Eyes reveal life history of fish

 If you look deep into the eyes of a fish, it will tell you its life story.

Scientists from the University of California, Davis, demonstrate that they can use stable isotopic analysis of the eye lenses of freshwater fish -- including threatened and endangered salmon -- to reveal a fish's life history and what it ate along the way.

They conducted their study, published today in the journal Methods in Ecology and Evolution, through field-based experiments in California's Central Valley. The study carries implications for managing floodplains, fish and natural resources; prioritizing habitat restoration efforts; and understanding how landscape disturbances impact fish.

The technique had previously been used in marine environments, but this is its first use for freshwater fish, many of which are threatened or endangered in California. Lead author Miranda Bell Tilcock, an assistant specialist with the UC Davis Center for Watershed Sciences, helped pioneer the technique for freshwater fish.

"Even the nerdiest fish biologists say, 'You can do what with fish eyes?'" said co-author and team co-lead Rachel Johnson, a research fisheries biologist with NOAA Fisheries' Southwest Fisheries Science Center and associate with the UC Davis Center for Watershed Sciences. "This is an exciting new tool we can use to measure the value of different habitats and focus conservation work."

THE EYES HAVE IT

Much like tree rings, fish eyeballs are archival. The lenses grow in layers throughout a fish's life, recording as chemical signatures the habitats used while each layer was forming and locking in the dietary value of what the fish ate in each habitat.

"It's like a little diet journal the fish keeps for us, which is really nice," Tilcock said.

To uncover that history, researchers perform what Tilcock said is "like peeling the world's tiniest onion." With fine-tipped forceps, they remove layer after layer, revealing a veritable Russian nesting doll of eye lenses. At the end is a tiny ball, like what you'd find in a silica packet, that can shatter like glass. This is the core, where the fish's eyes first began to develop.

Relative to other archival tissue, fish eyeballs are especially rich in protein. The isotopic values in the food webs bind to protein in the eye, leaving tell-tale geochemical fingerprints that isotopic analysis can uncover.

HABITAT IN THE EYES OF THE BEHOLDER

The first field-based experiments using the technique for freshwater fish took place on the Yolo Bypass of California's Central Valley. Here, fall-run, juvenile chinook salmon grew in three distinct food webs: river, floodplain and hatchery.

Scientists then conducted stable isotope analyses on the eye lenses of an adult salmon to reveal its diet history from birth to death. Stable isotopes are forms of atoms that don't decay into other elements and are incorporated into a fish's tissue through its diet. They can be used to trace origins, food webs and migratory patterns of species.

Taking the premise of "you are what you eat," the study's authors looked at the chemical crumbs of carbon, nitrogen and sulfur values in the eye lenses to determine which food webs and habitats the fish used at various life stages.

They found that fish on the floodplain grew quickly and appeared to grow additional laminae, or layers of lenses, during the 39-day study compared to fish reared in the river or hatchery. Also, the Yolo Bypass is home to rice fields, which decompose to add unique sulfur and carbon values -- a strong clue for researchers tracing which habitats fish use.

"This tool is not just unique to salmon in the Central Valley," Tilcock said. "There are many migratory species all over the world that need freshwater habitat. If you can isolate their habitat and value for diet, you can quantify it for long-term success."

For example, co-author and team co-leader Carson Jeffres, field and lab director at UC Davis' Center for Watershed Science, used the technique recently on fish in Brazil to look at changes in the food web there following a dam's construction.

EYES AND EARS WORK TOGETHER

Tilcock, Johnson and Jeffres are part of an "Eyes and Ears" project at UC Davis funded by the California Department of Fish and Wildlife. The project studies fish life history through eye lenses and otoliths, which are found within a fish's ears.

"You use the otolith to trace the river or hatchery where a fish was born based on the unique geology and water chemistry of the tributaries in the San Francisco Bay watershed," Johnson said. "Then you have the eye lens, which tells you where it's eating to help identify floodplain habitats."

"They really work together to present a fuller picture of how salmon move and what they eat as they use different mosaics of habitats across the landscape over their lifetime" said Jeffres. "Now we have the tool we have been looking for to link juvenile floodplain benefits across the salmon life cycle to adulthood. It's the holy grail of measuring restoration success."

Read more at Science Daily

Mira's last journey: Exploring the dark universe

 A team of physicists and computer scientists from the U.S. Department of Energy's (DOE) Argonne National Laboratory performed one of the five largest cosmological simulations ever. Data from the simulation will inform sky maps to aid leading large-scale cosmological experiments.

The simulation, called the Last Journey, follows the distribution of mass across the universe over time -- in other words, how gravity causes a mysterious invisible substance called "dark matter" to clump together to form larger-scale structures called halos, within which galaxies form and evolve.

