Thursday, July 30, 2020

Study Sheds Light on the Evolution of the Earliest Dinosaurs

Geological evidence suggests the known dinosaur groups diverged early on, supporting the traditional dinosaur family tree.

The classic dinosaur family tree has two subdivisions of early dinosaurs at its base: the Ornithischians, or bird-hipped dinosaurs, and the Saurischians, or lizard-hipped dinosaurs. In this photo-illustration, a drawing of a bird-hipped Ornithiscian is surrounded by fossils of a Pisanosaurus, a small bipedal dinosaur whose fossils have been analyzed in a new study.
The classic dinosaur family tree has two subdivisions of early dinosaurs at its base: the Ornithischians, or bird-hipped dinosaurs, and the Saurischians, or lizard-hipped dinosaurs. In this photo-illustration, a drawing of a bird-hipped Ornithiscian is surrounded by fossils of a Pisanosaurus, a small bipedal dinosaur whose fossils have been analyzed in a new study.
Image: Bone images courtesy of the researchers. Edited by MIT News.

The classic dinosaur family tree has two subdivisions of early dinosaurs at its base: the Ornithischians, or bird-hipped dinosaurs, which include the later Triceratops and Stegosaurus; and the Saurischians, or lizard-hipped dinosaurs, such as Brontosaurus and Tyrannosaurus.

In 2017, however, this classical view of dinosaur evolution was thrown into question with evidence that perhaps the lizard-hipped dinosaurs evolved first — a finding that dramatically rearranged the first major branches of the dinosaur family tree.

Now an MIT geochronologist, along with paleontologists from Argentina and Brazil, has found evidence to support the classical view of dinosaur evolution. The team’s findings are published today in the journal Scientific Reports.

The team reanalyzed fossils of Pisanosaurus, a small bipedal dinosaur that is thought to be the earliest preserved Ornithiscian in the fossil record. The researchers determined that the bird-hipped herbivore dates back to 229 million years ago, which is also around the time that the earliest lizard-hipped Saurischians are thought to have appeared.

The new timing suggests that Ornithiscians and Saurischians first appeared and diverged from a common ancestor at roughly the same time, giving support to the classical view of dinosaur evolution.

Paleontologists wrapping fossil bone fragments in a plaster jacket before transportation to the lab for preparation and detailed studies
Paleontologists wrapping fossil bone fragments in a plaster jacket before transportation to the lab for preparation and detailed studies
Courtesy of the researchers

The researchers also dated rocks from the Ischigualasto Formation, a layered sedimentary rock unit in Argentina that is known for having preserved an abundance of fossils of the very earliest dinosaurs. Based on these fossils and others across South America, scientists believe that dinosaurs first appeared in the southern continent, which at the time was fused together with the supercontinent of Pangaea. The early dinosaurs are then thought to have diverged and fanned out across the world.

However, in the new study, the researchers determined that the period over which the Ischigualasto Formation was deposited overlaps with the timing of another important geological deposit in North America, known as the Chinle Formation.

The middle layers of the Chinle Formation in the southwestern U.S. contain fossils of various fauna, including dinosaurs that appear to be more evolved than the earliest dinosaurs. The bottom layers of this formation, however, lack animal fossil evidence of any kind, let alone early dinosaurs. This suggests that conditions within this geological window prevented the preservation of any form of life, including early dinosaurs, if they walked this particular region of the world.

“If the Chinle and Ischigualasto formations overlap in time, then early dinosaurs may not have first evolved in South America, but may have also been roaming North America around the same time,” says Jahandar Ramezani, a research scientist in MIT’s Department of Earth, Atmospheric, and Planetary Sciences, who co-authored the study. “Those northern cousins just may not have been preserved.”

Field view of the fossil-rich Ischigualasto Formation (foreground) with the Sierra de Famatina mountains in the horizon
Field view of the fossil-rich Ischigualasto Formation (foreground) with the Sierra de Famatina mountains in the horizon
Courtesy of the researchers

The other researchers on the study are first author Julia Desojo from the National University of La Plata Museum, and a team of paleontologists from institutions across Argentina and Brazil.

“Following footsteps”

The earliest dinosaur fossils found in the Ischigualasto Formation are concentrated within what is now a protected provincial park known as “Valley of the Moon” in the San Juan Province. The geological formation also extends beyond the park, albeit with fewer fossils of early dinosaurs. Ramezani and his colleagues instead looked to study one of the accessible outcrops of the same rocks, outside of the park.

They focused on Hoyada del Cerro Las Lajas, a less-studied outcrop of the Ischigualasto Formation, in La Rioja Province, which another team of paleontologists explored in the 1960s.

“Our group got our hands on some of the field notes and excavated fossils from those early paleontologists, and thought we should follow their footsteps to see what we could learn,” Desojo says.

Over four expeditions between 2013 to 2019, the team collected fossils and rocks from various layers of the Las Lajas outcrop, including more than 100 new fossil specimens, though none of these fossils were of dinosaurs. Nevertheless, they analyzed the fossils and found they were comparable, in both species and relative age, to nondinosaur fossils found in the park region of the same Ischigualasto Formation. They also found out that the Ischigualasto Formation in Las Lajas was significantly thicker and much more complete than the outcrops in the park. This gave them confidence that the geological layers in both locations were deposited during the same critical time interval.

Ramezani then analyzed samples of volcanic ash collected from several layers of the Las Lajas outcrops. Volcanic ash contains zircon, a mineral that he separated from the rest of the sediment, and measured for isotopes of uranium and lead, the ratios of which yield the mineral’s age.



Microscopic crystals of the uranium-bearing mineral zircon were separated from the rock samples and analyzed by the U-Pb isotopic technique at the MIT Isotope Lab. These zircons yielded a precise age of 221.82 ± 0.10 Ma for the upper Ischigualasto Formation.
Microscopic crystals of the uranium-bearing mineral zircon were separated from the rock samples and analyzed by the U-Pb isotopic technique at the MIT Isotope Lab. These zircons yielded a precise age of 221.82 ± 0.10 Ma for the upper Ischigualasto Formation.
Courtesy of the researchers


With this high-precision technique, Ramezani dated samples from the top and bottom of the outcrop, and found that the sedimentary layers, and any fossils preserved within them, were deposited between 230 million and 221 million years ago. Since the team determined that the layered rocks in Las Lajas and the park match in both species and relative timing, they could also now determine the exact age of the park’s more fossil-rich outcrops.

Moreover, this window overlaps significantly with the time interval over which sediments were deposited, thousands of kilometers northward, in the Chinle Formation.

“For many years, people thought Chinle and Ischigualasto formations didn’t overlap, and based on that assumption, they developed a model of diachronous evolution, meaning the earliest dinosaurs appeared in South America first, then spread out to other parts of the world including North America,” Ramezani says. “We’ve now studied both formations extensively, and shown that diachronous evolution isn’t really based on sound geology.”

A family tree, preserved

Decades before Ramezani and his colleagues set out for Las Lajas, other paleontologists had explored the region and unearthed numerous fossils, including remains of Pisanosaurus mertii, a small, light-framed, ground-dwelling herbivore. The fossils are now preserved in an Argentinian museum, and scientists have gone back and forth on whether it is a true dinosaur belonging to the Ornithiscian group, or a “ basal dinosauromorph” — a kind of pre-dinosaur, with features that are almost, but not quite fully, dinosaurian.

“The dinosaurs we see in the Jurassic and Cretaceous are highly evolved, and ones we can nicely identify, but in the late Triassic, they all looked very much alike, so it’s very hard to distinguish them from each other, and from basal dinosauromorphs,” Ramezani explains.

His collaborator Max Langer from the University of São Paulo in Brazil painstakingly reanalyzed the museum-preserved fossil of Pisanosaurus, and concluded, based on certain key anatomical features, that it is indeed a dinosaur — and what’s more, that it is the earliest preserved Ornithiscian specimen. Based on Ramezani’s dating of the outcrop and the interpretation of Pisanosaurus, the researchers concluded that the earliest bird-hipped dinosaurs appeared around 229 million years ago — around the same time as their lizard-hipped counterparts.

“We can now say the earliest Ornithiscians first showed up in the fossil record roughly around the same time as the Saurischians, so we shouldn’t throw away the conventional family tree,” Ramezani says. “There are all these debates about where dinosaurs appeared, how they diversified, what the family tree looked like. A lot of those questions are tied to geochronology, so we need really good, robust age constraints to help answer these questions.”

This research was mainly funded by the National Council for Scientific and Technical Research (Argentina) and the São Paulo State Research Support Foundation (Brazil). Geochronologic research at the MIT Isotope Lab has been supported in part by the U.S. National Science Foundation.


