it for thousands of galaxies, so MaNGA gives us the statistical power to address a lot of important questions,” Bundy said.

MaNGA’s goal is to understand the “life history” of present-day galaxies, from their initial birth and assembly, through their ongoing growth via star formation and mergers, to their death from “quenching” of star formation at late times. Bundy and his students at UC Santa Cruz, for example, have discovered evidence in the MaNGA data for outflows of hot ionized gas in “dead” galaxies, supporting the idea that powerful winds driven out from a galaxy’s central black hole can shut down star formation. Bundy’s team is also finding clues to how galaxies were assembled over time by studying the motions of their stars and gas and by analyzing the chemical signatures of stars in different parts of galaxies.

MaNGA data release includes detailed maps of thousands of nearby galaxies
The Marvin web site offers easy access to a wealth of information about each galaxy in the MaNGA survey, including
 maps of key features such as star formation, stellar motion, emission lines, and dozens of other properties
important to astronomers [Credit: SDSS/MaNGA collaboration]

One of three programs in the fourth phase of SDSS, MaNGA will eventually study a representative sample of some 10,000 nearby galaxies. Bundy said the survey is more than half way toward that goal and on track to reach it by 2020. Data from 4,621 galaxies are now publicly available as part of the 15th SDSS data release (the third data release for SDSS-IV).

“This data release is a major milestone for us,” Bundy said. “MaNGA is already by far the largest survey of its kind, and this release includes both the data and the analytical tools the project has developed.”

A powerful new interface called Marvin provides access to the MaNGA data and galaxy maps based on analyses of the data. Marvin includes a wide range of tools for searching, accessing, and visualizing the data. The Marvin web site offers easy access to a wealth of information about each galaxy, including maps of key features such as star formation, stellar motion, emission lines, and dozens of other properties important to astronomers. Kyle Westfall, a project scientist at UC Observatories, led the development of the data analysis pipeline that produced the maps and other data products now publicly available for the first time.

Another important part of this data release is the MaNGA Stellar Library containing spectra of more than 3,000 stars in our Milky Way galaxy. When complete, it will include 5,000 to 6,000 stars. Researchers can use the spectra of these individual stars to try to reconstruct the spectrum of a galaxy and thereby figure out that galaxy’s unique mix of different star types.

MaNGA data release includes detailed maps of thousands of nearby galaxies
The MaNGA survey obtains spectra across the entire face of target galaxies using custom-designed fiber
bundles. The bottom right illustrates how the array of fibers spatially samples a particular galaxy.
The top right compares spectra observed by two fibers at different locations in the galaxy,
showing how the spectrum of the central regions differs dramatically from outer regions
[Credit: Dana Berry/SkyWorks Digital Inc., David Law, and the SDSS collaboration]

“The MaNGA Stellar Library is the largest library of stars ever compiled, with spectra from the same instruments used for the galaxies, so it’s a very powerful tool for understanding the nature of the stellar populations in these galaxies,” Bundy said.
MaNGA Survey Scientist Renbin Yan of the University of Kentucky led the development of the Stellar Library.

The MaNGA survey uses the two BOSS spectrographs at the 2.5-meter Sloan Foundation Telescope at Apache Point Observatory in New Mexico in a novel way. Specially designed “integral field units,” each composed of tightly packed arrays of optical fibers, enable the measurement of spectra at multiple points in the same galaxy. The MaNGA spectra provide continuous coverage from optical to near-infrared wavelengths.

Source: University of California – Santa Cruz [January 29, 2019]



Huge step forward in decoding genomes of small species

For the first time, scientists have read the whole genetic code of one single tiny mosquito. Traditionally, it has been difficult to extract enough DNA from insects and other small organisms to build a high quality genome for a single individual. Scientists from the Wellcome Sanger Institute and Pacific Biosciences worked in partnership to advance technology and lower the starting amount of DNA needed to just ‘half a mosquito-worth’, producing the first high quality whole genome of a single mosquito.

Huge step forward in decoding genomes of small species
Sanger Institute researchers, working with PacBio, have obtained a high-quality whole genome
from just a single mosquito’s DNA [Credit: James Gathany, CDC PHIL]

The results, reported in Genes, open the door to understanding the true genetic diversity of insects and other arthropods, which comprise the most diverse animal group in the tree of life.

In 2018, collaborating organisations around the world officially launched the Earth BioGenome Project, a global mission to sequence all 1.5 million known species of animals, plants, protozoa and fungi on Earth. The Earth BioGenome Project will ultimately create a new foundation for biology to drive solutions for preserving biodiversity and sustaining human societies.

When studying the biology of a species, the genome of a single individual can be used as a reference to explore the genetic differences attributing to varying susceptibility to disease, fitness and adaptation within others of the same species.

However, it is much easier to extract DNA and sequence the genome of some species over others. In particular, it has not been possible to assemble the genome from single small organisms such as insects using current sequencing technology. This leaves the genetic codes of individual insects and other similar-sized species inaccessible.

Until now, scientists have had to pool the DNA of multiple individuals of the same species, or inbreed them to produce genetically related individuals, in order to gather enough DNA to build a genome. This creates challenges when putting the genetic sequence back together again after it has been sequenced, as it can be difficult to know which genetic fragment came from which individual, resulting in genome sequences full of gaps and errors.

In the new study, Sanger Institute researchers worked with scientists at the sequencing technology provider, Pacific Biosciences (PacBio) to produce the first high-quality genome from a single insect using new technology that reduces the starting DNA needed.

Dr Mara Lawniczak, co-lead author from the Wellcome Sanger Institute, said: “This advancement in sequencing technology is vital to decoding the genomes of a huge number of species in the tree of life, giving us greater power to completely understand genetic diversity within even the tiniest species.”

