Planet Neuroscientists

- Wallabag.it! - Save to Instapaper - Save to Pocket -

NASA’s DART Spacecraft Smashes Into an Asteroid—on Purpose

in WIRED Science on 2022-09-26 23:28:58 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

NASA’s DART spacecraft just smashed into an asteroid — on purpose

Mission control rooms rarely celebrate crash landings. But the collision of NASA’s DART spacecraft with an asteroid was a smashing success.

At about 7:15 p.m. EDT on September 26, the spacecraft hurtled into Dimorphos, an asteroid moonlet orbiting a larger space rock named Didymos. The mission’s goal was to bump Dimorphos slightly closer to its parent asteroid, shortening its 12-hour orbit around Didymos by several minutes.

The Double Asteroid Redirection Test, or DART, is the world’s first attempt to change an asteroid’s motion by ramming a space probe into it (SN: 6/30/20). Neither Dimorphos nor Didymos poses a threat to Earth. But seeing how well DART’s maneuver worked will reveal how easy it is to tamper with an asteroid’s trajectory — a strategy that could protect the planet if a large asteroid is ever discovered on a collision course with Earth.

“We don’t know of any large asteroids that would be considered a threat to Earth that are coming any time in the next century,” says DART team member Angela Stickle, a planetary scientist at the Johns Hopkins University Applied Physics Laboratory in Laurel, Md. “The reason that we are doing something like DART is because there are asteroids that we haven’t discovered yet.”

Astronomers have spotted almost all the kilometer-size asteroids in the solar system that could end civilization if they hit Earth, says Jessica Sunshine, a planetary scientist at the University of Maryland in College Park who’s also on the DART team. But when it comes to space rocks around 150 meters wide, like Dimorphos, “we only know where about 40 percent of those are,” Sunshine says. “And that is something that, if it did hit, would certainly take out a city.”

Dimorphos is a safe asteroid to give an experimental nudge, says Mark Boslough, a physicist at Los Alamos National Laboratory in New Mexico who has studied planetary protection but is not involved in DART. “It’s not on a collision course” with Earth, he says, and DART “can’t hit it hard enough to put it on a collision course.” The DART spacecraft weighs only as much as a couple of vending machines, whereas Dimorphos is thought to be nearly as hefty as Egypt’s Great Pyramid of Giza.

After a 10-month voyage, DART met up with Didymos and Dimorphos near their closest approach to Earth, about 11 million kilometers away. Up until the very end of its journey, DART could see only the larger asteroid, Didymos. But about an hour before impact, DART spotted Dimorphos in its field of view. Using its onboard camera, the spacecraft steered itself toward the asteroid moonlet and slammed into it at some 6.1 kilometers per second, or nearly 14,000 miles per hour.

DART’s camera feed went dark after impact. But another probe nearby is expected to have caught the collision on camera. The Light Italian CubeSat for Imaging of Asteroids rode to Dimorphos aboard DART but detached a couple of weeks before impact to watch the event from a safe distance. Its mission was to whiz past Dimorphos about three minutes after DART’s impact to snap pictures of the crash site and the resulting plume of asteroid debris launched into space. The probe is expected to beam images of DART’s demise back to Earth within a couple of days.

“I was absolutely elated, especially as we saw the camera getting closer and just realizing all the science that we’re going to learn,” said Pam Melroy, NASA Deputy Administrator, after the impact. “But the best part was seeing, at the end, that there was no question there was going to be an impact, and to see the team overjoyed with their success.”

DART’s impact is expected to shove Dimorphos into a closer, shorter orbit around Didymos. Telescopes on Earth can clock the timing of that orbit by watching how the amount of light from the double asteroid system changes as Dimorphos passes in front of and behind Didymos.

“It’s really a beautifully conceived experiment,” Boslough says. In the coming weeks, dozens of telescopes across every continent will watch Dimorphos to see how much DART changed its orbit. The Hubble and James Webb space telescopes may also get images.