Contacts and sources:
Jennifer Chu,
Massachusetts Institute of Technology

Snow Ball Earth Trigger Found? Plunge in Incoming Sunlight Suspected



At least twice in Earth’s history, nearly the entire planet was encased in a sheet of snow and ice. These dramatic “Snowball Earth” events occurred in quick succession, somewhere around 700 million years ago, and evidence suggests that the consecutive global ice ages set the stage for the subsequent explosion of complex, multicellular life on Earth. The findings also suggest exoplanets lying within habitable zones may be susceptible to ice ages.

Scientists have considered multiple scenarios for what may have tipped the planet into each ice age. While no single driving process has been identified, it’s assumed that whatever triggered the temporary freeze-overs must have done so in a way that pushed the planet past a critical threshold, such as reducing incoming sunlight or atmospheric carbon dioxide to levels low enough to set off a global expansion of ice.

The trigger for “Snowball Earth” global ice ages may have been drops in incoming sunlight that happened quickly, in geological terms, according to an MIT study.
The trigger for “Snowball Earth” global ice ages may have been drops in incoming sunlight that happened quickly, in geological terms, according to an MIT study.
Image: Wikimedia, Oleg Kuznetsov

But MIT scientists now say that Snowball Earths were likely the product of “rate-induced glaciations.” That is, they found the Earth can be tipped into a global ice age when the level of solar radiation it receives changes quickly over a geologically short period of time. The amount of solar radiation doesn’t have to drop to a particular threshold point; as long as the decrease in incoming sunlight occurs faster than a critical rate, a temporary glaciation, or Snowball Earth, will follow.

These findings, published today in the Proceedings of the Royal Society A, suggest that whatever triggered the Earth’s ice ages most likely involved processes that quickly reduced the amount of solar radiation coming to the surface, such as widespread volcanic eruptions or biologically induced cloud formation that could have significantly blocked out the sun’s rays.

The findings may also apply to the search for life on other planets. Researchers have been keen on finding exoplanets within the habitable zone — a distance from their star that would be within a temperature range that could support life. The new study suggests that these planets, like Earth, could also ice over temporarily if their climate changes abruptly. Even if they lie within a habitable zone, Earth-like planets may be more susceptible to global ice ages than previously thought.

“You could have a planet that stays well within the classical habitable zone, but if incoming sunlight changes too fast, you could get a Snowball Earth,” says lead author Constantin Arnscheidt, a graduate student in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). “What this highlights is the notion that there’s so much more nuance in the concept of habitability.”

Arnscheidt has co-authored the paper with Daniel Rothman, EAPS professor of geophysics, and co-founder and co-director of the Lorenz Center.

A runaway snowball

Regardless of the particular processes that triggered past glaciations, scientists generally agree that Snowball Earths arose from a “runaway” effect involving an ice-albedo feedback: As incoming sunlight is reduced, ice expands from the poles to the equator. As more ice covers the globe, the planet becomes more reflective, or higher in albedo, which further cools the surface for more ice to expand. Eventually, if the ice reaches a certain extent, this becomes a runaway process, resulting in a global glaciation.


Credit: MIT

Global ice ages on Earth are temporary in nature, due to the planet’s carbon cycle. When the planet is not covered in ice, levels of carbon dioxide in the atmosphere are somewhat controlled by the weathering of rocks and minerals. When the planet is covered in ice, weathering is vastly reduced, so that carbon dioxide builds up in the atmosphere, creating a greenhouse effect that eventually thaws the planet out of its ice age.

Scientists generally agree that the formation of Snowball Earths has something to do with the balance between incoming sunlight, the ice-albedo feedback, and the global carbon cycle.

“There are lots of ideas for what caused these global glaciations, but they all really boil down to some implicit modification of solar radiation coming in,” Arnscheidt says. “But generally it’s been studied in the context of crossing a threshold.”

He and Rothman had previously studied other periods in Earth’s history where the speed, or rate at which certain changes in climate occurred had a role in triggering events, such as past mass extinctions.

“In the course of this exercise, we realized there was an immediate way to make a serious point by applying such ideas of rate-induced tipping, to Snowball Earth and habitability,” Rothman says.

“Be wary of speed”

The researchers developed a simple mathematical model of the Earth’s climate system that includes equations to represent relations between incoming and outgoing solar radiation, the surface temperature of the Earth, the concentration of carbon dioxide in the atmosphere, and the effects of weathering in taking up and storing atmospheric carbon dioxide. The researchers were able to tune each of these parameters to observe which conditions generated a Snowball Earth.

Ultimately, they found that a planet was more likely to freeze over if incoming solar radiation decreased quickly, at a rate that was faster than a critical rate, rather than to a critical threshold, or particular level of sunlight. There is some uncertainty in exactly what that critical rate would be, as the model is a simplified representation of the Earth’s climate. Nevertheless, Arnscheidt estimates that the Earth would have to experience about a 2 percent drop in incoming sunlight over a period of about 10,000 years to tip into a global ice age.

“It’s reasonable to assume past glaciations were induced by geologically quick changes to solar radiation,” Arnscheidt says.

The particular mechanisms that may have quickly darkened the skies over tens of thousands of years is still up for debate. One possibility is that widespread volcanoes may have spewed aerosols into the atmosphere, blocking incoming sunlight around the world. Another is that primitive algae may have evolved mechanisms that facilitated the formation of light-reflecting clouds. The results from this new study suggest scientists may consider processes such as these, that quickly reduce incoming solar radiation, as more likely triggers for Earth’s ice ages.

“Even though humanity will not trigger a snowball glaciation on our current climate trajectory, the existence of such a ‘rate-induced tipping point’ at the global scale may still remain a cause for concern,” Arnscheidt points out. “For example, it teaches us that we should be wary of the speed at which we are modifying Earth’s climate, not just the magnitude of the change. There could be other such rate-induced tipping points that might be triggered by anthropogenic warming. Identifying these and constraining their critical rates is a worthwhile goal for further research.”

This research was funded, in part, by the MIT Lorenz Center.




Contacts and sources:
Jennifer Chu,
Massachusetts Institute of Technology





Possible Sign of Neutron Star in Supernova 1987A Found

Artist's illustration of SN1987A
 
Credit: NRAO/AUI/NSF, B. Saxton

Two teams of astronomers have made a compelling case in the 33-year-old mystery surrounding Supernova 1987A. Based on observations of the Atacama Large Millimeter/submillimeter Array (ALMA) and a theoretical follow-up study, the scientists provide new insight for the argument that a neutron star is hiding deep inside the remains of the exploded star. This would be the youngest neutron star known to date.

Ever since astronomers witnessed one of the brightest explosions of a star in the night sky, creating Supernova 1987A (SN 1987A), they have been searching for a compact object that should have formed in the leftovers from the blast.
  

Because particles known as neutrinos were detected on Earth on the day of the explosion (23 February 1987), astronomers expected that a neutron star had formed in the collapsed center of the star. But when scientists could not find any evidence for that star, they started to wonder whether it subsequently collapsed into a black hole instead. For decades the scientific community has been eagerly awaiting a signal from this object that has been hiding behind a very thick cloud of dust.

The “blob”
Recently, observations from the ALMA radio telescope provided the first indication of the missing neutron star after the explosion. Extremely high-resolution images revealed a hot “blob” in the dusty core of SN 1987A, which is brighter than its surroundings and matches the suspected location of the neutron star.

Video zooming into the dusty core of Supernova 1987A, revealing a hot “blob” as seen with ALMA, which could be the location of the missing neutron star. The red color shows dust and cold gas in the center of the supernova remnant, taken at radio wavelengths with ALMA. The green and blue hues reveal where the expanding shock wave from the exploded star is colliding with a ring of material around the supernova. The green represents the glow of visible light, captured by NASA's Hubble Space Telescope. The blue color reveals the hottest gas and is based on data from NASA's Chandra X-ray Observatory. The ring was initially made to glow by the flash of light from the original explosion. Over subsequent years the ring material has brightened considerably as the explosion's shock wave slams into it.

Credit: ALMA (ESO/NAOJ/NRAO), P. Cigan and R. Indebetouw; NRAO/AUI/NSF, B. Saxton; NASA/ESA

“We were very surprised to see this warm blob made by a thick cloud of dust in the supernova remnant,” said Mikako Matsuura from Cardiff University and a member of the team that found the blob with ALMA. “There has to be something in the cloud that has heated up the dust and which makes it shine. That’s why we suggested that there is a neutron star hiding inside the dust cloud.”

Even though Matsuura and her team were excited about this result, they wondered about the brightness of the blob. “We thought that the neutron star might be too bright to exist, but then Dany Page and his team published a study that indicated that the neutron star can indeed be this bright because it is so very young,” said Matsuura.

Dany Page is an astrophysicist at the National Autonomous University of Mexico, who has been studying SN 1987A from the start. “I was halfway through my PhD when the supernova happened,” he said, “it was one of the biggest events in my life that made me change the course of my career to try to solve this mystery. It was like a modern holy grail.”