Sanger scientists extracted DNA from a single Anopheles coluzzii mosquito and sent it to PacBio in the United States.

To reduce the amount of starting DNA required for genome sequencing, the PacBio team tweaked the preparation chemistry for genomic sequencing. They removed two steps from the process that result in the loss of DNA: shearing — cutting the DNA fragments into certain size ranges, and size selection — removing the unwanted small fragments.

The team were able to generate a high quality genome from just 100 nanograms of DNA — about half a mosquito’s worth — which is over an order of magnitude less than the 5 micrograms of DNA previously required.

The resulting genome was quick to assemble, complete and accurate. As a result of the complete genomic picture, nearly half of the previously unplaced DNA fragments for this mosquito species could now be placed within the correct chromosomal context.

Dr Jonas Korlach, Chief Scientific Officer at Pacific Biosciences and co-lead author of the study, said: “This has been a real team effort and we’ve thoroughly enjoyed the collaboration in developing this protocol. It’s a great example of the significant advances we can bring to the scientific community when academia and industry work together.”

This advance could have positive potential for humans as well, for example in the future it could be possible to assemble the whole genetic code of a patient’s cancer, from a single biopsy.

Dr Peter Campbell from the Wellcome Sanger Institute, who was not involved in the study, said: “The sequencing technology also shows promise for reading the whole genetic code of an individual patient’s cancer biopsy. 100 nanograms of DNA collected with a needle prick could be enough to give a detailed view of the cancer’s genetics and inform targeted therapies for that specific patient.”

Source: Wellcome Trust Sanger Institute [January 29, 2019]



New Hellenistic and Roman era finds at ancient Kition

Works on the sewerage system of Larnaca continue to reveal archaeological finds from ancient Kition. Some of these are thought to be extremely important and of great historical value, as for example a section of the defense wall of the ancient city of Kition located on Teukros street. In 2016 a unique Roman mosaic, measuring 19×4.60m,  and featuring the Labours of Hercules was also discovered.

New Hellenistic and Roman era finds at ancient Kition
Mosaic floor found in Larnaca [Credit: Department of Antiquities of Cyprus]

As announced by Head of Antiquities Department, Dr Marina Ieronymidou-Solomidou, it is the first time that a mosaic has been found in Cyprus with such subject matter, i.e. the Labours of Hercules, usually associated with baths. According to the former there are five panels, two of which have been completely uncovered and another three in part. For the work to be revealed in its entirety, archaeologists are trying these last two years to overcome some practical issues as the mosaic extends diagonally towards apartment blocks and a private residence.

According to a report sent a few days ago to the Cypriot Parliament by Transport Minister Vasiliki Anastasiadou, work on the sewerage system of Larnaca has revealed a multitude of ancient artefacts made from various materials.

Specifically, many clay pots were found, which, as usual, make up most of the finds. Metal tools were also located and objects of prestige such as bone tools and jewellery, faience artefacts and imported raw materials such as semiprecious stones and gold jewellery.

The finds of each excavation are being examined by experts in each category of material (e.g. ceramics by specialists in ceramics) and also in groups of findings, such as the findings of a tomb, to come as close as possible to the historical conditions that created an archaeological assemblage; the key objective of scientific archaeological research.

Specifically regarding the gold jewellery in question, about which MP Christos Orphanides asked to be informed, Mrs Anastasiadou, according to the ‟Phileleutheros” newspaper, mentions in her letter that compared to the other categories of finds , the gold jewellery are small artefacts, limited in number, found in tombs from Hellenistic (310-58 B.C.) and Roman times (58 B.C.-330 B.C.).

Their small number and the fact they have been found sporadically in burials and not in large assemblages make it evident that they were important objects to their owners who were ordinary members of ancient Kition society.

New Hellenistic and Roman era finds at ancient Kition
Pottery found in Larnaca [Credit: Department of Antiquities of Cyprus]

Additionally, dozens of ancient carved tombs dating back from the Classical to the Roman period were found on Griva Digeni Street (Drosia district) and on Agisilaou, Aeolou, Gordiou Desmou, Liperti and Kultur streets.

Most of the burial monuments that have been excavated were unplundered and specifically the 10 tombs found on Gordion Desmos Street. This gave the Department of Antiquities the opportunity to collect valuable information about burial customs in ancient Kition.

During excavation work on the sewerage system in Teukrou Street, several clay female figurines were also found which may have come from the so-called shrine of Kamilarkon, located and excavated in 1894 by British archaeologist J.L. Myres.

The results of his excavation were published in the ‟Journal of Hellenic Studies” in 1897. These excavations located the foundations of a temple with many fragments of stone and clay statues and figurines in the Kamilarka district, where Teukrou and Nikodimou Mylonas Streets converge today.

In her letter, the minister says that most of these statues and figurines are female, depicting the ‟goddess with raised arms”, various types of Astarte, the goddess with child, Kourotrophoi, women worshippers and musicians. There are also a few male figures such as musicians, riders, worshippers et al. The findings date the use of the site as a sanctuary from the Cypro-archaic to the Hellenistic period (7th-3rd centuries B.C.).

It comes as no surprise to the Department of Antiquities that archaeological remains of great historical value are still being discovered, since it is well known that under the modern city of Larnaca there are layers of the place’s older history, first inhabited in the Early Bronze Age at the end of the 3rd millennium B.C.

Regarding the construction works of the sewerage system, the Department of Antiquities, in cooperation with the Larnaca Sewerage Board, is proceeding, where necessary, in changing the route of sewerage pipes, so that those archaeological remains that cannot be moved, are kept in the ground and made available to researchers in the future.

Source: Archaeology & Arts [January 29, 2019]




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