The scientists performed the simulation on Argonne's supercomputer Mira. The same team of scientists ran a previous cosmological simulation called the Outer Rim in 2013, just days after Mira turned on. After running simulations on the machine throughout its seven-year lifetime, the team marked Mira's retirement with the Last Journey simulation.

The Last Journey demonstrates how far observational and computational technology has come in just seven years, and it will contribute data and insight to experiments such as the Stage-4 ground-based cosmic microwave background experiment (CMB-S4), the Legacy Survey of Space and Time (carried out by the Rubin Observatory in Chile), the Dark Energy Spectroscopic Instrument and two NASA missions, the Roman Space Telescope and SPHEREx.

"We worked with a tremendous volume of the universe, and we were interested in large-scale structures, like regions of thousands or millions of galaxies, but we also considered dynamics at smaller scales," said Katrin Heitmann, deputy division director for Argonne's High Energy Physics (HEP) division.

The code that constructed the cosmos

The six-month span for the Last Journey simulation and major analysis tasks presented unique challenges for software development and workflow. The team adapted some of the same code used for the 2013 Outer Rim simulation with some significant updates to make efficient use of Mira, an IBM Blue Gene/Q system that was housed at the Argonne Leadership Computing Facility (ALCF), a DOE Office of Science User Facility.

Specifically, the scientists used the Hardware/Hybrid Accelerated Cosmology Code (HACC) and its analysis framework, CosmoTools, to enable incremental extraction of relevant information at the same time as the simulation was running.

"Running the full machine is challenging because reading the massive amount of data produced by the simulation is computationally expensive, so you have to do a lot of analysis on the fly," said Heitmann. "That's daunting, because if you make a mistake with analysis settings, you don't have time to redo it."

The team took an integrated approach to carrying out the workflow during the simulation. HACC would run the simulation forward in time, determining the effect of gravity on matter during large portions of the history of the universe. Once HACC determined the positions of trillions of computational particles representing the overall distribution of matter, CosmoTools would step in to record relevant information -- such as finding the billions of halos that host galaxies -- to use for analysis during post-processing.

"When we know where the particles are at a certain point in time, we characterize the structures that have formed by using CosmoTools and store a subset of data to make further use down the line," said Adrian Pope, physicist and core HACC and CosmoTools developer in Argonne's Computational Science (CPS) division. "If we find a dense clump of particles, that indicates the location of a dark matter halo, and galaxies can form inside these dark matter halos."

The scientists repeated this interwoven process -- where HACC moves particles and CosmoTools analyzes and records specific data -- until the end of the simulation. The team then used features of CosmoTools to determine which clumps of particles were likely to host galaxies. For reference, around 100 to 1,000 particles represent single galaxies in the simulation.

"We would move particles, do analysis, move particles, do analysis," said Pope. "At the end, we would go back through the subsets of data that we had carefully chosen to store and run additional analysis to gain more insight into the dynamics of structure formation, such as which halos merged together and which ended up orbiting each other."

Using the optimized workflow with HACC and CosmoTools, the team ran the simulation in half the expected time.

Community contribution

The Last Journey simulation will provide data necessary for other major cosmological experiments to use when comparing observations or drawing conclusions about a host of topics. These insights could shed light on topics ranging from cosmological mysteries, such as the role of dark matter and dark energy in the evolution of the universe, to the astrophysics of galaxy formation across the universe.

"This huge data set they are building will feed into many different efforts," said Katherine Riley, director of science at the ALCF. "In the end, that's our primary mission -- to help high-impact science get done. When you're able to not only do something cool, but to feed an entire community, that's a huge contribution that will have an impact for many years."

The team's simulation will address numerous fundamental questions in cosmology and is essential for enabling the refinement of existing models and the development of new ones, impacting both ongoing and upcoming cosmological surveys.

"We are not trying to match any specific structures in the actual universe," said Pope. "Rather, we are making statistically equivalent structures, meaning that if we looked through our data, we could find locations where galaxies the size of the Milky Way would live. But we can also use a simulated universe as a comparison tool to find tensions between our current theoretical understanding of cosmology and what we've observed."

Looking to exascale

"Thinking back to when we ran the Outer Rim simulation, you can really see how far these scientific applications have come," said Heitmann, who performed Outer Rim in 2013 with the HACC team and Salman Habib, CPS division director and Argonne Distinguished Fellow. "It was awesome to run something substantially bigger and more complex that will bring so much to the community."

As Argonne works towards the arrival of Aurora, the ALCF's upcoming exascale supercomputer, the scientists are preparing for even more extensive cosmological simulations. Exascale computing systems will be able to perform a billion billion calculations per second -- 50 times faster than many of the most powerful supercomputers operating today.

"We've learned and adapted a lot during the lifespan of Mira, and this is an interesting opportunity to look back and look forward at the same time," said Pope. "When preparing for simulations on exascale machines and a new decade of progress, we are refining our code and analysis tools, and we get to ask ourselves what we weren't doing because of the limitations we have had until now."