Extremely high-resolution ALMA images revealed a hot "blob" in the dusty core of Supernova 1987A (inset), which could be the location of the missing neutron star. The red color shows dust and cold gas in the center of the supernova remnant, taken at radio wavelengths with ALMA. The green and blue hues reveal where the expanding shock wave from the exploded star is colliding with a ring of material around the supernova. The green represents the glow of visible light, captured by NASA's Hubble Space Telescope. The blue color reveals the hottest gas and is based on data from NASA's Chandra X-ray Observatory. The ring was initially made to glow by the flash of light from the original explosion. Over subsequent years the ring material has brightened considerably as the explosion's shock wave slams into it.

Credit: ALMA (ESO/NAOJ/NRAO), P. Cigan and R. Indebetouw; NRAO/AUI/NSF, B. Saxton; NASA/ESA

The theoretical study by Page and his team, published today in The Astrophysical Journal, strongly supports the suggestion made by the ALMA team that a neutron star is powering the dust blob. “In spite of the supreme complexity of a supernova explosion and the extreme conditions reigning in the interior of a neutron star, the detection of a warm blob of dust is a confirmation of several predictions,” Page explained.

These predictions were the location and the temperature of the neutron star. According to supernova computer models, the explosion has “kicked away” the neutron star from its birthplace with a speed of hundreds of kilometers per second (tens of times faster than the fastest rocket). The blob is exactly at the place where astronomers think the neutron star would be today. And the temperature of the neutron star, which was predicted to be around 5 million degrees Celsius, provides enough energy to explain the brightness of the blob.

Not a pulsar or a black hole

Contrary to common expectations, the neutron star is likely not a pulsar
Credit: The National Radio Astronomy Observatory

“A pulsar’s power depends on how fast it spins and on its magnetic field strength, both of which would need to have very finely tuned values to match the observations,” said Page, “while the thermal energy emitted by the hot surface of the young neutron star naturally fits the data.”

“The neutron star behaves exactly like we expected,” added James Lattimer of Stony Brook University in New York, and a member of Page’s research team. Lattimer has also followed SN 1987A closely, having published prior to SN 1987A predictions of a supernova’s neutrino signal that subsequently matched the observations. “Those neutrinos suggested that a black hole never formed, and moreover it seems difficult for a black hole to explain the observed brightness of the blob. We compared all possibilities and concluded that a hot neutron star is the most likely explanation.”

This neutron star is a 25 km wide, extremely hot ball of ultra-dense matter. A teaspoon of its material would weigh more than all the buildings within New York City combined. Because it can only be 33 years old, it would be the youngest neutron star ever found. The second youngest neutron star that we know of is located in the supernova remnant Cassiopeia A and is 330 years old.

Only a direct picture of the neutron star would give definite proof that it exists, but for that astronomers may need to wait a few more decades until the dust and gas in the supernova remnant become more transparent.

Even though many telescopes have made images of SN 1987A, none of them have been able to observe its core with such high precision as ALMA. Earlier (3-D) observations with ALMA already showed the types of molecules found in the supernova remnant and confirmed that it produced massive amounts of dust.

“This discovery builds upon years of ALMA observations, showing the core of the supernova in more and more detail thanks to the continuing improvements to the telescope and data processing,” said Remy Indebetouw of the National Radio Astronomy Observatory and the University of Virginia, who has been a part of the ALMA imaging team.

The National Radio Astronomy Observatory is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.


Credit: The National Radio Astronomy Observatory





Contacts and sources:
Iris Nijman
The National Radio Astronomy Observatory





Publication: ALMA observation of the "blob": "High Angular Resolution ALMA Images of Dust and Molecules in the SN 1987A Ejecta", by P. Cigan et al., The Astrophysical Journal. https://doi.org/10.3847/1538-4357/ab4b46

Theoretical study favoring a neutron star: "NS 1987A in SN 1987A", by D. Page et al., The Astrophysical Journal. https://doi.org/10.3847/1538-4357/ab93c2







COVID-19 Economic and Food Supply Chain Disruptions Endanger Global Food Security



COVID-19 has led to a global economic slowdown that is affecting all four pillars of food security - availability, access, utilization, and stability - according to a new article from researchers at the International Food Policy Research Institute (IFPRI), published in the journal Science. Agricultural and food markets are facing continuous disruptions due to labor shortages caused by lockdowns, as well as large shifts in food demand arising from income losses and the closure of schools and restaurants. The key findings highlight the impact of COVID-19 on food systems, the global economy, poverty, health, and trade.

A photograph of nearly empty shelves of meat at a supermarket in Littleton, CO during the 2020 COVID-19 virus outbreak.
File:Empty meat shelves Colorado.jpg
Credit: Seraphimblade / Wikimedia Commons

"The most important impact of the pandemic on food security is through income declines that put food access at risk", said article co-author and IFPRI Director-General Johan Swinnen. "This is especially a concern for the extreme poor, who spend on average about 70 percent of their total income on food."

The International Monetary Fund (IMF) projects a 5% decline in the world economy in 2020, a deeper global recession than during 2008-2009 financial crisis. Model-based simulations by IFPRI suggest that such a deep recession would push 150 million more people into extreme poverty; an increase of 24% from current levels. Most of the rise in poverty will be concentrated in sub-Saharan Africa and South Asia. "Disruptions in food systems both contribute to increases in poverty, by affecting a critical source of income for many of the world's poor, and also exacerbate the impacts of poverty by reducing access to food, particularly nutritious foods," said Swinnen.

The researchers note that income declines will particularly affect consumption of nutrition-rich foods, such as fruits, vegetables, and animal-source products. New evidence from Ethiopia confirms this impact and further indicates that it is expected to increase micronutrient deficiencies among its population, contributing to poor health and greater susceptibility to COVID-19.

Credit: International Food Policy Research Institute (IFPRI)

Governments all over the world have made attempts to ensure availability of staple foods and these supply chains have generally held up well, even in countries with strict social distancing requirements. But food supply chains differ across countries and crops, as do the impacts of COVID-19 on supplies. Capital-intensive food value chains that are highly mechanized (predominant in rich countries for staple crops such as wheat, maize and soybeans) have continued functioning with few disruptions. In contrast, food production in poor countries tends to be more labor-intensive; and production of many non-staples, such as fruits and vegetables, worldwide requires workers be in close proximity. These food value chains have shown more supply disruptions owing to the risk of disease transmission, labor shortages, and disruptions in transportation and logistics. Parts of food processing sectors in rich countries have also been susceptible to such disruptions, as evident in the case of United States and Europe, where 30,000 workers in meat processing tested positive for COVID-19, causing many plant closures.

"It is critical to exempt agricultural practices and actors from COVID-19 lockdown measures to ensure the adequate flow of food from farm to fork", said IFPRI's Markets, Trade and Institutions Division Director Rob Vos. The researchers point to the "green lanes" the Chinese government created to ease the transport, production processes, and distribution of agricultural inputs and food products as an example.

Trade is also essential to address issues of availability and stability. It ensures diversification of supplies, reduces gaps in production and helps stabilize of world markets. Export restrictions on staple foods including rice and wheat, imposed by 21 countries in the early months of the pandemic, created volatility and upward pressure on world prices for food staples. "Fortunately, many of these export restrictions have since been lifted, and world market prices for rice, for instance, declined after the end of Vietnam's export ban," said article co-author and IFPRI Senior Research Fellow David Laborde. The researchers recommend governments avoid further use of disruptive policies like export restrictions on food, keep policies consistent with rules agreed at the WTO and maintain open trade channels.

Fiscal challenges facing low- and middle-income countries could create strong international spillover effects for the economic consequences of COVID-19. Support and response from high-income countries and international organizations is crucial for poor countries with limited fiscal space. "Such support would not only aid global economic recovery but also mitigate the enormous humanitarian costs associated with the health tragedy of COVID-19 and the consequent food crisis," said article co-author and IFPRI Senior Research Fellow Will Martin.


Read the full article in the journal Science: https://science.sciencemag.org/cgi/doi/10.1126/science.abc4765





Contacts and sources:
Drew SampleInternational Food Policy Research Institute (IFPRI)






Wednesday, July 29, 2020

Ancient Economy in The Grip of Plague and Climate Change Collapsed, Lessons from Grape Pips



While we all try to understand the new reality imposed by the COVID-19 pandemic, many look to the past for historical precedents such as the Spanish flu of 1918 and the Black Plague of the 14th century. The first historically attested wave of what later became known as the Black Plague (caused by the bacterium Yersinia pestis) spread throughout the Byzantine Empire and beyond, in 541 CE. Known as Justinianic Plague, after the emperor Justinian who contracted the disease but survived, it caused high mortality and had a range of socio-economic effects.

