. Scientific Frontline

Friday, August 27, 2021

Covid-19, not vaccination, presents biggest blood clot risks

Researchers from the University of Oxford have today announced the results of a study into

thrombocytopenia (a condition with low platelet counts) and thromboembolic events (blood clots) following vaccination for Covid-19, some of the same events which have led to restricted use of the Oxford-AstraZeneca vaccine in a number of countries.

  1. Study compares risks of thrombocytopenia and thromboembolic events following ChAdOx1 nCov-19 (Oxford-AstraZeneca), BNT162b2 mRNA (Pfizer-BioNTech) vaccination, and SARS-CoV-2 (Covid-19) infection
  2. Study shows increased risk of thrombocytopenia and venous thromboembolism with ChAdOx1 nCoV-19, and increased risk of arterial thromboembolism following BNT162b2 mRNA
  3. Risks of these adverse events were however much higher following SARS-CoV-2 infection
  4. Study authors fully independent from Oxford vaccine developers

Researchers from the University of Oxford have today announced the results of a study into thrombocytopenia (a condition with low platelet counts) and thromboembolic events (blood clots) following vaccination for Covid-19, some of the same events which have led to restricted use of the Oxford-AstraZeneca vaccine in a number of countries. 

Writing in the British Medical Journal (BMJ), they detail the findings from over 29 million people vaccinated with first doses of either the ChAdOx1 nCov-19 ‘Oxford-AstraZeneca’ vaccine or the BNT162b2 mRNA ‘Pfizer-BioNTech’ vaccine. They conclude that with both of these vaccines, for short time intervals following the first dose, there are increased risks of some hematological and vascular adverse events leading to hospitalization or death.

Julia Hippisley-Cox, Professor of Clinical Epidemiology and General Practice at the University of Oxford, lead author of the paper, said:

‘People should be aware of these increased risks after Covid-19 vaccination and seek medical attention promptly if they develop symptoms, but also be aware that the risks are considerably higher and over longer periods of time if they become infected with SARS-CoV-2’ 

The authors further note that the risk of these adverse events is substantially higher and for a longer period of time, following infection from the SARS-CoV-2 ‘coronavirus’ than after either vaccine.

All of the coronavirus vaccines currently in use have been tested in randomized clinical trials, which are unlikely to be large enough to detect very rare adverse events. When rare events are uncovered, then regulators perform a risk-benefit analysis of the medicine; to compare the risks of the adverse events if vaccinated versus the benefits of avoidance of the disease – in this case, Covid-19.

In this paper, the team of authors from the University of Oxford, University of Leicester, Guys and St Thomas’ NHS Foundation Trust, the Intensive Care National Audit & Research Centre, the London School of Hygiene and Tropical Medicine, the University of Cambridge, the University of Edinburgh and the University of Nottingham, compared rates of adverse events after vaccination with Pfizer-BioNTech and Oxford-AstraZeneca vaccines with rates of the same events after a positive SARS-CoV-2 test result.

For this, they used routinely collected electronic health records to evaluate the short-term risks (within 28 days) of hospital admission with thrombocytopenia, venous thromboembolism (VTE) and arterial thromboembolism (ATE), using data collected from across England between December 1, 2020 and April 24, 2021. Other outcomes studied were cerebral venous sinus thrombosis (CVST), ischemic stroke, myocardial infarction and other rare arterial thrombotic events.

Prof. Hippisley-Cox added:

‘This research is important as many other studies, while useful, have been limited by small numbers and potential biases. Electronic healthcare records, which contain detailed recording of vaccinations, infections, outcomes and confounders, have provided us with a rich source of data with which to perform a robust evaluation of these vaccines, and compare to risks associated with Covid-19 infection.’

The authors detail the following limitations to their study:

  1. restricting the analysis to first vaccine dose only
  2. a short vaccination exposure window
  3. the lack of formal adjudication of routinely acquired outcomes, and the potential for misclassification of outcomes or exposures
  4. admissions where patients were still in hospital by the study end date being excluded.
  5. However, they believe that any bias, if present, is likely to not change with respect to each vaccine and so the comparisons between vaccines are unlikely to be affected.

Andrew Morris, Director, Health Data Research UK and Lead, Data and Connectivity National Core Study:

‘Congratulations to the team at Oxford who have worked with colleagues across the UK on this important research. This is truly health data science in action – the use of secure, large scale, linked datasets to develop real-world insights on the safety of COVID-19 vaccines. The analyses in this paper are a vital addition to all of the work enabled by HDR UK to enhance our understanding of the virus, and a key output from the Data and Connectivity National Core Study.’