The Last Journey was a gravity-only simulation, meaning it did not consider interactions such as gas dynamics and the physics of star formation. Gravity is the major player in large-scale cosmology, but the scientists hope to incorporate other physics in future simulations to observe the differences they make in how matter moves and distributes itself through the universe over time.

Read more at Science Daily

Making wheat and peanuts less allergenic

 The United States Department of Agriculture identifies a group of "big eight" foods that causes 90% of food allergies. Among these foods are wheat and peanuts.

Sachin Rustgi, a member of the Crop Science Society of America, studies how we can use breeding to develop less allergenic varieties of these foods. Rustgi recently presented his research at the virtual 2020 ASA-CSSA-SSSA Annual Meeting.

Allergic reactions caused by wheat and peanuts can be prevented by avoiding these foods, of course. "While that sounds simple, it is difficult in practice," says Rustgi.

Avoiding wheat and peanuts means losing out on healthy food options. These two foods are nutritional powerhouses.

Wheat is a great source of energy, fiber, and vitamins. Peanuts provide proteins, good fats, vitamins and minerals.

"People with food allergies can try hard to avoid the foods, but accidental exposure to an allergen is also possible," says Rustgi. Allergen exposure can lead to hospitalization, especially for people with peanut allergies.

"For others, avoiding wheat and peanuts is not easy due to geographical, cultural, or economic reasons," explains Rustgi.

Rustgi and his colleagues are using plant breeding and genetic engineering to develop less allergenic varieties of wheat and peanuts. Their goal is to increase food options for people with allergies.

For wheat, researchers focus on a group of proteins, called gluten.

The gluten in bread flour makes dough elastic. Gluten also contributes to the chewy texture of bread.

But gluten can cause an immune reaction for individuals with Celiac disease. In addition, others experience non-celiac gluten sensitivity, leading to a variety of adverse symptoms.

Researchers have been trying to breed varieties of wheat with lower gluten content. The challenge, in part, lies in the complicated nature of gluten genetics. The information needed to make gluten is embedded in the DNA in wheat cells.

But gluten isn't a single protein -- it's a group of many different proteins. The instructions cells needed to make the individual gluten proteins are contained within different genes.

In wheat, these gluten genes are distributed all over a cell's DNA. Since so many portions of the DNA play a role in creating gluten, it is difficult for plant breeders to breed wheat varieties with lower gluten levels.

"When we started this research, a major question was whether it would be possible to work on a characteristic controlled by so many genes," says Rustgi.

For peanuts, the situation is similar. Peanuts contain 16 different proteins recognized as allergens.

"Not all peanut proteins are equally allergenic," says Rustgi. Four proteins trigger an allergic reaction in more than half of peanut sensitive individuals.

Like the gluten genes in wheat, the peanut allergen genes are spread throughout the peanut DNA.

"Affecting this many targets is not an easy task, even with current technology," says Rustgi.

Rustgi and the research team are testing many varieties of wheat and peanuts to find ones that are naturally less allergenic than others.

These low-allergenic varieties can be bred with crop varieties that have desirable traits, such as high yields or pest resistance. The goal is to develop low-allergenic wheat that can be grown commercially.

In addition to traditional breeding efforts, Rustgi is also using genetic engineering to reduce allergenic proteins in wheat and peanuts.

For example, a technology called CRISPR allows scientists to make very precise changes to a cell's DNA.

Rustgi is using CRISPR to target gluten genes in wheat. Recent improvements in CRISPR technology allow researchers to target many genes at once.

Genes targeted by CRISPR are changed or mutated. This means that cells can no longer 'read' these genes to make the specific proteins.

"Disrupting the gluten genes in wheat could yield wheat with significantly lower levels of gluten. A similar approach would work in peanuts," says Rustgi.

Other approaches include understanding how gluten production is regulated in wheat cells. As it turns out, one protein serves as a 'master regulator' for many gluten genes.

That's important because disrupting this master regulator could lead to reduced amounts of gluten in wheat. Targeting a single gene is much easier than trying to disrupt the several gluten genes.

"Wheat and peanuts are the major sources of proteins to many, especially those living in resource-deprived conditions," says Rustgi. "Finding affordable ways to make wheat and peanuts available for all is very important."

Developing wheat and peanuts with reduced allergen levels is a key step toward this goal.

Read more at Science Daily

Detecting trace amounts of multiple classes of antibiotics in foods

 Widespread use of antibiotics in human healthcare and livestock husbandry has led to trace amounts of the drugs ending up in food products. Long-term consumption could cause health problems, but it's been difficult to analyze more than a few antibiotics at a time because they have different chemical properties. Now, researchers reporting in ACS' Journal of Agricultural and Food Chemistry have developed a method to simultaneously measure 77 antibiotics in a variety of foods.