St Sebastian pleading for the life of a gravedigger afflicted with plague during the 7th-century Plague of Justinian.
Plaguet03.jpg
Credit: Josse Lieferinxe / Wikimedia Commons

 Around the same time, an enormous volcanic eruption in late 535 or early 536 CE marked the beginning of the coldest decade in the last two thousand years (another volcano of similar proportions erupted in 539 CE). However, scholars disagree as to just how far-reaching and devastating the mid-6th century epidemic and climate change were. This scholarly debate is unsurprising considering that even today, leaders and policymakers around the world differ on the severity and correct response to COVID-19, not to mention climate change. One reason that hindsight is not 20/20 when it comes to ancient plagues is that ancient reports tend to exaggerate, or underrepresent, the human tolls, while archaeological evidence for the social and economic effects of plague are very hard to find.

Recently, a team of Israeli archaeologists discovered new and compelling evidence for a significant economic downturn on the fringe of the Byzantine Empire in the aftermath of a major pandemic in the mid-6th century CE. The research, published today in the Proceedings of the National Academy of Sciences (PNAS), reconstructs the rise and fall of commercial viticulture in the middle of Israel's arid Negev desert.

Daniel Fuks, a PhD student in the Martin (Szusz) Department of Land of Israel Studies and Archaeology at Bar-Ilan University, led the study as a researcher in Prof. Ehud Weiss' Archaeobotany Lab, and as a team member of the Negev Byzantine Bio-Archaeology Research Program, "Crisis on the Margins of the Byzantine Empire", headed by Prof. Guy Bar-Oz of the University of Haifa. This project seeks to discover when and why the agricultural settlement of the Negev Highlands was abandoned.

Vine seeds discovered in the area
Vine seeds discovered in the area
Credit: Bar-Ilan University

Agriculture in this arid desert was made possible through rainwater runoff farming which reached its peak in the Byzantine period, as seen at sites like Elusa, Shivta and Nessana. At Negev Highland sites today, the ruins of well-built stone structures attest to their former glory, but Bar-Oz's team, guided by field archaeologists from the Israel Antiquities Authority (IAA), Dr. Yotam Tepper and Dr. Tali Erickson-Gini, discovered even more compelling evidence about life during that period in an unexpected place: the trash. "Your trash says a lot about you. In the ancient trash mounds of the Negev, there is a record of residents' daily lives - in the form of plant remains, animal remains, ceramic sherds, and more," explains Bar-Oz. "In the 'Crisis on the Margins' project, we excavated these mounds to uncover the human activity behind the trash, what it included, when it flourished, and when it declined."

The study of seeds found in archaeological excavations is part of the field known as archaeobotany (aka paleoethnobotany). The Bar-Ilan University Archaebotany Lab in which most of this research was conducted is the only lab in Israel dedicated to the identification of ancient seeds and fruits. Prof. Ehud Weiss, the lab's head, explains that the task of archaeobotany is to "get into the pantry - or, in this case, the trash - of ancient people and study their interactions with plants. 

Archaeobotany reconstructs ancient economy, environment and culture, but the way there is not easy. Grain by grain must be sorted through endless sediment samples, looking for seeds, identifying them and counting each one, as it is written '...if one can count the dust of the earth, then your seed too can be counted' (Genesis 13:16)." For the present study, nearly 10,000 seeds of grape, wheat and barley were retrieved and counted from 11 trash mounds at three sites. "Identifying seed and fruit remains is a unique capability of our lab," says Weiss, "and it relies on the Israel National Reference Collection of Plant Seeds and Fruit held in our lab, and on years of experience in retrieving, processing, and analyzing plant remains from sites of all periods in Israeli archaeology."

One of the researchers' first observations was the high numbers of grape seeds in the ancient trash mounds. This fit well with previous scholars' suggestions that the Negev was involved in export-bound viticulture. Byzantine texts laud the vinum Gazetum or "Gaza wine" as a sweet white wine exported from the port of Gaza throughout the Mediterranean and beyond. This wine was generally transported in a type of amphora known as "Gaza Jars" or "Gaza Wine Jars", which are also found in sites throughout the Mediterranean. In Byzantine Negev trash mounds, these Gaza Jars appear in high quantities.

Roman-era Palestinian amphorae, Bodrum Castle, Turkey
Credit: Ad Meskens  - Own work / Wikimedia Commons

Daniel Fuks, the Bar-Ilan University PhD student, sought to determine whether there were any interesting trends in the relative frequency of grape pips in the rubbish. In a Ted-style talk hosted by Bet Avichai last year, he said, "Imagine you're an ancient farmer with a plot of land to feed your family. On most of it, you plant cereals like wheat and barley because that's how you get your bread. On a smaller part, you plant a vineyard and other crops like legumes, vegetables and fruit trees, for your family's needs.

"But one day you realize that you could sell the excellent wine you produce, for export, and earn enough cash to buy bread and a bit more. Little by little you expand your vineyard and move from subsistence farming to commercial viticulture.

"If we look at your trash and count the seeds, we'll discover a rise in the proportion of grape pips relative to cereal grains. And that's exactly what we discovered: A significant rise in the ratio of grape pips to cereal grains between the 4th century CE and the mid-6th century. Then suddenly, it declines."

Meanwhile, Fuks and Dr. Tali Erickson-Gini, an expert in ancient Negev pottery, took this to the next level. They checked whether there were similar trends in the proportion of Gaza Wine Jars to Bag-Shaped Jars, the latter being much less suited to camelback transport from the Negev Highlands to the port at Gaza. Indeed, the rise and initial decline of Gaza Jars tracked the rise and fall of the grape pips.

The researchers concluded that the commercial scale of viticulture in the Negev, as seen in the grape pip ratios, was connected to Mediterranean trade, attested to by the Gaza Jar ratios. In other words, a novel archaeological testimony to an international commercial economy from some 1,500 years ago was discovered!

View of the Negev Highlands from the ancient Nabataean city of Avdat

Credit: Andrew Shiva / Wikipedia

Like today, this situation brought unprecedented prosperity, but also greater vulnerability to shocks. In the mid-6th century, there were a few such shocks that could explain the decline. One of them was Justinianic plague, which had a high death toll in Byzantium and other parts of the empire. In the article, the authors explain that the resulting "contracting market for Gaza products would have detrimentally impacted the Negev economy, even while trade at nearby Gaza may have continued... If the plague reached the Negev, it could also have harmed the local production capacity and supply of agricultural products in general by inducing a shortage of agricultural laborers."

A different shock of that period was a volcanic eruption of global proportions in late 535/early 536 CE, which covered the Northern Hemisphere's atmosphere with dust and caused decade-long global cooling (another eruption of similar magnitude occurred in 539 CE). This led to drought in Europe, but may have increased precipitation, possibly including high-intensity flash flooding, in the southern Levant, causing detriment to local agriculture.

The Sisyphean task of sorting and counting seeds may not appear to be the most exciting, but the research on archaeological plant finds is innovative and influential, while also demonstrating the ingenuity and insightfulness involved in ancient peoples' interactions with plants. Guy Bar-Oz, of the University of Haifa, states,: "The discovery of the rise and fall of commercial viticulture in the Byzantine Negev supports other recent evidence unearthed by the 'Crisis on the Margins' project for major agricultural and settlement expansion in the 5th to mid-6th century followed by decline. It appears that agricultural settlement in the Negev Highlands received such a blow that it was not revived until modern times. Significantly, the decline came nearly a century before the Islamic conquest of the mid-seventh century."

Two of the most likely triggers for the mid-6th century collapse - climate change and plague - reveal inherent vulnerabilities in political-economic systems, then and now. "The difference is that the Byzantines didn't see it coming," explains Fuks. "We can actually prepare ourselves for the next outbreak or the imminent consequences of climate change. The question is, will we be wise enough to do so?"




Contacts and sources:
Elana OberlanderBar-Ilan University







50% Global Reduction in Human-Linked Earth Vibrations Due to COVID-19 Lockdowns



The lack of human activity during lockdown caused human-linked vibrations in the Earth to drop by an average of 50% between March and May 2020.

This quiet period, likely caused by the total global effect of social distancing measures, closure of services and industry, and drops in tourism and travel, is the longest and most pronounced quiet period of seismic noise in recorded history.
Credit: Imperial College London / Lecocq et al.

Our study uniquely highlights just how much human activities impact the solid Earth, and could let us see more clearly than ever what differentiates human and natural noise.Dr Stephen HicksDepartment of Earth Science and Engineering

The new research, led by the Royal Observatory of Belgium and five other institutions around the world including Imperial College London, showed that the dampening of ‘seismic noise’ caused by humans was more pronounced in more densely populated areas.

The relative quietness allowed researchers to listen in to previously concealed earthquake signals, and could help us differentiate between human and natural seismic noise more clearly than ever before.

Co-author Dr Stephen Hicks, from Imperial’s Department of Earth Science and Engineering, said: “This quiet period is the longest and largest dampening of human-caused seismic noise since we started monitoring the Earth in detail using vast monitoring networks of seismometers.