Aziz Sheikh, Professor of Primary Care Research & Development and Director of the Usher Institute at The University of Edinburgh and a co-author of the paper, said:

‘This enormous study, using data on over 29 million vaccinated people, has shown that there is a very small risk of clotting and other blood disorders following first dose Covid-19 vaccination.  Though serious, the risk of these same outcomes is much higher following SARS-CoV-2 infection.

‘On balance, this analysis therefore clearly underscores the importance of getting vaccinated to reduce the risk of these clotting and bleeding outcomes in individuals, and because of the substantial public health benefit that Covid-19 vaccinations offer.’

Source / Credit: University of Oxford

Together, but still apart

 Social disconnection is a lack of social, emotional and physical engagement with other people. This

results in isolation and loneliness. Risk factors such as the shrinking of family sizes, lack of family support and declining health have made it hard for older adults to keep up with social and economic activities and maintain social connections, which ultimately results in social disconnection and isolation. The social distancing measures brought about by the ongoing COVID-19 pandemic have exacerbated social isolation, especially among the elderly.

In the Singapore Chinese Health Study done by a team led by Professor Koh Woon Puay, from the Healthy Longevity Translational Research Program at the NUS Yong Loo Lin School of Medicine and Associate Professor Feng Qiushi of the Faculty of Arts and Social Sciences showed that from 16,943 community-dwelling seniors, 78.8% of socially disconnected older adults are living with family, compared to 14.4% of socially disconnected adults who are living alone. Hence, although older adults living alone are more likely to be socially disconnected, in Singapore, the majority of socially isolated older adults still stay with their families. Among those living alone, men were twice as likely to experience social disconnection, compared to the women. This study was published in Gerontology on 16 June 2021.

In this cohort, the team also studied the factors associated with social isolation in this cohort, to see if they had similar effects among those living alone and those living with their families. The salient findings were:

Regardless of the living arrangements, factors such as low education level, cognitive impairment, fair or poor self-rated health, depression, and limitations with daily living activities were independently associated with social disconnection.

Among those living alone, men were twice as likely to experience social disconnection compared to women.

From these findings, Prof Koh recommends targeting community interventions to elderly men living alone, and extending its scope to older adults in poor health who live with their families. The Singapore Government has made much effort in the area of eldercare which has helped most older people to stay socially connected. Despite this, social alienation is increasingly present due to the demographic trends of population ageing and solo-living and extra effort is needed to help vulnerable individuals, especially older men. Interventions that encourage individual and personal productivity, such as paid work, volunteerism and learning new skills should be promoted among older adults to create opportunities for social interaction and maintenance of cognitive functions, Prof Koh adds.

In addition to social isolation, older adults are also at increased risk of chronic age-related diseases, as well as gradual loss of bodily functions and independence in activities of daily living. Prof Koh and Associate Professor Feng have collaborated with other scientists within NUS and other research institutions to establish the SG70 Towards Healthy Longevity cohort study, as the next study to examine the effects of biological, lifestyle and socioeconomic factors that prevent people from ageing healthily and productively. This cohort will recruit 3,000 participants, from the ages of 65 to 75 years old comprising of the three major ethnic groups in Singapore. This age group has been identified as the vulnerable period where the average Singaporean may transit from good health to poor health, and the research team will study this ageing process in the SG70 participants for the next 10 to 15 years.

The eventual aim of this SG70 cohort study is to gather scientific evidence that will form the basis for intervention studies in the near future that may slow, halt or reverse the ageing process, in order to help people age more healthily, avoid age-related diseases and maintain a good quality of life in their twilight years.

Source / Credit: NUS Yong Loo Lin School of Medicine

Thursday, August 26, 2021

Plants evolved ability to actively control water-loss earlier than previously thought


Fern stomata Credit: University of Birmingham
New research has shed light on when plants first evolved the ability to respond to changing humidity in the air around them, and was probably a feature of a common ancestor of both flowering plants and ferns.

New research has shed light on when plants first evolved the ability to respond to changing humidity in the air around them, and was probably a feature of a common ancestor of both flowering plants and ferns.

Key to the regulation mechanism are tiny holes, or pores, on the surface of leaves, called stomata. These enable the plant to regulate the uptake of CO2 gas as fuel for photosynthesis, and the loss of water vapour – a constant balancing act that requires the pores to open and close according to changing conditions. This ability is important to agriculture because it helps crops to use less water to grow.

Plants first evolved stomata soon after they moved from water to land, some 450 million years ago, but scientists are still uncertain about the evolutionary pathway they took and the point at which plants became able to choose whether to open or close the pores in response to their environment.