Antibiotics can be present at trace amounts in meat, eggs and milk if the animals aren't withdrawn from the drugs for a sufficient period of time before the products are collected. Also, antibiotics can accumulate in cereals, vegetables and fruits from manure fertilizer or treated wastewater applied to crops. Consuming these foods over a long period of time could lead to increased antibiotic resistance of bacterial pathogens or to an imbalance in the gut microbiome. However, most previous monitoring methods for antibiotics in foods have been limited to a few compounds at a time, usually within a single class of antibiotics with similar structures and chemical properties. Other methods have analyzed multiple antibiotics in only a single food type, such as eggs or milk. Yujie Ben and colleagues wanted to develop a time- and cost-effective method that could detect a wide range of antibiotics in different types of foods.

The researchers added trace amounts of 81 antibiotics from seven categories to vegetable samples and tested 20 different methods for extracting the drugs from the food. Only one extraction process, which involved treating freeze-dried, homogenized food samples with an acidified acetonitrile solution and a mixture of magnesium sulfate and sodium acetate, allowed the researchers to isolate 77 of the antibiotics. After establishing that their method was sensitive and accurate with spiked antibiotics in several foods, the team applied it to store-bought samples of wheat flour, mutton, eggs, milk, cabbage and bananas, detecting a total of 10 antibiotics. One of them, roxithromycin, was detected at trace amounts in all six food types. The new method should help with understanding, monitoring and regulating antibiotic levels in foods, the researchers say.

From Science Daily

Simulating 800,000 years of California earthquake history to pinpoint risks

 Massive earthquakes are, fortunately, rare events. But that scarcity of information blinds us in some ways to their risks, especially when it comes to determining the risk for a specific location or structure.

"We haven't observed most of the possible events that could cause large damage," explained Kevin Milner, a computer scientist and seismology researcher at the Southern California Earthquake Center (SCEC) at the University of Southern California. "Using Southern California as an example, we haven't had a truly big earthquake since 1857 -- that was the last time the southern San Andreas broke into a massive magnitude 7.9 earthquake. A San Andreas earthquake could impact a much larger area than the 1994 Northridge earthquake, and other large earthquakes can occur too. That's what we're worried about."

The traditional way of getting around this lack of data involves digging trenches to learn more about past ruptures, collating information from lots of earthquakes all around the world and creating a statistical model of hazard, or using supercomputers to simulate a specific earthquake in a specific place with a high degree of fidelity.

However, a new framework for predicting the likelihood and impact of earthquakes over an entire region, developed by a team of researchers associated with SCEC over the past decade, has found a middle ground and perhaps a better way to ascertain risk.

A new study led by Milner and Bruce Shaw of Columbia University, published in the Bulletin of the Seismological Society of America in January 2021, presents results from a prototype Rate-State earthquake simulator, or RSQSim, that simulates hundreds of thousands of years of seismic history in California. Coupled with another code, CyberShake, the framework can calculate the amount of shaking that would occur for each quake. Their results compare well with historical earthquakes and the results of other methods, and display a realistic distribution of earthquake probabilities.

According to the developers, the new approach improves the ability to pinpoint how big an earthquake might occur in a given location, allowing building code developers, architects, and structural engineers to design more resilient buildings that can survive earthquakes at a specific site.

"For the first time, we have a whole pipeline from start to finish where earthquake occurrence and ground-motion simulation are physics-based," Milner said. "It can simulate up to 100,000s of years on a really complicated fault system."

Applying massive computer power to big problems

RSQSim transforms mathematical representations of the geophysical forces at play in earthquakes -- the standard model of how ruptures nucleate and propagate -- into algorithms, and then solves them on some of the most powerful supercomputers on the planet. The computationally-intensive research was enabled over several years by government-sponsored supercomputers at the Texas Advanced Computing Center, including Frontera -- the most powerful system at any university in the world -- Blue Waters at the National Center for Supercomputing Applications, and Summit at the Oak Ridge Leadership Computing Facility.

"One way we might be able to do better in predicting risk is through physics-based modeling, by harnessing the power of systems like Frontera to run simulations," said Milner. "Instead of an empirical statistical distribution, we simulate the occurrence of earthquakes and the propagation of its waves."

"We've made a lot of progress on Frontera in determining what kind of earthquakes we can expect, on which fault, and how often," said Christine Goulet, Executive Director for Applied Science at SCEC, also involved in the work. "We don't prescribe or tell the code when the earthquakes are going to happen. We launch a simulation of hundreds of thousands of years, and just let the code transfer the stress from one fault to another."

The simulations began with the geological topography of California and simulated over 800,000 virtual years how stresses form and dissipate as tectonic forces act on the Earth. From these simulations, the framework generated a catalogue -- a record that an earthquake occurred at a certain place with a certain magnitude and attributes at a given time. The catalog that the SCEC team produced on Frontera and Blue Waters was among the largest ever made, Goulet said. The outputs of RSQSim were then fed into CyberShake that again used computer models of geophysics to predict how much shaking (in terms of ground acceleration, or velocity, and duration) would occur as a result of each quake.