“Our study uniquely highlights just how much human activities impact the solid Earth, and could let us see more clearly than ever what differentiates human and natural noise.”

The paper is published today in Science.

Anthropause

Measured by instruments called seismometers, seismic noise is caused by vibrations within the Earth, which travel like waves. The waves can be triggered by earthquakes, volcanoes, and bombs - but also by daily human activity like travel and industry.

via GIPHY

via GIPHY  Lecocq et al.

Although 2020 has not seen a reduction in earthquakes, the drop in human-caused seismic noise is unprecedented. The strongest drops were found in urban areas, but the study also found signatures of the lockdown on sensors buried hundreds of metres underground and in more remote areas.

Human-generated noise usually dampens during quiet periods like over the Christmas/New Year period and Chinese New Year, and during weekends and overnight. However, the drop in vibrations caused by COVID-19 lockdown measures eclipse even those seen during these periods.

Drop in UK seismic activity and recreation/retail activity, pre- and post-lockdown

Credit: Imperial College London,  Lecocq et al.

Some researchers are dubbing this drop in anthropogenic (human-caused) noise and pollution the ‘anthropause’.

Dr Hicks said: “This is the first global study of the impact of the coronavirus anthropause on the solid Earth beneath our feet.”

To gather the data, researchers looked at seismic data from a global network of 268 seismic stations in 117 countries and found significant noise reductions compared to before any lockdown at 185 of those stations. Beginning in China in late January 2020, and followed by Europe and the rest of the world in March to April 2020, researchers tracked the ‘wave’ of quietening between March and May as worldwide lockdown measures took hold.

With increasing urbanisation and growing global populations, more people will be living in geologically hazardous areas. It will therefore become more important than ever to differentiate between natural and human-caused noiseDr Thomas LecocqRoyal Observatory of Belgium

The largest drops in vibrations were seen in the most densely populated areas, like Singapore and New York City, but drops were also seen in remote areas like Germany’s Black Forest and Rundu in Namibia.

Citizen-owned seismometers, which tend to measure more localised noise, noted large drops around universities and schools around Cornwall, UK and Boston, USA – a drop in noise 20 per cent larger than seen during school holidays.

Countries like Barbados, where lockdown coincided with the tourist season, saw a 50 per cent decrease in noise. This coincided with flight data that suggested tourists returned home in the weeks before official lockdown.
Listening in

Over the past few decades, seismic noise has gradually increased as economies and populations have grown.

The drastic changes to daily life caused by the pandemic have provided a unique opportunity to study their environmental impacts, such as reductions in emissions and pollution in the atmosphere. The changes have also given us the opportunity to listen in to the Earth’s natural vibrations without the distortions of human input.

Ctizen seismometer known as a 'Raspberry Shake'
Photo of seismometer: Stephen Hicks/Imperial College London

The study reports the first evidence that previously concealed earthquake signals, especially during daytime, appeared much clearer on seismometers in urban areas during lockdown.

The researchers say the lockdown quietening could also help them differentiate between human-caused noise and natural signals that might warn of upcoming natural disasters.

Lead author Dr Thomas Lecocq from the Royal Observatory of Belgium said: "With increasing urbanisation and growing global populations, more people will be living in geologically hazardous areas. It will therefore become more important than ever to differentiate between natural and human-caused noise so that we can ‘listen in’ and better monitor the ground movements beneath our feet. This study could help to kick-start this new field of study.”

The study’s authors hope that their work will spawn further research on the seismic lockdown, as well as finding previously hidden signals from earthquakes and volcanoes.

Dr Hicks said: “The lockdowns caused by the coronavirus pandemic may have given us a glimmer of insight into how human and natural noise interacts with the Earth. We hope this insight will spawn new studies that help us listen better to the Earth and understand natural signals we would otherwise have missed.”

268 seismometers (red) in 117 countries detected a drop on seismic noise.






Credits:  Lecocq et al.




Contacts and sources:
Caroline Brogan
Imperial College London

Publication: “Global quieting of high-frequency seismic noise due to COVID-19 pandemic lockdown measures” by Thomas Lecocq et al., published Thursday 23 July 2020 in Science





Deep Sea Microbes Dormant for 100 Million Years, Brought Back to Life, Now Hungry and Ready to Multiply



For decades, scientists have gathered ancient sediment samples from below the seafloor to better understand past climates, plate tectonics and the deep marine ecosystem. In a new study published in Nature Communications, researchers reveal that given the right food in the right laboratory conditions, microbes collected from sediment as old as 100 million years can revive and multiply, even after laying dormant since large dinosaurs prowled the planet.

Yuki Morono (left) and Steven D’Hondt (far right) aboard the research drillship JOIDES Resolution with sediment cores gathered from the South Pacific Gyre. 
Yuki Morono (left) and Steven D’Hondt (far right) aboard the research drillship JOIDES Resolution with sediment cores gathered from the South Pacific Gyre. (Photo courtesy of IODP JRSO)
Photo courtesy of IODP JRSO

The research team behind the new study, from the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), the URI Graduate School of Oceanography, the National Institute of Advanced Industrial Science and Technology, the Kochi University and Marine Works Japan, gathered the ancient sediment samples ten years ago during an expedition to the South Pacific Gyre, the part of the ocean with the lowest productivity and fewest nutrients available to fuel the marine food web.

“Our main question was whether life could exist in such a nutrient-limited environment or if this was a lifeless zone,” said the paper’s lead author Yuki Morono, senior scientist at JAMSTEC. “And we wanted to know how long the microbes could sustain their life in a near-absence of food.”

On the seafloor, there are layers of sediment consisting of marine snow (organic debris continually sourced from the sea surface), dust, and particles carried by the wind and ocean currents. Small life forms such as microbes become trapped in this sediment.

Aboard the research drillship JOIDES Resolution, the team drilled numerous sediment cores 100 meters below the seafloor and nearly 6,000 meters below the ocean’s surface. The scientists found that oxygen was present in all of the cores, suggesting that if sediment accumulates slowly on the seafloor at a rate of no more than a meter or two every million years, oxygen will penetrate all the way from the seafloor to the basement. Such conditions make it possible for aerobic microorganisms—those that require oxygen to live—to survive for geological time scales of millions of years.

With fine-tuned laboratory procedures, the scientists, led by Morono, incubated the samples to coax their microbes to grow. The results demonstrated that rather than being fossilized remains of life, the microbes in the sediment had survived, and were capable of growing and dividing.

“We knew that there was life in deep sediment near the continents where there’s a lot of buried organic matter,” said URI Graduate School of Oceanography professor and co-author of the study Steven D’Hondt. “But what we found was that life extends in the deep ocean from the seafloor all the way to the underlying rocky basement.”

Morono was initially taken aback by the results. “At first I was skeptical, but we found that up to 99.1% of the microbes in sediment deposited 101.5 million years ago were still alive and were ready to eat,” he said.

With the newly developed ability to grow, manipulate and characterize ancient microorganisms, the research team is looking forward to applying a similar approach to other questions about the geological past. According to Morono, life for microbes in the subseafloor is very slow compared to life above it, and so the evolutionary speed of these microbes will be slower. “We want to understand how or if these ancient microbes evolved,” he said. “This study shows that the subseafloor is an excellent location to explore the limits of life on Earth.”

Before looking ahead to future research, D’Hondt took time to reflect on Morono’s achievement. “What’s most exciting about this study is that it shows that there are no limits to life in the old sediment of the world’s ocean,” said D’Hondt. “In the oldest sediment we’ve drilled, with the least amount of food, there are still living organisms, and they can wake up, grow and multiply.”

This study was supported by the Japan Society for the Promotion of Science (JSPS), the Funding Program for Next Generation World-Leading Researchers, and the U.S. National Science Foundation. This study was conducted using core samples collected during Expedition 329, “South Pacific Gyre Subseafloor Life,” of the Integrated Ocean Drilling Program.



Contacts and sources:
Peter J. Hanlon
University of Rhode Island

Publication: Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years. Morono, Y., Ito, M., Hoshino, T. et al. Nat Commun, 2020 DOI: 10.1038/s41467-020-17330-1




Possibility of Life Supported by Cosmic Rays Below the Surface of Mars Investigation

Recent findings suggest the presence of traces of water on Mars, raising the question of the possibility of a life-supporting environment.

Although no life has been detected on the Martian surface, a new study from astrophysicist and research scientist at the Center for Space Science at NYU Abu Dhabi, Dimitra Atri finds that conditions below the surface could potentially support it. The subsurface – which is less harsh and has traces of water – has never been explored. According to Atri, the steady bombardment of penetrating Galactic Cosmic Rays (GCRs) might provide the energy needed to catalyze organic activity there.

fikret-science-club07
Credit: NYU 

Atri’s findings are reported in the study Investigating the biological potential of galactic cosmic ray-induced radiation-driven chemical disequilibrium in the Martian subsurface environment in the journal Scientific Reports, Springer Nature.