In the most recently evolved plants – flowering plants – stomata closure in response to drought is actively triggered by a number of internal signals, including a hormone called abscisic acid (ABA), but scientists have been struggling to understand if this mechanism is also present in older groups of plants. In a new study, published in Current Biology, researchers at the University of Birmingham have found evidence that the fern species Ceratopteris richardii actively closes its stomata using similar signals.

This semi-aquatic tropical fern has recently become the first model for exploring genetic control of development in the fern family, and is now helping scientists to unpick the long evolutionary history between the earliest land-living plants (mosses, liverworts and hornworts) and the modern flowering plants that dominate today’s ecosystems.

The team used RNA sequencing technology to identify the genetic mechanisms behind different stomatal responses and was able to demonstrate the fern’s ability to close stomata in response to low humidity or in response to ABA involves copies of genes already known to control stomata in flowering plants.

The results suggest that both ferns and flowering plants evolved using similar stomatal closure methods. This indicates that these mechanisms were present – at least in some form – in the stomata of the last common ancestor of both groups.

Dr Andrew Plackett, of the University of Birmingham’s School of Biosciences, led the research in collaboration with groups at the University of Bristol and the University of Oxford. He said: “We know that plants have possessed stomata for most of their evolutionary history, but the point in evolution where plants became able to actively open and close them has been controversial.

“We’ve been able to show the same active closure mechanisms found in flowering plants are also present in ferns, a much older group of plants. Being able to better understand how these mechanisms have changed during plant evolution gives us useful tools to learn more about how they work. This will be important for helping our crops to adapt to future environmental changes.”

Prof Alistair Hetherington of Bristol’s School of Biological Sciences added: “This new work confirms that the earliest plants were able to actively control the water they lost through the microscopic valve like structures on the surfaces of leaves known as stomata. This is important because it shows that the intracellular machinery allowing stomata to open and close was present in the earliest land plants. The research also shows that, whether stomata respond actively or passively is dictated by the environment in which the plants lived. "

Source / Credit: University of Bristol

Farmed carnivores may become disease reservoirs posing human health risk

 Farming large numbers of carnivores, like mink, could allow the formation of undetected ‘disease reservoirs’, in which a pathogen could spread to many animals and mutate to become a risk to human health.

Research led by the University of Cambridge has discovered that carnivores have a defective immune system, which makes them likely to be asymptomatic carriers of disease-causing pathogens.

Three key genes in carnivores that are critical for gut health were found to have lost their function. If these genes were working, they would produce protein complexes called inflammasomes to activate inflammatory responses and fight off pathogens. The study is published today in the journal Cell Reports.

The researchers say that the carnivorous diet, which is high in protein, is thought to have antimicrobial properties that could compensate for the loss of these immune pathways in carnivores – any gut infection is expelled by the production of diarrhoea. But the immune deficiency means that other pathogens can reside undetected elsewhere in these animals.

“We’ve found that a whole cohort of inflammatory genes is missing in carnivores - we didn’t expect this at all,” said Professor Clare Bryant in the University of Cambridge’s Department of Veterinary Medicine, senior author of the paper. 

She added: “We think that the lack of these functioning genes contributes to the ability of pathogens to hide undetected in carnivores, to potentially mutate and be transmitted becoming a human health risk.”

Zoonotic pathogens are those that live in animal hosts before jumping to infect humans. The COVID-19 pandemic, thought to originate in a wild animal, has shown the enormous damage that can be wrought by a novel human disease. Carnivores include mink, dogs, and cats, and are the biggest carriers of zoonotic pathogens. 

Three genes appear to be in the process of being lost entirely in carnivores: the DNA is still present but it is not expressed, meaning they have become ‘pseudogenes’ and are not functioning. A third gene important for gut health has developed a unique mutation, causing two proteins called caspases to be fused together to change their function so they can no longer respond to some pathogens in the animal’s body.

“When you have a large population of farmed carnivorous animals, like mink, they can harbour a pathogen - like SARS-CoV-2 and others - and it can mutate because the immune system of the mink isn’t being activated. This could potentially spread into humans,” said Bryant.

The researchers say that the results are not a reason to be concerned about COVID-19 being spread by dogs and cats. There is no evidence that these domestic pets carry or transmit COVID-19. It is when large numbers of carnivores are kept together in close proximity that a large reservoir of the pathogen can build up amongst them, and potentially mutate.

This research was funded by Wellcome.