“It’ll be really interesting to see what comes out,” says Amy Mainzer, a planetary scientist at the University of Arizona in Tucson who is not involved in DART. “Asteroids have a way of surprising us,” she says, because it’s hard to know a space rock’s precise chemical makeup and internal structure based on observations from Earth. So Dimorphos’ motion post-impact may not exactly match researchers’ expectations.

The DART team will compare data on Dimorphos’ new orbit with their computer simulations to see how close those models were to predicting the asteroid’s actual behavior and tweak them accordingly. “If we can get our models to reproduce what actually happened, then you can use those models to [plan for] other scenarios that might show up in the future” — like the discovery of a real killer asteroid, says DART team member Wendy Caldwell, a mathematician and planetary scientist at Los Alamos National Laboratory.

“No matter what happens,” she says, “we will get information that is valuable to the scientific community and to the planetary defense community.” 

in Science News on 2022-09-26 23:17:37 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Hurricane Ian Blows Back NASA’s Artemis Launch

in WIRED Science on 2022-09-26 19:15:14 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

In Maya society, cacao use was for everyone, not just royals

In ancient Maya civilization, cacao wasn’t just for the elites.

Traces of the sacred plant show up in ceramics from all types of neighborhoods and dwellings in and around a former Maya city, researchers report September 26 in the Proceedings of the National Academy of Sciences. The finding suggests that, contrary to previous thinking, cacao was consumed at every social level of Maya society.

“Now we know that the rituals the elite depict with cacao were likely played out, like Thanksgiving, like any other ritual, by everyone,” says Anabel Ford, an archaeologist at the University of California, Santa Barbara.

Cacao — which chocolate is made from — was sacred to the ancient Maya, consumed in rituals and used as a currency. The cacao tree (Theobroma cacao) itself was linked to Hun Hunahpu, the maize god. Previous research found cacao in ceremonial vessels and elite burials, suggesting that its use was restricted to those at the top.

To explore the extent to which cacao was used in broader Maya society, Ford and colleagues examined 54 ceramic shards dating from A.D. 600 to 900 (SN: 9/27/18). The shards come from jars, mixing bowls, serving plates and vases thought to be drinking vessels. All the pieces were found in residential and ceremonial civic areas of varying size and status from city centers, foothills, upland areas and the valley around the former Maya city of El Pilar, on the present-day border of Guatemala and Belize.

To identify cacao, the researchers searched for theophylline, a compound found in trace amounts in the plant. The team found the compound on more than half of the samples, on all types of ceramics and distributed throughout social contexts.

Future research will move beyond who consumed cacao and explore the role of farmers in managing the critical resource. “A better question is to understand who grew it,” Ford says, because those people probably had greater access to the prized commodity.

in Science News on 2022-09-26 19:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Mangrove forests expand and contract with a lunar cycle

The glossy leaves and branching roots of mangroves are downright eye-catching, and now a study finds that the moon plays a special role in the vigor of these trees.

Long-term tidal cycles set in motion by the moon drive, in large part, the expansion and contraction of mangrove forests in Australia, researchers report in the Sept. 16 Science Advances. This discovery is key to predicting when stands of mangroves, which are good at sequestering carbon and could help fight climate change, are most likely to proliferate (SN: 11/18/21). Such knowledge could inform efforts to protect and restore the forests.

Mangroves are coastal trees that provide habitat for fish and buffer against erosion (SN: 9/14/22). But in some places, the forests face a range of threats, including coastal development, pollution and land clearing for agriculture. To get a bird’s-eye view of these forests, Neil Saintilan, an environmental scientist at Macquarie University in Sydney, and his colleagues turned to satellite imagery. Using NASA and U.S. Geological Survey Landsat data from 1987 to 2020, the researchers calculated how the size and density of mangrove forests across Australia changed over time.

After accounting for persistent increases in these trees’ growth — probably due to rising carbon dioxide levels, higher sea levels and increasing air temperatures — Saintilan and his colleagues noticed a curious pattern. Mangrove forests tended to expand and contract in both extent and canopy cover in a predictable manner. “I saw this 18-year oscillation,” Saintilan says.