There is growing evidence suggesting the presence of an aqueous environment on ancient Mars, raising the question of the possibility of a life-supporting environment. The erosion of the Martian atmosphere resulted in drastic changes in its climate, surface water disappeared, shrinking habitable spaces on the planet, with only a limited amount of water remaining near the surface in form of brines and water-ice deposits. Life, if it ever existed, would have had to adapt to harsh modern conditions, which include low temperatures and surface pressure, and high radiation dose. 

The NYU Abu Dhabi Center for Space Science will be carrying out scientific research based on the observations and data collected by the Emirates Mars Mission Hope probe.
Credit: NYU Abu Dhabi Center for Space Science

The subsurface of Mars has traces of water in the form of water-ice and brines, and undergoes radiation-driven redox chemistry. Using a combination of numerical models, space mission data, and studies of deep-cave ecosystems on Earth for his research, Atri proposes mechanisms through which life, if it ever existed on Mars, could survive and be detected with the upcoming ExoMars mission (2022) by the European Space Agency and Roscosmos. He hypothesizes that galactic cosmic radiation, which can penetrate several meters below the surface, will induce chemical reactions that can be used for metabolic energy by extant life, and host organisms using mechanisms seen in similar chemical and radiation environments on Earth.

“It is exciting to contemplate that life could survive in such a harsh environment, as few as two meters below the surface of Mars. When the Rosalind Franklin rover on board the ExoMars mission (ESA and Roscosmos), equipped with a subsurface drill, is launched in 2022, it will be well-suited to detect extant microbial life and hopefully provide some important insights.” says research Scientist Dimitra Atri


Credit: NYU


The NYU Abu Dhabi Center for Space Science will be carrying out scientific research based on the observations and data collected by the Emirates Mars Mission Hope probe. The Center will look to tackle a slew of questions about Mars. How did it lose its atmosphere and how does solar activity impact the exploration of Mars? The probe will provide insight into our distant planetary neighbor and it will also help answer questions that have captured humanity’s imagination for generations.

Is there life on Mars?

Can we live on the red planet?

“Studying detailed physical processes on Mars and Martian atmospheres will greatly inform our understanding of potential habitability for terrestrial planets throughout other solar systems,” said Dimitra Atri, a research scientist at the NYUAD Center for Space Science.

The Hope Probe, set to reach the red planet’s orbit in 2021, will be the first probe to provide a complete picture of the Martian atmosphere and its layers. NYUAD researchers at the Center will begin to study the data in spring.

Scientists from NYUAD will build models demonstrating atmospheric losses at Mars and researching how it lost a thicker atmosphere in the past and how its present atmosphere might evolve in the future.

“One of the main objectives of the UAE Space Agency and the Mohammed bin Rashid Space Centre is to carry out scientific research from mission data in the UAE, train the local population and engage the general public. We have made plans to be involved in all of the above,” said Atri.

As part of its efforts to support the Emirates Mars Mission, the NYU Abu Dhabi Center for Space Science will be utilizing its expertise and research capabilities to carry out scientific research based on observations and data collected from this mission. The Center, aligned with the UAE’s National Space Strategy 2030, will continue to work in close coordination with the relevant government organizations.


Contacts and sources:
Naser Al Wasmi
New York University (NYU)
Center for Space Science at NYU Abu Dhabi

Publication: Investigating the biological potential of galactic cosmic ray-induced radiation-driven chemical disequilibrium in the Martian subsurface environment. Dimitra Atri. Scientific Reports, 2020; 10 (1) DOI: 10.1038/s41598-020-68715-7




Artificial Intelligence Stops To Smell the Roses Now It's Ready to Works on Flavors and Fragrances


 A University of California Riverside study applies machine learning to olfaction with possible vast applications in flavors and fragrances.

A pair of researchers at the University of California, Riverside, has used machine learning to understand what a chemical smells like -- a research breakthrough with potential applications in the food flavor and fragrance industries.

"We now can use artificial intelligence to predict how any chemical is going to smell to humans," said Anandasankar Ray, a professor of molecular, cell and systems biology, and the senior author of the study that appears in iScience. "Chemicals that are toxic or harsh in, say, flavors, cosmetics, or household products can be replaced with natural, softer, and safer chemicals."

Anandasankar Ray is a professor of molecular, cell and systems biology at UC Riverside. 
Credit:  L. Duka.

Humans sense odors when some of their nearly 400 odorant receptors, or ORs, are activated in the nose. Each OR is activated by a unique set of chemicals; together, the large OR family can detect a vast chemical space. A key question in olfaction is how the receptors contribute to different perceptual qualities or percepts.

"We tried to model human olfactory percepts using chemical informatics and machine learning," Ray said. "The power of machine learning is that it is able to evaluate a large number of chemical features and learn what makes a chemical smell like, say, a lemon or a rose or something else. The machine learning algorithm can eventually predict how a new chemical will smell even though we may initially not know if it smells like a lemon or a rose."

According to Ray, digitizing predictions of how chemicals smell creates a new way of scientifically prioritizing what chemicals can be used in the food, flavor, and fragrance industries.

"It allows us to rapidly find chemicals that have a novel combination of smells," he said. "The technology can help us discover new chemicals that could replace existing ones that are becoming rare, for example, or which are very expensive. It gives us a vast palette of compounds that we can mix and match for any olfactory application. For example, you can now make a mosquito repellent that works on mosquitoes but is pleasant smelling to humans."

The researchers first developed a method for a computer to learn chemical features that activate known human odorant receptors. They then screened roughly half a million compounds for new ligands -- molecules that bind to receptors -- for 34 odorant receptors. Next, they focused on whether the algorithm that could estimate odorant receptor activity could also predict diverse perceptual qualities of odorants.

"Computers might help us better understand human perceptual coding, which appears, in part, to be based on combinations of differently activated ORs," said Joel Kowalewski, a student in the Neuroscience Graduate Program working with Ray and the first author of the research paper. "We used hundreds of chemicals that human volunteers previously evaluated, selected ORs that best predicted percepts on a portion of chemicals, and tested that these ORs were also predictive of new chemicals."

Joel Kowalewski is a student in the Neuroscience Graduate Program at UC Riverside.
 Credit: Joel Kowalewski, UC Riverside.


Ray and Kowalewski showed the activity of ORs successfully predicted 146 different percepts of chemicals. To their surprise, few rather than all ORs were needed to predict some of these percepts. Since they could not record activity from sensory neurons in humans, they tested this further in the fruit fly (Drosophila melanogaster) and observed a similar result when predicting the fly's attraction or aversion to different odorants.

"If predictions are successful with less information, the task of decoding odor perception would then become easier for a computer," Kowalewski said.

Ray explained that many items available to consumers use volatile chemicals to make themselves appealing. About 80% of what is considered flavor in food actually stems from the odors that affect smell. Fragrances for perfuming cosmetics, cleaning products, and other household goods play an important role in consumer behavior.

"Our digital approach using machine learning could open up many opportunities in the food, flavor, and fragrance industries," he said. "We now have an unprecedented ability to find ligands and new flavors and fragrances. Using our computational approach, we can intelligently design volatile chemicals that smell desirable for use and also predict ligands for the 34 human ORs."


The study was partially funded by UCR and the National Science Foundation.
The technology has been disclosed to the UCR Office of Technology Partnerships, assigned UC case number 2019-131, is patent pending, titled "Methods for identifying, compounds identified and compositions thereof," and licensed to the startup company Sensorygen Inc. Founded by Ray in 2015, Sensorygen utilizes computational biology and artificial intelligence to discover natural replacements for toxic and harsh chemicals in everyday products, including finding new flavors and insect repellents.

The research paper is titled "Predicting human olfactory perception from activities of odorant receptors."



Contacts and sources:
Iqbal PittalwalaUniversity of California Riverside





Artificial Intelligence Identifies Prostate Cancer with Near-Perfect Accuracy



A study published today in The Lancet Digital Health by UPMC and University of Pittsburgh researchers demonstrates the highest accuracy to date in recognizing and characterizing prostate cancer using an artificial intelligence (AI) program.

"Humans are good at recognizing anomalies, but they have their own biases or past experience," said senior author Rajiv Dhir, M.D., M.B.A., chief pathologist and vice chair of pathology at UPMC Shadyside and professor of biomedical informatics at Pitt. "Machines are detached from the whole story. There's definitely an element of standardizing care."

To train the AI to recognize prostate cancer, Dhir and his colleagues provided images from more than a million parts of stained tissue slides taken from patient biopsies. Each image was labeled by expert pathologists to teach the AI how to discriminate between healthy and abnormal tissue. The algorithm was then tested on a separate set of 1,600 slides taken from 100 consecutive patients seen at UPMC for suspected prostate cancer.