Source / Credit: University of Cambridge

Climate change is accelerating, according to comprehensive study

 Climate change is happening and accelerating. Earth will continue to warm. And these changes are unequivocally caused by human activities. Those are among the conclusions of the report published by the International Panel on Climate Change (IPCC), with University of Hawaiʻi at Mānoa Assistant Professor of oceanography Malte Stuecker as a contributing author.

Ocean temperature (blue=cold, red=warm) simulated at ultra-high resolution. Photo credit: IBS/ICCP‘s Aleph

“The latest IPCC report shows clearly that if we do not drastically curb our emissions, we will head towards temperatures that Earth has not seen in millions of years,” Stuecker summarizes. “Moreover, we can now say with certainty that all of the global warming that occurred since the mid-19th century is due to human activity. While these are sobering facts, we should certainly not despair. In fact, if societies choose a pathway of large reductions in greenhouse gas emissions now, the report also shows that we will avoid the worst possible future outcomes and Earth will experience only moderate additional warming over this century that we can likely adapt to.”

In addition to global warming, regional climate in many parts of the world is impacted by the cycling between warm El Niño and cold La Niña conditions in the eastern Pacific Ocean—commonly referred to as the El Niño-Southern Oscillation (ENSO). ENSO—has persisted without major interruptions for thousands to millions of years. This may also change in a future warmer world, though the recent IPCC report highlights uncertainties in potential changes in ENSO.

Rainfall will be more extreme as the climate warms. (Photo credit: Max LaRochelle via Unsplash)

Two additional studies

Continuing the long tradition of contributing to developing theories and advancing climate models around ENSO, researchers from the UH Mānoa School of Ocean and Earth Science and Technology (SOEST) recently published two additional studies addressing the complexity of this most important climate phenomenon.

SOEST atmospheric scientists, Associate Professor Christina Karamperidou and Professor Fei-Fei Jin, and Stuecker co-authored a review paper published in Nature Reviews Earth & Environment wherein they synthesized recent advancements in research on ENSO.

There is an emerging consensus among simulations of future climate under strong greenhouse gas emissions with the most recent generation of climate models that the variability of future ENSO sea surface temperature may increase as the climate warms.

“There is however still much uncertainty on the degree to which ENSO may change and the time at which these potential changes will emerge from ENSO’s natural variability,” said Karamperidou. “This is partly due to incomplete understanding of the phenomenon, partly due to known limitations of models in representing and resolving relevant processes, and partly due to the inherent limitations on our understanding imposed by the short length of the instrumental record.”

Additionally, led by researchers at the IBS Center for Climate Physics in Korea, Stuecker co-authored another study published in Nature Climate Change that produced a series of global climate model simulations with unprecedented spatial resolution. Boosted by the power of one of South Korea’s fastest supercomputers (Aleph), the new ultra-high-resolution simulations realistically represented processes that are usually missing from other models, though they play fundamental roles in the generation and termination of El Niño and La Niña events.

“From this highest resolution future climate model simulation that has been done to date, we conclude that it’s possible that ENSO variability could collapse under strong greenhouse warming in the future,” said Stuecker.

Further investigation is needed

This apparent contradiction in findings raises many interesting questions and highlights the need for further investigation.

“Regardless of the details of how El Niño changes in the future, rainfall and drought will become more extreme in the future due to the fact that we will be living in a warmer world with a hydrological cycle on steroids,” said Stuecker.

“Despite the spread of model projections on how ENSO may change under strong anthropogenic forcing, both the IPCC report and the Nature Reviews article demonstrate that its impacts on rainfall are very likely to be enhanced which has significant implications across the globe and the Pacific, including Hawaiʻi,” said Karamperidou.

Source / Credit: University of Hawaiʻi

Wednesday, August 25, 2021

Astrophysical data to unravel the universe’s mysteries

 The University of Washington and Carnegie Mellon University have announced an expansive,

Rubin Observatory summit facility in Cerro Pachón, Chile.Rubin Observatory/NSF/AURA

multiyear collaboration to create new software platforms to analyze large astronomical datasets generated by the upcoming Legacy Survey of Space and Time, or LSST, which will be carried out by the Vera C. Rubin Observatory in northern Chile. The open-source platforms are part of the new LSST Interdisciplinary Network for Collaboration and Computing — known as LINCC — and will fundamentally change how scientists use modern computational methods to make sense of big data.

Through the LSST, the Rubin Observatory, a joint initiative of the National Science Foundation and the Department of Energy, will collect and process more than 20 terabytes of data each night — and up to 10 petabytes each year for 10 years — and will build detailed composite images of the southern sky. Over its expected decade of observations, astrophysicists estimate the Department of Energy’s LSST Camera will detect and capture images of an estimated 30 billion stars, galaxies, stellar clusters and asteroids. Each point in the sky will be visited around 1,000 times over the survey’s 10 years, providing researchers with valuable time series data.