"The framework outputs a full slip-time history: where a rupture occurs and how it grew," Milner explained. "We found it produces realistic ground motions, which tells us that the physics implemented in the model is working as intended." They have more work planned for validation of the results, which is critical before acceptance for design applications.

The researchers found that the RSQSim framework produces rich, variable earthquakes overall -- a sign it is producing reasonable results -- while also generating repeatable source and path effects.

"For lots of sites, the shaking hazard goes down, relative to state-of-practice estimates" Milner said. "But for a couple of sites that have special configurations of nearby faults or local geological features, like near San Bernardino, the hazard went up. We are working to better understand these results and to define approaches to verify them."

The work is helping to determine the probability of an earthquake occurring along any of California's hundreds of earthquake-producing faults, the scale of earthquake that could be expected, and how it may trigger other quakes.

Support for the project comes from the U.S. Geological Survey (USGS), National Science Foundation (NSF), and the W.M. Keck Foundation. Frontera is NSF's leadership-class national resource. Compute time on Frontera was provided through a Large-Scale Community Partnership (LSCP) award to SCEC that allows hundreds of U.S. scholars access to the machine to study many aspects of earthquake science. LSCP awards provide extended allocations of up to three years to support long-lived research efforts. SCEC -- which was founded in 1991 and has computed on TACC systems for over a decade -- is a premier example of such an effort.

The creation of the catalog required eight days of continuous computing on Frontera and used more than 3,500 processors in parallel. Simulating the ground shaking at 10 sites across California required a comparable amount of computing on Summit, the second fastest supercomputer in the world.

"Adoption by the broader community will be understandably slow," said Milner. "Because such results will impact safety, it is part of our due diligence to make sure these results are technically defensible by the broader community," added Goulet. But research results such as these are important in order to move beyond generalized building codes that in some cases may be inadequately representing the risk a region face while in other cases being too conservative.

Read more at Science Daily

Purported phosphine on Venus more likely to be ordinary sulfur dioxide

 In September, a team led by astronomers in the United Kingdom announced that they had detected the chemical phosphine in the thick clouds of Venus. The team's reported detection, based on observations by two Earth-based radio telescopes, surprised many Venus experts. Earth's atmosphere contains small amounts of phosphine, which may be produced by life. Phosphine on Venus generated buzz that the planet, often succinctly touted as a "hellscape," could somehow harbor life within its acidic clouds.

Since that initial claim, other science teams have cast doubt on the reliability of the phosphine detection. Now, a team led by researchers at the University of Washington has used a robust model of the conditions within the atmosphere of Venus to revisit and comprehensively reinterpret the radio telescope observations underlying the initial phosphine claim. As they report in a paper accepted to the Astrophysical Journal and posted Jan. 25 to the preprint site arXiv, the U.K.-led group likely wasn't detecting phosphine at all.

"Instead of phosphine in the clouds of Venus, the data are consistent with an alternative hypothesis: They were detecting sulfur dioxide," said co-author Victoria Meadows, a UW professor of astronomy. "Sulfur dioxide is the third-most-common chemical compound in Venus' atmosphere, and it is not considered a sign of life."

The team behind the new study also includes scientists at NASA's Caltech-based Jet Propulsion Laboratory, the NASA Goddard Space Flight Center, the Georgia Institute of Technology, the NASA Ames Research Center and the University of California, Riverside.

The UW-led team shows that sulfur dioxide, at levels plausible for Venus, can not only explain the observations but is also more consistent with what astronomers know of the planet's atmosphere and its punishing chemical environment, which includes clouds of sulfuric acid. In addition, the researchers show that the initial signal originated not in the planet's cloud layer, but far above it, in an upper layer of Venus' atmosphere where phosphine molecules would be destroyed within seconds. This lends more support to the hypothesis that sulfur dioxide produced the signal.

Both the purported phosphine signal and this new interpretation of the data center on radio astronomy. Every chemical compound absorbs unique wavelengths of the electromagnetic spectrum, which includes radio waves, X-rays and visible light. Astronomers use radio waves, light and other emissions from planets to learn about their chemical composition, among other properties.

In 2017 using the James Clerk Maxwell Telescope, or JCMT, the U.K.-led team discovered a feature in the radio emissions from Venus at 266.94 gigahertz. Both phosphine and sulfur dioxide absorb radio waves near that frequency. To differentiate between the two, in 2019 the same team obtained follow-up observations of Venus using the Atacama Large Millimeter/submillimeter Array, or ALMA. Their analysis of ALMA observations at frequencies where only sulfur dioxide absorbs led the team to conclude that sulfur dioxide levels in Venus were too low to account for the signal at 266.94 gigahertz, and that it must instead be coming from phosphine.