Prostate biopsy with cancer probability (blue is low, red is high). This case was originally diagnosed as benign but changed to cancer upon further review. The AI accurately detected cancer in this tricky case.
Credit: Ibex Medical Analytics

During testing, the AI demonstrated 98% sensitivity and 97% specificity at detecting prostate cancer -- significantly higher than previously reported for algorithms working from tissue slides.

Also, this is the first algorithm to extend beyond cancer detection, reporting high performance for tumor grading, sizing and invasion of the surrounding nerves. These all are clinically important features required as part of the pathology report.

AI also flagged six slides that were not noted by the expert pathologists.

But Dhir explained that this doesn't necessarily mean that the machine is superior to humans. For example, in the course of evaluating these cases, the pathologist could have simply seen enough evidence of malignancy elsewhere in that patient's samples to recommend treatment. For less experienced pathologists, though, the algorithm could act as a failsafe to catch cases that might otherwise be missed.

"Algorithms like this are especially useful in lesions that are atypical," Dhir said. "A nonspecialized person may not be able to make the correct assessment. That's a major advantage of this kind of system."

While these results are promising, Dhir cautions that new algorithms will have to be trained to detect different types of cancer. The pathology markers aren't universal across all tissue types. But he didn't see why that couldn't be done to adapt this technology to work with breast cancer, for example.

Additional authors on the study include Liron Pantanowitz, M.B.B.Ch., of the University of Michigan; Gabriela Quiroga-Garza, M.D., of UPMC; Lilach Bien, Ronen Heled, Daphna Laifenfeld, Ph.D., Chaim Linhart, Judith Sandbank, M.D., Manuela Vecsler, of Ibex Medical Analytics; Anat Albrecht-Shach, M.D., of Shamir Medical Center; Varda Shalev, M.D., M.P.A., of Maccabbi Healthcare Services; and Pamela Michelow, M.S., and Scott Hazelhurst, Ph.D., of the University of the Witwatersrand.

Funding for this study was provided by Ibex, which also created this commercially available algorithm. Pantanowitz, Shalev and Albrecht-Shach report fees paid by Ibex, and Pantanowitz and Shalev serve on the medical advisory board. Bien and Linhart are authors on pending patents US 62/743,559 and US 62/981,925. Ibex had no influence over the design of the study or the interpretation of the results.



Contacts and sources:
Erin Hare / Cyndy Patton
University of Pittsburgh







Combating a Pandemic Is 500 Times More Expensive Than Preventing One Says New Research

Investing in wildlife monitoring and deforestation could prevent costly pandemics.

According to new research, the failure to protect tropical rain forests has cost trillions of dollars stemming from the coronavirus pandemic, which has wreaked economic havoc and caused historic levels of unemployment in the United States and around the world.

Deforestation of Rainforest
Credit: Daniele Gidsicki   / Wikimedia Commons

For decades, scientists and environmental activists have been trying to draw the world's attention to the many harms caused by the rapid destruction of tropical forests. One of these harms is the emergence of new diseases that are transmitted between wild animals and humans, either through direct contact or through contact with livestock that is then eaten by humans. The SARS-CoV-2 virus--which has so far infected more than 15 million people worldwide--appears to have been transmitted from bats to humans in China.

"Much of this traces back to our indifference about what has been occurring at the edges of tropical forests," says Les Kaufman, a Boston University professor of biology.

He recently brought together 18 experts from Princeton University, Duke University, Conservation International, and other institutions, to better understand the economic costs of reducing transmission of viruses like the novel coronavirus. Looking at existing research, they made a startling realization.

They discovered that significantly reducing transmission of new diseases from tropical forests would cost, globally, between $22.2 and $30.7 billion each year. In stark contrast, they found that the COVID-19 pandemic will likely end up costing between $8.1 and $15.8 trillion globally--roughly 500 times as costly as what it would take to invest in proposed preventive measures. To estimate the total financial cost of COVID-19, researchers included both the lost gross domestic product and the economic and workforce cost of hundreds of thousands of deaths worldwide. They published their findings in a policy brief in Science.

Deforestation - Caceres (Mato Grosso, Brasile), Satellite Landsat 5 TM (227/071 - 1996, 453 RGB)
File:Deforestation Carceres Braasil 1996.jpg
Credit: NASA / Wikimedia Commons

The researchers say disease transmission from wild animals to humans occurs frequently near the edges of tropical forests, where human incursions increase the likelihood of contact with animals. These incursions take the form of logging, cattle ranching, and other livestock businesses, and the exotic animal trade, among others. Tropical forests are often cut down in a patchwork or checkerboard pattern, increasing the amount of land that lies at the edges of the forest and thus increasing the risk for disease transmission between species that would normally live in different ecosystems.

To reduce disease transmission, Kaufman and his collaborators propose expanding wildlife trade monitoring programs, investing in efforts to end the wild meat trade in China, investing in policies to reduce deforestation by 40 percent, and fighting the transmission of disease from wild animals to livestock.

In China alone, wildlife farming (a government-monitored effort to sustainably hunt wild animals without overhunting them) is an approximately $20 billion industry, employing 15 million people, say Kaufman and his peers. In many China communities, the purchase of wildlife and bushmeat--meat from wildlife species--is a status symbol.

The researchers also propose to increase funding for creating an open source library of the unique genetic signatures of known viruses, which could help quickly pinpoint the source of emerging diseases and catch them more quickly, before they can spread.

Every year, two new viruses are estimated to transfer from animals to humans, the researchers say. Historically, these have included HIV, MERS, SARS-CoV-1, H1N1, and most recently, the SARS-CoV-2 virus that causes COVID-19. Kaufman and his colleagues hope that their report will spur governments around the world, including the US government, to help fund these preventive measures.

There are some signs of hope, they say, including the February announcement by the Standing Committee of the National People's Congress that wildlife consumption for food or related trade would be banned in China.

"The pandemic gives an incentive to do something addressing concerns that are immediate and threatening to individuals, and that's what moves people," says Kaufman. "There are many people who might object to the United States fronting money, but it's in our own best interest. Nothing seems more prudent than to give ourselves time to deal with this pandemic before the next one comes."




Contacts and sources:
Hilary Katulak
Jeremy Schwab
Boston University






Trustworthy Volcanoes Hiding Explosive Secret Say Volcanologists

An international team of volcanologists working on remote islands in the Galápagos Archipelago has found that volcanoes which reliably produce small basaltic lava eruptions hide chemically diverse magmas in their underground plumbing systems - including some with the potential to generate explosive activity.

Many volcanoes produce similar types of eruption over millions of years. For example, volcanoes in Iceland, Hawai'i and the Galápagos Islands consistently erupt lava flows - comprised of molten basaltic rock - which form long rivers of fire down their flanks. Although these lava flows are potentially damaging to houses close to the volcano, they generally move at a walking pace and do not pose the same risk to life as larger explosive eruptions, like those at Vesuvius or Mt. St. Helens. This long-term consistency in a volcano's eruptive behaviour informs hazard planning by local authorities.

The 2015 eruption at Wolf volcano in the Galapagos Archipelago. 
Credit:  Gabriel Salazar, La Pinta Yacht Expedition


The research team, led by Dr Michael Stock from Trinity College Dublin and comprising scientists from the US, UK and Ecuador, studied two Galápagos volcanoes, which have only erupted compositionally uniform basaltic lava flows at the Earth's surface for their entire lifetimes. By deciphering the compositions of microscopic crystals in the lavas, the team was able to reconstruct the chemical and physical characteristics of magmas stored underground beneath the volcanoes.

The results of the study show that - in contrast with the monotonous basaltic lavas erupted at the Earth's surface - magmas beneath the volcanoes are extremely diverse and include compositions similar to those erupted at Mt. St. Helens.

The team believes that volcanoes consistently erupt compositionally uniform basaltic lavas when the amount of magma flushing through the ground beneath the edifice is high enough to "overprint" any chemical diversity. This can occur when volcanoes are located close to a "hot spot" - a plume of hot magma rising towards the surface from deep within the Earth.

The team collects samples from solidified lava flows on Wolf volcano with assistance from a Galápagos National Park ranger. 
Credit:  Dr Benjamin Bernard.

However, the chemically diverse magmas which the team discovered could become mobile and ascend towards the surface under certain circumstances. In this case, volcanoes that have reliably produced basaltic lava eruptions for millennia might undergo unexpected changes to more explosive activity in the future.

Dr Stock, from Trinity's School of Natural Sciences, and lead author on the paper, said:

"This was really unexpected. We started the study wanting to know why these volcanoes were so boring and what process caused the erupted lava compositions to remain constant over long timescales. Instead we found that they aren't boring at all - they just hide these secret magmas under the ground."

"Although there's no sign that these Galápagos volcanoes will undergo a transition in eruption style any time soon, our results show why other volcanoes might have changed their eruptive behaviour in the past. The study will also help us to better understand the risks posed by volcanoes in other parts of the world - just because they've always erupted a particular way in the past doesn't mean you can rely on them to continue doing the same thing indefinitely into the future."