That regularity got the researchers thinking about the moon. Earth’s nearest celestial neighbor has long been known to help drive the tides, which deliver water and necessary nutrients to mangroves. A rhythm called the lunar nodal cycle could explain the mangroves’ growth pattern, the team hypothesized.

Over the course of 18.6 years, the plane of the moon’s orbit around Earth slowly tips. When the moon’s orbit is the least tilted relative to our planet’s equator, semidiurnal tides — which consist of two high and two low tides each day — tend to have a larger range. That means that in areas that experience semidiurnal tides, higher high tides and lower low tides are generally more likely. The effect is caused by the angle at which the moon tugs gravitationally on the Earth.  

Saintilan and his colleagues found that mangrove forests experiencing semidiurnal tides tended to be larger and denser precisely when higher high tides were expected based on the moon’s orbit. The effect even seemed to outweigh other climatic drivers of mangrove growth, such as El Niño conditions. Other regions with mangroves, such as Vietnam and Indonesia, probably experience the same long-term trends, the team suggests.

Having access to data stretching back decades was key to this discovery, Saintilan says. “We’ve never really picked up before some of these longer-term drivers of vegetation dynamics.”

It’s important to recognize this effect on mangrove populations, says Octavio Aburto-Oropeza, a marine ecologist at the Scripps Institution of Oceanography in La Jolla, Calif., who was not involved in the research.

Scientists now know when some mangroves are particularly likely to flourish and should make an extra effort at those times to promote the growth of these carbon-sequestering trees, Aburto-Oropeza says. That might look like added limitations on human activity nearby that could harm the forests, he says. “We should be more proactive.” 

in Science News on 2022-09-26 13:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Here’s how olivine may trigger deep earthquakes

Cocooned within the bowels of the Earth, one mineral’s metamorphosis into another may trigger some of the deepest earthquakes ever detected.

These cryptic tremors — known as deep-focus earthquakes — are a seismic conundrum. They violently rupture at depths greater than 300 kilometers, where intense temperatures and pressures are thought to force rocks to flow smoothly. Now, experiments suggest that those same hellish conditions might also sometimes transform olivine — the primary mineral in Earth’s mantle — into the mineral wadsleyite. This mineral switch-up can destabilize the surrounding rock, enabling earthquakes at otherwise impossible depths, mineral physicist Tomohiro Ohuchi and colleagues report September 15 in Nature Communications.

“It’s been a real puzzle for many scientists because earthquakes shouldn’t occur deeper than 300 kilometers,” says Ohuchi, of Ehime University in Matsuyama, Japan.

Deep-focus earthquakes usually occur at subduction zones where tectonic plates made of oceanic crust — rich in olivine — plunge toward the mantle (SN: 1/13/21). Since the quakes’ seismic waves lose strength during their long ascent to the surface, they aren’t typically dangerous. But that doesn’t mean the quakes aren’t sometimes powerful. In 2013, a magnitude 8.3 deep-focus quake struck around 609 kilometers below the Sea of Okhotsk, just off Russia’s eastern coast.

Past studies hinted that unstable olivine crystals could spawn deep quakes. But those studies tested other minerals that were similar in composition to olivine but deform at lower pressures, Ohuchi says, or the experiments didn’t strain samples enough to form faults.

He and his team decided to put olivine itself to the test. To replicate conditions deep underground, the researchers heated and squeezed olivine crystals up to nearly 1100° Celsius and 17 gigapascals. Then the team used a mechanical press to further compress the olivine slowly and monitored the deformation.

From 11 to 17 gigapascals and about 800° to 900° C, the olivine recrystallized into thin layers containing new wadsleyite and smaller olivine grains. The researchers also found tiny faults and recorded bursts of sound waves — indicative of miniature earthquakes. Along subducting tectonic plates, many of these thin layers grow and link to form weak regions in the rock, upon which faults and earthquakes can initiate, the researchers suggest.

“The transformation really wreaks havoc with the [rock’s] mechanical stability,” says geophysicist Pamela Burnley of the University of Nevada, Las Vegas, who was not involved in the research. The findings help confirm that olivine transformations are enabling deep-focus earthquakes, she says.