Scientists plan to use this data to address fundamental questions about our universe, such as the formation of our solar system, the course of near-Earth asteroids, the birth and death of stars, the nature of dark matter and dark energy, the universe’s murky early years and its ultimate fate, among other things.

“Tools that utilize the power of cloud computing will allow any researcher to search and analyze data at the scale of the LSST, not just speeding up the rate at which we make discoveries but changing the scientific questions that we can ask,” said Andrew Connolly, a UW professor of astronomy, director of the eScience Institute and former director of the Data Intensive Research in Astrophysics and Cosmology Institute — commonly known as the DiRAC Institute.

The Rubin Observatory will produce an unprecedented data set through the LSST. To take advantage of this opportunity, the LSST Corporation created the LSST Interdisciplinary Network for Collaboration and Computing, whose launch was announced Aug. 9 at the Rubin Observatory Project & Community Workshop. One of LINCC’s primary goals is to create new and improved analysis infrastructure that can accommodate the data’s scale and complexity that will result in meaningful and useful pipelines of discovery for LSST data.

“Many of the LSST’s science objectives share common traits and computational challenges. If we develop our algorithms and analysis frameworks with forethought, we can use them to enable many of the survey’s core science objectives,” said Rachel Mandelbaum, professor of physics and member of the McWilliams Center for Cosmology at Carnegie Mellon.

Connolly and Mandelbaum will co-lead the project, which will consist of programmers and scientists based at the UW and Carnegie Mellon, who will create platforms using professional software engineering practices and tools. Specifically, they will create a “cloud-first” system that also supports high-performance computing systems in partnership with the Pittsburgh Supercomputing Center, a joint effort of Carnegie Mellon and the University of Pittsburgh, and the National Science Foundation’s NOIRLab. The LSST Corporation will run programs to engage the LSST Science Collaborations and broader science community in the design, testing and use of the new tools.

The complete focal plane of the LSST Camera is more than 2 feet wide and contains 189 individual sensors that will produce 3200-megapixel images.Jacqueline Orrell/SLAC National Accelerator Laboratory/NSF/DOE/Rubin Observatory/AURA

The LINCC analysis platforms are supported by Schmidt Futures, a philanthropic initiative founded by Eric and Wendy Schmidt that “bets early on exceptional people making the world better.” This project is part of Schmidt Futures’ work in astrophysics, which aims to accelerate our knowledge about the universe by supporting the development of software and hardware platforms to facilitate research across the field of astronomy.

“Many years ago, the Schmidt family provided one of the first grants to advance the original design of the Vera C. Rubin Observatory. We believe this telescope is one of the most important and eagerly awaited instruments in astrophysics in this decade. By developing platforms to analyze the astronomical datasets captured by the LSST, Carnegie Mellon University and the University of Washington are transforming what is possible in the field of astronomy,” said Stuart Feldman, chief scientist at Schmidt Futures. "The software funded by this gift will magnify the scientific return on the public investment by the National Science Foundation and the Department of Energy to build and operate Rubin Observatory’s revolutionary telescope, camera and data systems,” said Adam Bolton, director of the Community Science and Data Center at NSF’s NOIRLab. The center will collaborate with LINCC scientists and engineers to make the LINCC framework accessible to the broader astronomical community.

Through this new project, new algorithms and processing pipelines developed at LINCC will be able to be used across fields within astrophysics and cosmology to sift through false signals, filter out noise in the data and flag potentially important objects for follow-up observations. The tools developed by LINCC will support a “census of our solar system” that will chart the courses of asteroids; help researchers to understand how the universe changes with time; and build a 3D view of the universe’s history.

“Our goal is to maximize the scientific output and societal impact of Rubin LSST, and these analysis tools will go a huge way toward doing just that,” said Jeno Sokoloski, director for science at the LSST Corporation. “They will be freely available to all researchers, students, teachers and members of the general public.”

Northwestern University and the University of Arizona, in addition to the UW and Carnegie Mellon, are hub sites for LINCC. The University of Pittsburgh will partner with the Carnegie Mellon hub.