In this new study by the UW-led group, the researchers started by modeling conditions within Venus' atmosphere, and using that as a basis to comprehensively interpret the features that were seen -- and not seen -- in the JCMT and ALMA datasets.

"This is what's known as a radiative transfer model, and it incorporates data from several decades' worth of observations of Venus from multiple sources, including observatories here on Earth and spacecraft missions like Venus Express," said lead author Andrew Lincowski, a researcher with the UW Department of Astronomy.

The team used that model to simulate signals from phosphine and sulfur dioxide for different levels of Venus' atmosphere, and how those signals would be picked up by the JCMT and ALMA in their 2017 and 2019 configurations. Based on the shape of the 266.94-gigahertz signal picked up by the JCMT, the absorption was not coming from Venus' cloud layer, the team reports. Instead, most of the observed signal originated some 50 or more miles above the surface, in Venus' mesosphere. At that altitude, harsh chemicals and ultraviolet radiation would shred phosphine molecules within seconds.

"Phosphine in the mesosphere is even more fragile than phosphine in Venus' clouds," said Meadows. "If the JCMT signal were from phosphine in the mesosphere, then to account for the strength of the signal and the compound's sub-second lifetime at that altitude, phosphine would have to be delivered to the mesosphere at about 100 times the rate that oxygen is pumped into Earth's atmosphere by photosynthesis."

The researchers also discovered that the ALMA data likely significantly underestimated the amount of sulfur dioxide in Venus' atmosphere, an observation that the U.K.-led team had used to assert that the bulk of the 266.94-gigahertz signal was from phosphine.

"The antenna configuration of ALMA at the time of the 2019 observations has an undesirable side effect: The signals from gases that can be found nearly everywhere in Venus' atmosphere -- like sulfur dioxide -- give off weaker signals than gases distributed over a smaller scale," said co-author Alex Akins, a researcher at the Jet Propulsion Laboratory.

This phenomenon, known as spectral line dilution, would not have affected the JCMT observations, leading to an underestimate of how much sulfur dioxide was being seen by JCMT.

"They inferred a low detection of sulfur dioxide because of that artificially weak signal from ALMA," said Lincowski. "But our modeling suggests that the line-diluted ALMA data would have still been consistent with typical or even large amounts of Venus sulfur dioxide, which could fully explain the observed JCMT signal."

"When this new discovery was announced, the reported low sulfur dioxide abundance was at odds with what we already know about Venus and its clouds," said Meadows. "Our new work provides a complete framework that shows how typical amounts of sulfur dioxide in the Venus mesosphere can explain both the signal detections, and non-detections, in the JCMT and ALMA data, without the need for phosphine."

Read more at Science Daily

How heavy is dark matter? Scientists radically narrow the potential mass range for the first time

 Scientists have calculated the mass range for Dark Matter -- and it's tighter than the science world thought.

Their findings -- due to be published in Physics Letters B in March -- radically narrow the range of potential masses for Dark Matter particles, and help to focus the search for future Dark Matter-hunters. The University of Sussex researchers used the established fact that gravity acts on Dark Matter just as it acts on the visible universe to work out the lower and upper limits of Dark Matter's mass.

The results show that Dark Matter cannot be either 'ultra-light' or 'super-heavy', as some have theorised, unless an as-yet undiscovered force also acts upon it.

The team used the assumption that the only force acting on Dark Matter is gravity, and calculated that Dark Matter particles must have a mass between 10-3 eV and 107 eV. That's a much tighter range than the 10-24 eV -- 1019 GeV spectrum which is generally theorised.

What makes the discovery even more significant is that if it turns out that the mass of Dark Matter is outside of the range predicted by the Sussex team, then it will also prove that an additional force -- as well as gravity -- acts on Dark Matter.

Professor Xavier Calmet from the School of Mathematical and Physical Sciences at the University of Sussex, said:

"This is the first time that anyone has thought to use what we know about quantum gravity as a way to calculate the mass range for Dark Matter. We were surprised when we realised no-one had done it before -- as were the fellow scientists reviewing our paper.

"What we've done shows that Dark Matter cannot be either 'ultra-light' or 'super-heavy' as some theorise -- unless there is an as-yet unknown additional force acting on it. This piece of research helps physicists in two ways: it focuses the search area for Dark Matter, and it will potentially also help reveal whether or not there is a mysterious unknown additional force in the universe."

Folkert Kuipers, a PhD student working with Professor Calmet, at the University of Sussex, said:

"As a PhD student, it's great to be able to work on research as exciting and impactful as this. Our findings are very good news for experimentalists as it will help them to get closer to discovering the true nature of Dark Matter."

The visible universe -- such as ourselves, the planets and stars -- accounts for 25 per cent of all mass in the universe. The remaining 75 per cent is comprised of Dark Matter.