Dr Benjamin Bernard, a volcanologist involved in monitoring Galápagos volcanoes at Instituto Geofísico and co-author on the paper, added:

"This discovery is a game-changer because it allows us to reconcile apparently divergent observations, such as the presence of explosive deposits at several Galápagos volcanoes. It also allows us to better understand the behaviour of these volcanoes, which is essential for volcano monitoring and hazard assessment."

This work was published in the leading international journal Nature Communications and was funded by the Charles Darwin and Galápagos Islands Fund at Christ's College, University of Cambridge. It was conducted with support from the Ecuadorian Instituto Geofísico, Galápagos National Park and Charles Darwin Foundation.



Contacts and sources:
Michael StockTrinity College Dublin

Publication: Cryptic evolved melts beneath monotonous basaltic shield volcanoes in the Galápagos Archipelago Michael J. Stock, Dennis Geist, David A. Neave, Matthew L. M. Gleeson, Benjamin Bernard, Keith A. Howard, Iris Buisman & John Maclennan Nature Communications volume 11, Article number: 3767 (2020 https://www.nature.com/articles/s41467-020-17590-x http://dx.doi.org/10.1038/s41467-020-17590-x





Tuesday, July 28, 2020

People with Neanderthal Gene Variant Feel More Pain

People who inherited a special ion channel from Neanderthals experience more pain.

Pain is mediated through specialized nerve cells that are activated when potentially harmful things affect various parts of our bodies. These nerve cells have a special ion channel that has a key role in starting the electrical impulse that signals pain and is sent to the brain. According to a new study by researchers at the Max Planck Institute for Evolutionary Anthropology in Germany and the Karolinska Institutet in Sweden people who inherited the Neanderthal variant of this ion channel experience more pain.


Neanderthals and modern humans have mixed and exchanged genes several times over the millennia. Researchers have discovered that people who have inherited a gene variant for an ion channel from Neanderthals have a lower pain threshold.
Credit: © Science Photo Library / Daynes, Elisabeth

As several Neanderthal genomes of high quality are now available researchers can identify genetic changes that were present in many or all Neanderthals, investigate their physiological effects and look into their consequences when they occur in people today. Looking into one gene that carries such changes, Hugo Zeberg, Svante Pääbo and colleagues found that some people, especially from central and south America but also in Europe, have inherited a Neanderthal variant of a gene that encodes an ion channel that initiates the sensation of pain.

By using data from a huge population study in the UK, the authors show that people in the UK who carry the Neanderthal variant of the ion channel experience more pain. “The biggest factor for how much pain people report is their age. But carrying the Neanderthal variant of the ion channel makes you experience more pain similar to if you were eight years older”, says lead author Hugo Zeberg, a researcher at the Max Planck Institute for Evolutionary Anthropology and Karolinska Institutet. “The Neanderthal variant of the ion channel carries three amino acid differences to the common, ‘modern’ variant”, explains Zeberg. “While single amino acid substitutions do not affect the function of the ion channel, the full Neanderthal variant carrying three amino acid substitutions leads to heightened pain sensitivity in present-day people.”

On a molecular level, the Neanderthal ion channel is more easily activated which may explain why people who inherited it have a lowered pain threshold. “Whether Neanderthals experienced more pain is difficult to say because pain is also modulated both in the spinal cord and in the brain”, says Pääbo. “But this work shows that their threshold for initiating pain impulses was lower than in most present-day humans.”


Contacts and sources:
Sandra Jacobs
Max Planck Institute for Evolutionary Anthropology

Publication: A Neanderthal Sodium Channel Increases Pain Sensitivity in Present-Day Humans.
Hugo Zeberg, Michael Dannemann, Kristoffer Sahlholm, Kristin Tsuo, Tomislav Maricic, Victor Wiebe, Wulf Hevers, Hugh P.C. Robinson, Janet Kelso, Svante Pääbo. Current Biology, 2020; DOI: 10.1016/j.cub.2020.06.045





Researchers Identify Evolutionary Origins of SARS-CoV-2, First Emerged 40-70 Years Ago

By reconstructing the evolutionary history of SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic, an international research team of Chinese, European and U.S. scientists has discovered that the lineage that gave rise to the virus has been circulating in bats for decades and likely includes other viruses with the ability to infect humans. The findings have implications for the prevention of future pandemics stemming from this lineage.

"Coronaviruses have genetic material that is highly recombinant, meaning different regions of the virus's genome can be derived from multiple sources," said Maciej Boni, associate professor of biology, Penn State. "This has made it difficult to reconstruct SARS-CoV-2's origins. You have to identify all the regions that have been recombining and trace their histories. To do that, we put together a diverse team with expertise in recombination, phylogenetic dating, virus sampling, and molecular and viral evolution."

The team used three different bioinformatic approaches to identify and remove the recombinant regions within the SARS-CoV-2 genome. Next, they reconstructed phylogenetic histories for the non-recombinant regions and compared them to each other to see which specific viruses have been involved in recombination events in the past. They were able to reconstruct the evolutionary relationships between SARS-CoV-2 and its closest known bat and pangolin viruses. Their findings appear today (July 28) in Nature Microbiology.

The researchers found that the lineage of viruses to which SARS-CoV-2 belongs diverged from other bat viruses about 40-70 years ago. Importantly, although SARS-CoV-2 is genetically similar (about 96%) to the RaTG13 coronavirus, which was sampled from a Rhinolophus affinis horseshoe bat in 2013 in Yunnan province, China, the team found that it diverged from RaTG13 a relatively long time ago, in 1969.

By reconstructing the evolutionary history of SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic, an international research team of Chinese, European and U.S. scientists has discovered that the lineage that gave rise to the virus has been circulating in bats for decades and likely includes other viruses with the ability to infect humans.
Two horseshoe bats hanging upside down
Image: Creative =Nature_nl, iStock

"The ability to estimate divergence times after disentangling recombination histories, which is something we developed in this collaboration, may lead to insights into the origins of many different viral pathogens," said Philippe Lemey, principal investigator in the Department of Evolutionary and Computational Virology, KE Leuven.

The team found that one of the older traits that SARS-CoV-2 shares with its relatives is the receptor-binding domain (RBD) located on the Spike protein, which enables the virus to recognize and bind to receptors on the surfaces of human cells.

"This means that other viruses that are capable of infecting humans are circulating in horseshoe bats in China," said David L. Robertson, professor of computational virology, MRC-University of Glasgow Centre for Virus Research.

Will these viruses be capable of jumping directly from bats into humans or will an intermediate species be required to make the leap? According to Robertson, for SARS-CoV-2, other research groups incorrectly proposed that key evolutionary changes occurred in pangolins.

"SARS-CoV-2's RBD sequence has so far only been found in a few pangolin viruses," said Robertson. "Furthermore, the other key feature thought to be instrumental to SARS-CoV-2's ability to infect humans -- a polybasic cleavage site insertion in the Spike protein -- has not yet been seen in another close bat relative of the SARS-CoV-2 virus. Yet, while it is possible that pangolins may have acted as an intermediate host facilitating transmission of SARS-CoV-2 to humans, no evidence exists to suggest that pangolin infection is a requirement for bat viruses to cross into humans. Instead, our research suggests that SARS-CoV-2 likely evolved the ability to replicate in the upper respiratory tract of both humans and pangolins."

The team concluded that preventing future pandemics will require better sampling within wild bats and the implementation of human disease surveillance systems that are able to identify novel pathogens in humans and respond in real time.

"The key to successful surveillance," said Robertson, "is knowing which viruses to look for and prioritizing those that can readily infect humans. We should have been better prepared for a second SARS virus."

Boni added, "We were too late in responding to the initial SARS-CoV-2 outbreak, but this will not be our last coronavirus pandemic. A much more comprehensive and real-time surveillance system needs to be put in place to catch viruses like this when case numbers are still in the double digits."

Support for this research was provided by the European Research Council, the Medical Research Council, the Research Foundation -- Flanders and the National Natural Science Foundation of China.



Contacts and sources:
Sara LaJeunesse
Penn State


Publication: Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic Maciej F. Boni, Philippe Lemey, Xiaowei Jiang, Tommy Tsan-Yuk Lam, Blair W. Perry, Todd A. Castoe, Andrew Rambaut & David L. Robertson Nature Microbiology (2020) https://www.nature.com/articles/s41564-020-0771-4 http://dx.doi.org/10.1038/s41564-020-0771-4
Other authors on the paper include: Xiaowei Jiang, lecturer in bioinformatics, Xi'an Jiaotong-Liverpool University; Tommy Tsan-Yuk Lam, assistant professor of public health, University of Hong Kong; Blair Perry, graduate student, University of Texas Arlington; Todd Castoe, associate professor of biology, University of Texas Arlington; and Andrew Rambaut, professor of molecular evolution, Institute of Evolutionary Biology, University of Edinburgh.