UW, Carnegie Mellon to pioneer platforms that harness astrophysical data to unravel the universe’s mysteries

Source / Credit: University of Washington

Antarctic Ocean Flows: an excerpt from Atlas of a Changing Earth

In this visualization of Antarctica, we cruise along the coastline of the Amundsen Sea from Cape Dart to the Pine Island Glacier. Initially we pass the massive Getz Ice Shelf on our right stretching over 300 miles (500 km) along the coast. As we approach the Smith Glacier and the Dotson Ice Shelf, the sea surface becomes transparent allowing us to see the ocean flows moving under the surface. These flows portray the direction, speed and temperature of the ocean circulation based on version 3 of the ECCO ocean circulation model. The flows are colored by temperature, spanning the range from 29.75 degrees Fahrenheit (-1.25 degrees Celsius) shown in blue to 34.25 degrees Fahrenheit (+1.25 degrees Celsius) shown in red. We see the ocean flows circulating around the Pine Island Bay and under the adjacent floating ice tongue of the Thwaites Glacier.  

As we approach the Pine Island Glacier, we dip below the surface of the bay and see the stratification of the temperature in the ocean flows, with the coldest water shown in blue near the surface and the warmer water shown in red at lower depths. We move forward under the floating ice of the Pine Island Glacier and see how the warmer ocean flows are circulating under the glacier's floating tongue, eroding the ice from beneath.  

The topography in this visualization has been exaggerated by 4x above sea level and 15x below sea level in order to more clearly observe the change in ocean temperature at various depths.

Credit / Source: NASA's Scientific Visualization Studio

Peabody fossils illuminate dinosaur evolution in eastern North America

Tyrannosaurus rex, the fearsome predator that once roamed what is now western North America, appears to have had an East Coast cousin.

A new study by Yale undergraduate Chase Doran Brownstein describes two dinosaurs that once roamed the eastern United States from fossils housed at the Yale Peabody Museum of Natural History: an herbivorous hadrosaur (depicted in the silhouette) and a tyrannosaur.

A new study by Yale undergraduate Chase Doran Brownstein describes two dinosaurs that inhabited Appalachia — a once isolated land mass that today composes much of the eastern United States — about 85 million years ago: a herbivorous duck-billed hadrosaur and a carnivorous tyrannosaur. The findings were published Aug. 25 in the journal Royal Society Open Science.

Chase Doran Brownstein

The two dinosaurs, which Brownstein described from specimens housed at Yale’s Peabody Museum of Natural History, help fill a major gap in the North American fossil record from the Late Cretaceous and provide evidence that dinosaurs in the eastern portion of the continent evolved distinctly from their counterparts in western North America and Asia, Brownstein said.

“These specimens illuminate certain mysteries in the fossil record of eastern North America and help us better understand how geographic isolation— large water bodies separated Appalachia from other landmasses — affected the evolution of dinosaurs,” said Brownstein, who is entering his junior year at Yale College. “They’re also a good reminder that while the western United States has long been the source of exciting fossil discoveries, the eastern part of the country contains its share of treasures.”

For most of the second half of the Cretaceous, which ended 66 million years ago, North America was divided into two land masses, Laramidia in the West and Appalachia in the East, with the Western Interior Seaway separating them. While famous dinosaur species like T. rex and Triceratops lived throughout Laramidia, much less is known about the animals that inhabited Appalachia. One reason is that Laramidia’s geographic conditions were more conducive to the formation of sediment-rich fossil beds than Appalachia’s, Brownstein explained.

The specimens described in the new study were discovered largely during the 1970s at the Merchantville Formation in present day New Jersey and Delaware. They constitute one of the only known dinosaur assemblages from the late Santonian to early Campanian stages of the Late Cretaceous in North America. This fossil record period, dating from about 85 to 72 million years ago, is limited, Brownstein noted.

Brownstein examined a partial skeleton of a large predatory therapod, concluding that it is probably a tyrannosaur. He noted that the fossil shares several features in its hind limbs with Dryptosaurus, a tyrannosaur that lived about 67 million years ago in what is now New Jersey. The dinosaur has different hands and feet than T. rex, including massive claws on its forelimbs, suggesting that it represents a distinct family of the predators that evolved solely in Appalachia.

“Many people believe that all tyrannosaurs must have evolved a specific set of features to become apex predators,” Brownstein said. “Our fossil suggests they evolved into giant predators in a variety of ways as it lacks key foot or hand features that one would associate with western North American or Asian tyrannosaurs.”

The partial skeleton of the hadrosaur provided important new information on the evolution of the shoulder girdle in that group of dinosaurs, Brownstein found. The hadrosaur fossils also provide one of the best records of this group from east of the Mississippi and include some of the only infant/perinate (very young) dinosaur fossils found in this region.