Read more at Science Daily

Pace of prehistoric human innovation could be revealed by 'linguistic thermometer'

 Multi-disciplinary researchers at The University of Manchester have helped develop a powerful physics-based tool to map the pace of language development and human innovation over thousands of years -- even stretching into pre-history before records were kept.

Tobias Galla, a professor in theoretical physics, and Dr Ricardo Bermúdez-Otero, a specialist in historical linguistics, from The University of Manchester, have come together as part of an international team to share their diverse expertise to develop the new model, revealed in a paper entitled 'Geospatial distributions reflect temperatures of linguistic feature' authored by Henri Kauhanen, Deepthi Gopal, Tobias Galla and Ricardo Bermúdez-Otero, and published by the journal Science Advances.

Professor Galla has applied statistical physics -- usually used to map atoms or nanoparticles -- to help build a mathematically-based model that responds to the evolutionary dynamics of language. Essentially, the forces that drive language change can operate across thousands of years and leave a measurable "geospatial signature," determining how languages of different types are distributed over the surface of the Earth.

Dr Bermúdez-Otero explained: "In our model each language has a collection of properties or features and some of those features are what we describe as 'hot' or 'cold'.

"So, if a language puts the object before the verb, then it is relatively likely to get stuck with that order for a long period of time -- so that's a 'cold' feature. In contrast, markers like the English article 'the' come and go a lot faster: they may be here in one historical period, and be gone in the next. In that sense, definite articles are 'hot' features.

"The striking thing is that languages with 'cold' properties tend to form big clumps, whereas languages with 'hot' properties tend to be more scattered geographically."

This method therefore works like a thermometer, enabling researchers to retrospectively tell whether one linguistic property is more prone to change in historical time than another. This modelling could also provide a similar benchmark for the pace of change in other social behaviours or practices over time and space.

"For example, suppose that you have a map showing the spatial distribution of some variable cultural practice for which you don't have any historical records -- this could be be anything, like different rules on marriage or on the inheritance of possessions," added Dr Bermúdez-Otero.

"Our method could, in principle, be used to ascertain whether one practice changes in the course of historical time faster than another, ie whether people are more innovative in one area than in another, just by looking at how the present-day variation is distributed in space."

The source data for the linguistic modelling comes from present-day languages and the team relied on The World Atlas of Language Structures (WALS). This records information of 2,676 contemporary languages.

Professor Galla explained: "We were interested in emergent phenomena, such as how large-scale effects, for example patterns in the distribution of language features arise from relatively simple interactions. This is a common theme in complex systems research.

Read more at Science Daily

From fins to limbs

 When tetrapods (four-limbed vertebrates) began to move from water to land roughly 390 million years ago it set in motion the rise of lizards, birds, mammals, and all land animals that exist today, including humans and some aquatic vertebrates such as whales and dolphins.

The earliest tetrapods originated from their fish ancestors in the Devonian period and are more than twice as old as the oldest dinosaur fossils. They resembled a cross between a giant salamander and a crocodile and were about 1-2 meters long, had gills, webbed feet and tail fins, and were still heavily tied to water. Their short arms and legs had up to eight digits on each hand and foot and they were probably ambush predators, lurking in shallow water waiting for prey to come near.

Scientists know how the fins of fish transformed into the limbs of tetrapods, but controversies remain about where and how the earliest tetrapods used their limbs. And, while many hypotheses have been proposed, very few studies have rigorously tested them using the fossil record.

In a paper published January 22 in Science Advances an international team of researchers examined three-dimensional digital models of the bones, joints, and muscles of the fins and limbs of two extinct early tetrapods and a closely related fossil fish to reveal how function of the forelimb changed as fins evolved into limbs. The research led by Julia Molnar, Assistant Professor at New York Institute of Technology College of Osteopathic Medicine and Stephanie Pierce, Thomas D. Cabot Associate Professor of Organismic and Evolutionary Biology at Harvard University, discovered three distinct functional stages in the transition from fins to limbs, and that these early tetrapods had a very distinct pattern of muscle leverage that didn't look like a fish fin or modern tetrapod limbs.

To reconstruct how limbs of the earliest known tetrapods functioned, Molnar, Pierce and co-authors John Hutchinson (Royal Veterinary College), Rui Diogo (Howard University), and Jennifer Clack (University of Cambridge) first needed to figure out what muscles were present in the fossil animals. A challenging task as muscles are not preserved in fossils, and the muscles of modern fish fins are completely different from those of tetrapod limbs. The team spent several years trying to answer the question, how exactly did the few simple muscles of a fin become dozens of muscles that perform all sorts of functions in a tetrapod limb?

"Determining what muscles were present in a 360-million-year-old fossil took many years of work just to get to the point where we could begin to build very complicated musculoskeletal models," said Pierce. "We needed to know how many muscles were present in the fossil animals and where they attached to on the bones so we could test how they functioned."