Next, Ohuchi’s team plans to experiment on olivine at even higher pressures to gain insights into the mineral’s deformation at greater depths.

in Science News on 2022-09-26 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Viruses to Fight Superbugs? Scientists Are Working on It

in WIRED Science on 2022-09-26 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

A Wheel Made of ‘Odd Matter’ Spontaneously Rolls Uphill

in WIRED Science on 2022-09-25 12:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Next Open NeuroFedora meeting: 26 September 1300 UTC

Photo by William White on Unsplash.

Please join us at the next regular Open NeuroFedora team meeting on Monday 26 September at 1300 UTC. The meeting is a public meeting, and open for everyone to attend. You can join us over:

• Matrix (using your web-browser)
• IRC

You can use this link to convert the meeting time to your local time. Or, you can also use this command in the terminal:

$ date --date='TZ="UTC" 1300 2022-09-26'

The meeting will be chaired by @ankursinha. The agenda for the meeting is:

• New introductions and roll call.
• Tasks from last meeting.
• Open Pagure tickets.
• Package health check.
• Open package reviews check.
• CompNeuro lab compose status check for Fedora 36/37.
• Neuroscience query of the week
• Next meeting day, and chair.
• Open floor.

We hope to see you there!

in NeuroFedora blog on 2022-09-24 12:43:24 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Philadelphia’s Diatom Archive Is a Way, Way, Wayback Machine

in WIRED Science on 2022-09-24 12:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Weekend reads: ‘Papermill alarm’ software; questions about a study of prosthetics; what do publishers stand for?

in Retraction watch on 2022-09-24 11:30:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

How to Find Your Vaccine History—and Store It Safely

in WIRED Science on 2022-09-24 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

UCLA walks back claim that application for $50 million grant included fake data

in Retraction watch on 2022-09-23 18:07:37 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Here is the first direct look at Neptune’s rings in more than 30 years

Humankind is seeing Neptune’s rings in a whole new light thanks to the James Webb Space Telescope.

In an infrared image released September 21, Neptune and its gossamer diadems of dust take on an ethereal glow against the inky backdrop of space. The stunning portrait is a huge improvement over the rings’ previous close-up, which was taken more than 30 years ago.

Unlike the dazzling belts encircling Saturn, Neptune’s rings appear dark and faint in visible light, making them difficult to see from Earth. The last time anyone saw Neptune’s rings was in 1989, when NASA’s Voyager 2 spacecraft, after tearing past the planet, snapped a couple grainy photos from roughly 1 million kilometers away (SN: 8/7/17). In those photos, taken in visible light, the rings appear as thin, concentric arcs.

As Voyager 2 continued to interplanetary space, Neptune’s rings once again went into hiding — until July. That’s when the James Webb Space Telescope, or JWST, turned its sharp, infrared gaze toward the planet from roughly 4.4 billion kilometers away (SN: 7/11/22).

Neptune itself appears mostly dark in the new image. That’s because methane gas in the planet’s atmosphere absorbs much of its infrared light. A few bright patches mark where high-altitude methane ice clouds reflect sunlight.

And then there are the ever-elusive rings. “The rings have lots of ice and dust in them, which are extremely reflective in infrared light,” says Stefanie Milam, a planetary scientist at NASA’s Goddard Space Flight Center in Greenbelt, Md., and one of JWST’s project scientists. The enormity of the telescope’s mirror also makes its images extra sharp. “JWST was designed to look at the first stars and galaxies across the universe, so we can really see fine details that we haven’t been able to see before,” Milam says.