Brownstein, who works as a research associate at the Stamford Museum and Nature Center in Stamford, Connecticut, has previously published his paleontological research in several peer-journals, including Scientific Reports, the Journal of Paleontology, and the Zoological Journal of the Linnaean Society. In addition to eastern North American fossils, he currently focuses his research on the evolution of fishes, lizards, and birds. He is particularly interested in how geographic change and other factors contribute to how fast different types of living things evolve.

He currently works in the lab of Thomas J. Near, curator of the Peabody Museum’s ichthyology collections and professor and chair of the Department of Ecology and Evolutionary Biology at Yale. Brownstein also collaborates with Yale paleontologists Jacques Gauthier and Bhart-Anjan Bhullar in the Department of Earth and Planetary Sciences.

While Brownstein is considering pursuing an academic career in evolutionary biology, he says his research is driven by enjoyment.

“Doing research and thinking about these things makes me happy,” he said. “Like biking, it’s something I love to do”

Source / Credit: Yale University
By Mike Cummings

Tuesday, August 24, 2021

Emerging from the deep: Stawell’s dark matter lab takes shape

Construction of the Southern Hemisphere’s first dark matter underground physics laboratory is progressing with the concrete slab now in place and the world-class facility on schedule to welcome scientists by Christmas.

The ancillary area where scientists can shower before going into the lab to work.
Image: Stawell Gold Mines

Dr Leonie Walsh, Victoria’s first lead scientist, first woman president of the Australian Innovation Research Group and representative on the Forum of Australian Chief Scientists is interim chair of the company that will operate and manage the Stawell Underground Physics Laboratory (SUPL).

Dr Walsh recently visited the underground laboratory in regional Victorian, seeing first-hand the work underway to ensure that the lab, one kilometer underground,  has an excellent chance of detecting the universe’s elusive dark matter.

“We saw the cavern walls where the lab is being built, being sprayed with a product called Tekflex to reduce the potential for interference from background radon gas in the rock mass, in experiments,” Dr Walsh said. “As an industrial scientist, I have worked across a broad range of industrial sites around the world, but none as unique as SUPL.”

It takes half an hour to journey underground to the site of the lab. Dr Walsh completed the journey after undergoing the strict safety induction and personal protective equipment (PPE) fit-out.

“Researchers will start their day with a 10km drive down a maze of tunnels in protective equipment to the cavernous laboratory, 1100 meters underground to work on their dark matter experiments with equipment designed and built for the purpose of finding dark matter – this thing that makes up 85 per cent of our universe, but which continues to be a mystery,” she said.

“The disused section of Stawell’s gold mine in regional Victoria, has turned out to be the ideal location to progress our understanding of dark matter.”

The 33 meters long, 10 meters wide lab is funded by a $10 million grant from the Federal and State Governments, supported by a $35 million Australian Research Council for the Centre of Excellence for Dark Matter Particle Physics based at the University of Melbourne.

Tom Kelly, the University of Melbourne’s Senior Project Manager, said that major pieces of the plant as well as plumbing, electrical and communications cable and mechanical ductwork and piping are expected to be in place by early October.

“We anticipate the handover to be on time and to commence the installation of experimental equipment before Christmas,” Mr Kelly said.

The five research institutions that will work at Stawell are Melbourne University, Swinburne University of Technology, Adelaide University, the Australian National University and the Australian Nuclear Science and Technology Organization (ANSTO).

ANSTO’s representative on the SUPL company board, Professor Andrew Peele, accompanied Dr Walsh on the inspection and said: “Science goes to extreme lengths to find answers, and in this case, to a very sheltered environment a kilometer underground. It is impressive to see the progress made first-hand and pleasing to see the preparations for the range of activities that will advance our understanding of dark matter.

“ANSTO is delighted to be part of this project and to share our expertise in ultra-sensitive radiation measurement. This is critical to the operation of the instruments that will be housed in SUPL and will also make possible high-precision radiation measurements needed to better understand environmental and other samples.”

Dr Walsh is pictured above at left with Professor Elisabetta Barberio, the Director of the Stawell Underground Physics Laboratory, and board member designate, Professor Andrew Peele, from the Australian Nuclear Science and Technology Organization (ANSTO).

Source / Credit: The University of Melbourne

Monday, August 23, 2021

Alex Jordan: "Fish are not stupid, they're different!"

Alex Jordan is a behavioral ecologist at the Max Planck Institute of Animal Behavior in Konstanz, Germany. His main interest: he wants to know why animals do what they do. He is especially devoted to fish, having been a hobbyist since a young age, and seeing the value of being able to study animals equally well in the wild as in captivity.

Alex, a few years ago you conducted a study that resonated strongly in the scientific community on the reaction of cleaner wrasses to their mirror image. What did you find out in the process?