They built three-dimensional musculoskeletal models of the pectoral fin in Eusthenopteron (a fish closely related to tetrapods that lived during the Late Devonian period about 385 million years ago) and the forelimbs of two early tetrapods, Acanthostega (365 million years old living towards the end of the Late Devonian period) and Pederpes (348-347 million years old living during the early Carboniferous period). For comparison, they also built similar models of the pectoral fins of living fishes (coelacanth, lungfish) and forelimbs of living tetrapods (salamander, lizard).

To determine how the fins and limbs worked, the researchers used computational software originally developed to study human locomotion. This technique had been used recently to study locomotion in the ancestors of humans and also dinosaurs like T. rex, but never in something as old as an early tetrapod.

Manipulating the models in the software, the team were able to measure two functional traits: the joint's maximum range of motion and the muscles' ability to move the fin or limb joints. The two measurements would reveal trade-offs in the locomotor system and allow the researchers to test hypotheses of function in extinct animals.

The team found the forelimbs of all terrestrial tetrapods passed through three distinct functional stages: a "benthic fish" stage that resembled modern lungfish, an "early tetrapod" stage unlike any extinct animal, and a "crown tetrapod" stage with characteristics of both lizards and salamanders.

"The fin from Eusthenopteron had a pattern that was reminiscent of the lungfish, which is one of the closest living relatives of tetrapods," said Pierce. "But the early tetrapod limbs showed more similarities to each other than either fish or modern tetrapods."

"That was perhaps the most surprising," said Molnar. "I thought Pederpes, and possibly Acanthostega, would fall pretty well within the range of modern tetrapods. But they formed their own distinct cluster that didn't look like a modern tetrapod limb or a fish fin. They were not smack dab in the middle but had their own collection of characteristics that probably reflected their unique environment and behaviors."

The results showed that early tetrapod limbs were more adapted for propulsion rather than weight bearing. In the water, animals use their limbs for propulsion to move themselves forward or backward allowing the water to support their body weight. Moving on land, however, requires the animal act against gravity and push downward with their limbs to support their body mass.

This doesn't mean that early tetrapods were incapable of moving on land, but rather they didn't move like a modern-day living tetrapod. Their means of locomotion was probably unique to these animals that were still very much tied to the water, but were also venturing onto land, where there were many opportunities for vertebrate animals but little competition or fear from predators.

"These results are exciting as they independently support a study I published last year using completely different fossils and methods," said Pierce. "That study, which focused on the upper arm bone, indicated that early tetrapods had some capacity for land movement but that they may not have been very good at it."

The researchers are closer to reconstructing the evolution of terrestrial locomotion, but more work is needed. They plan to next model the hind limb to investigate how all four limbs worked together. It has been suggested that early tetrapods were using their forelimbs for propulsion, but modern tetrapods get most of their propulsive power from the hind limb.

Read more at Science Daily

Climate change in antiquity: Mass emigration due to water scarcity

 The absence of monsoon rains at the source of the Nile was the cause of migrations and the demise of entire settlements in the late Roman province of Egypt. This demographic development has been compared with environmental data for the first time by professor of ancient history, Sabine Huebner of the University of Basel -- leading to a discovery of climate change and its consequences.

The oasis-like Faiyum region, roughly 130 km south-west of Cairo, was the breadbasket of the Roman Empire. Yet at the end of the third century CE, numerous formerly thriving settlements there declined and were ultimately abandoned by their inhabitants. Previous excavations and contemporary papyri have shown that problems with field irrigation were the cause. Attempts by local farmers to adapt to the dryness and desertification of the farmland -- for example, by changing their agricultural practices -- are also documented.

Volcanic eruption and monsoon rains

Basel professor of ancient history Sabine R. Huebner has now shown in the US journal Studies in Late Antiquity that changing environmental conditions were behind this development. Existing climate data indicates that the monsoon rains at the headwaters of the Nile in the Ethiopian Highlands suddenly and permanently weakened. The result was lower high-water levels of the river in summer. Evidence supporting this has been found in geological sediment from the Nile Delta, Faiyum and the Ethiopian Highlands, which provides long-term climate data on the monsoons and the water level of the Nile.

A powerful tropical volcanic eruption around 266 CE, which in the following year brought a below-average flood of the Nile, presumably also played a role. Major eruptions are known from sulfuric acid deposits in ice cores from Greenland and Antarctica, and can be dated to within three years. Particles hurled up into the stratosphere lead to a cooling of the climate, disrupting the local monsoon system.

New insights into climate, environment, and society

In the third century CE, the entire Roman Empire was hit by crises that are relatively well documented in the province of Egypt by more than 26,000 preserved papyri (documents written on sheets of papyrus). In the Faiyum region, these include records of inhabitants who switched to growing vines instead of grain or to sheep farming due to the scarcity of water. Others accused their neighbors of water theft or turned to the Roman authorities for tax relief. These and other adaptive strategies of the population delayed the death of their villages for several decades.

Read more at Science Daily