Upcoming JWST observations will look at Neptune with other scientific instruments. That should provide new intel on the rings’ composition and dynamics, as well as on how Neptune’s clouds and storms evolve, Milam says. “There’s more to come.”

in Science News on 2022-09-23 13:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

The Physics of Going Fast—but Not Too Fast—on a Giant Slide

in WIRED Science on 2022-09-23 13:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Call for Papers! Introducing BMC Cancer’s New Collection: Extracellular Vesicles in Cancer Progression

In recognition of the growing field of research, BMC Cancer have launched this Collection to bring together research on:

• The role of extracellular vesicles in modulating the behaviour of resident and host cells in the tumor microenvironment.
• The role of circulating extracellular vesicles in setting up the pre-metastatic niche
• The role of extracellular vesicles in therapeutic resistance.
• Investigating the cargos of cancer-related extracellular vesicles as potential diagnostic, prognostic and predictive biomarkers.
• Changes in the mechanisms of extracellular vesicles biogenesis, release and uptake in cancer.
• The use of extracellular vesicles as delivery vehicles for therapeutics.
• The role of extracellular vesicles as therapeutic targets.
• Advances in the isolation and characterisation of cancer-related extracellular vesicles.

This Collection is now open for submissions!

This Collection welcomes submission of Research Articles. Before submitting your manuscript, please ensure you have read our submission guidelines. During the submission process you will be prompted to declare whether you are submitting to a Collection or thematic series, select “yes” and then select from the following options “Extracellular vesicles in cancer progression”.

Articles will undergo the journal’s standard peer-review process and are subject to all of the journal’s standard policies. Articles will be added to the Collection as they are published.

Data sets and descriptions relevant to the Collection will be considered in BMC Research Notes as Data Notes. You can find out more about this article type here. This type of content will be published in BMC Research Notes and included in the final Collection.

Submission deadline: 31st of March 2023.

To find out more and read the articles within the Collection, click here.

The post Call for Papers! Introducing BMC Cancer’s New Collection: Extracellular Vesicles in Cancer Progression appeared first on BMC Series blog.

in BMC Series blog on 2022-09-23 12:53:55 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Has AlphaFold actually solved biology’s protein-folding problem?

As people around the world marveled in July at the most detailed pictures of the cosmos snapped by the James Webb Space Telescope, biologists got their first glimpses of a different set of images — ones that could help revolutionize life sciences research.

The images are the predicted 3-D shapes of more than 200 million proteins, rendered by an artificial intelligence system called AlphaFold. “You can think of it as covering the entire protein universe,” said Demis Hassabis at a July 26 news briefing. Hassabis is cofounder and CEO of DeepMind, the London-based company that created the system. Combining several deep-learning techniques, the computer program is trained to predict protein shapes by recognizing patterns in structures that have already been solved through decades of experimental work using electron microscopes and other methods.

The AI’s first splash came in 2021, with predictions for 350,000 protein structures — including almost all known human proteins. DeepMind partnered with the European Bioinformatics Institute of the European Molecular Biology Laboratory to make the structures available in a public database.

July’s massive new release expanded the library to “almost every organism on the planet that has had its genome sequenced,” Hassabis said. “You can look up a 3-D structure of a protein almost as easily as doing a key word Google search.”

These are predictions, not actual structures. Yet researchers have used some of the 2021 predictions to develop potential new malaria vaccines, improve understanding of Parkinson’s disease, work out how to protect honeybee health, gain insight into human evolution and more. DeepMind has also focused AlphaFold on neglected tropical diseases, including Chagas disease and leishmaniasis, which can be debilitating or lethal if left untreated.

Expanding the protein universe 

Decades of slow-going experiments have revealed the structure of more than 194,000 proteins, all housed in the Protein Data Bank. In 2021, the AlphaFold project released predicted structures for about 1 million proteins, including almost all known human proteins. This year, the AlphaFold database exploded with predicted structures for more than 200 million proteins.

Total number of protein structures identified and predicted

The release of the vast dataset was greeted with excitement by many scientists. But others worry that researchers will take the predicted structures as the true shapes of proteins. There are still things AlphaFold can’t do — and wasn’t designed to do — that need to be tackled before the protein cosmos completely comes into focus.

Having the new catalog open to everyone is “a huge benefit,” says Julie Forman-Kay, a protein biophysicist at the Hospital for Sick Children and the University of Toronto. In many cases, AlphaFold and RoseTTAFold, another AI researchers are excited about, predict shapes that match up well with protein profiles from experiments. But, she cautions, “it’s not that way across the board.”