We placed marks on the cleaner wrasses' bodies that they could only see in a mirror. The fish then tried to remove these marks. We performed various tests to make sure that the fish only reacted to marks that they saw on their own bodies in the mirror an nothing else.

A mirror test passed in this way is considered by researchers to be evidence of self-awareness. Only a few species score positively in this test, for example apes, corvids, dolphins - and now cleaner wrasses.

What do you conclude from this? Are the fish aware of themselves?

No, I don't think so. I suspect the wrasses have simply learned that a mirror creates an image of something - in this case, themselves. Since dark spots on fish bodies are an important signal for wrasses by nature - they usually represent parasites, which the wrasses feed on - they are naturally particularly interested in this. However, they probably do not possess self-awareness or even self-consciousness.

In any case, the test demonstrates that the fish are extremely adaptive and can exploit new opportunities for themselves. 

What can the mirror test then tell us in the first place?

In my opinion, the mirror test is not well suited for studying self-awareness in animals. We also did the test with African cichlids from Lake Tanganyika. They didn't care about the marks on their bodies at all. Also the cleaner wrasses passed the test only if the marks were brown. They didn’t care about marks of other colors. It is important to remember that other highly evolved animals, such as dogs or cats, do not pass the test either.

There are different reasons why an animal does not react to the marks, so in my opinion the test is not suitable to answer the question about self-awareness. It was developed by humans for humans. For most animals, it just doesn't fit.

How can you find out what other organisms think, feel, perceive?

That is very difficult in principle. Even you and I differ in how we perceive things. But you can at least describe your cognitive status to me. Since we can hardly or not at all communicate with animals, we can only infer what they feel, want, think. Some degree of uncertainty will always remain, because we can't help but take ourselves as the measure of all things. To leave our human world of experience and to put ourselves into the world of a fish is all but easy.

How could we nevertheless get an idea of what is going on inside a fish?

We want to try this with a completely new approach. We will measure the activity of nerve cells in the brain when zebrafish react to conspecifics or when they face their mirror image. If there are different activation patterns in the brain in the two cases, this would indicate that the fish are not seeing a conspecific, but themselves. That would be a strong hint for the fish being self-aware.

Fish are commonly regarded as primitive and not very intelligent. Is this justified?

Not at all. We need to stop seeing ourselves as the pinnacle of evolution and ranking other animals in descending order below. All organisms on earth are the result of millions of years of evolution. They and their predecessors have always managed to defy all odds and adapt. Seen in this light, even a bacterium is highly evolved.

Consequently, fish are not dumber or worse than us, they are just different!

How smart are fish?

We don't know exactly yet, but there are definitely differences between species. Fish that migrate in large anonymous schools through the ocean probably need less higher mental abilities than those that defend territories, for example. So I would expect more from a Tanganyika cichlid than from a mackerel.

It is known from other groups of animals that species with a narrow food spectrum are less capable cognitively than those that eat a variety of foods. Thus, the omnivores among fishes might generally be "smarter" than specialists.

Marine fish often exhibit more complex behaviors than freshwater species - simply because inland waters have not existed as long as the oceans, and therefore they have less time to develop such behaviors.

What can fish do?

Some fish are very sophisticated. They can play and use tools, they predict the actions of others, and they even cheat and reconciliate. Some species thus possess higher cognitive abilities than other vertebrates. They may not be that far from apes and humans.

Fish can also recognize people. They know who to expect food from and who not to expect it from, as many aquarium owners can attest. In our research area in Lake Tanganyika, for example, predatory fish from the genus Lepidiolamprologus have learned that they can prey  when my colleague and I are out diving. In doing so, they don't follow me, but her, because she flushes out most of the fish.

And not only that: some species can also distinguish conspecifics individually. Damselfish, for example, have individual color markings on their faces that are only visible in ultraviolet light, which they use to recognize each other.

Another fascinating example, which we plan to investigate ourselves, is how mullet and wrasses work together in the Mediterranean. When a mullet is foraging and scavenging on the sand, it is often accompanied by a wrasse, which preys on small critters scared up by the mullet. This alone would be nothing special, but the wrasse keeps touching the mullet - it literally caresses it. Probably the mullet knows in this way that there is no danger from above while it burrows underground. The "masseur" thus ensures that the mullet stays in its territory.

What do these findings mean for how we treat fish today?

Even if there is still a lot we don't know, one thing is clear: fish can do more than we have given them credit for up to now. They are sentient animals capable of cognitive engagement with the world around them, including social interactions, fear, suffering, and enjoyment.

Thank you for this interview!

Interview by Harald Rösch


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