Predictions are more accurate for some proteins than for others. Erroneous predictions could leave some scientists thinking they understand how a protein works when really, they don’t. Painstaking experiments remain crucial to understanding how proteins fold, Forman-Kay says. “There’s this sense now that people don’t have to do experimental structure determination, which is not true.”

F20H23.2

Source organism:

Thale cress (Arabidopsis thaliana)

Importance:

This plant protein is a kinase, which tacks phosphates onto other molecules, potentially changing their functions.

Note: The confidence level of AlphaFold’s predictions vary within each protein. Dark blue and light blue regions on a predicted structure mean the algorithm is relatively sure. Less certain predictions are colored yellow and orange.

Plodding progress

Proteins start out as long chains of amino acids and fold into a host of curlicues and other 3-D shapes. Some resemble the tight corkscrew ringlets of a 1980s perm or the pleats of an accordion. Others could be mistaken for a child’s spiraling scribbles.

A protein’s architecture is more than just aesthetics; it can determine how that protein functions. For instance, proteins called enzymes need a pocket where they can capture small molecules and carry out chemical reactions. And proteins that work in a protein complex, two or more proteins interacting like parts of a machine, need the right shapes to snap into formation with their partners.

Knowing the folds, coils and loops of a protein’s shape may help scientists decipher how, for example, a mutation alters that shape to cause disease. That knowledge could also help researchers make better vaccines and drugs.

For years, scientists have bombarded protein crystals with X-rays, flash frozen cells and examined them under high­powered electron microscopes, and used other methods to discover the secrets of protein shapes. Such experimental methods take “a lot of personnel time, a lot of effort and a lot of money. So it’s been slow,” says Tamir Gonen, a membrane biophysicist and Howard Hughes Medical Institute investigator at the David Geffen School of Medicine at UCLA.

Ice nucleation protein

Source organism:

Pseudomonas bacteria (Pseudomonas syringae)

Importance:

Leads to frost damage on plants by triggering ice crystals at relatively high temperatures. It might be used for seeding clouds and food preservation.

Such meticulous and expensive experimental work has uncovered the 3-D structures of more than 194,000 proteins, their data files stored in the Protein Data Bank, supported by a consortium of research organizations. But the accelerating pace at which geneticists are deciphering the DNA instructions for making proteins has far outstripped structural biologists’ ability to keep up, says systems biologist Nazim Bouatta of Harvard Medical School. “The question for structural biologists was, how do we close the gap?” he says.

For many researchers, the dream has been to have computer programs that could examine the DNA of a gene and predict how the protein it encodes would fold into a 3-D shape.

Here comes AlphaFold

Over many decades, scientists made progress toward that AI goal. But “until two years ago, we were really a long way from anything like a good solution,” says John Moult, a computational biologist at the University of Maryland’s Rockville campus.

Moult is one of the organizers of a competition: the Critical Assessment of protein Structure Prediction, or CASP. Organizers give competitors a set of proteins for their algorithms to fold and compare the machines’ predictions against experimentally determined structures. Most AIs failed to get close to the actual shapes of the proteins.

Then in 2020, AlphaFold showed up in a big way, predicting the structures of 90 percent of test proteins with high accuracy, including two-thirds with accuracy rivaling experimental methods.

Deciphering the structure of single proteins had been the core of the CASP competition since its inception in 1994. With AlphaFold’s performance, “suddenly, that was essentially done,” Moult says.

Since AlphaFold’s 2021 release, more than half a million scientists have accessed its database, Hassabis said in the news briefing. Some researchers, for example, have used AlphaFold’s predictions to help them get closer to completing a massive biological puzzle: the nuclear pore complex. Nuclear pores are key portals that allow molecules in and out of cell nuclei. Without the pores, cells wouldn’t work properly. Each pore is huge, relatively speaking, composed of about 1,000 pieces of 30 or so different proteins. Researchers had previously managed to place about 30 percent of the pieces in the puzzle.

The nuclear pore

Researchers previously solved about 30 percent of the 1,000-piece puzzle that is the nuclear pore complex. AlphaFold helped make sense of experimental data to complete 60 percent of the structure.

That puzzle is now almost 60 percent complete, after combining AlphaFold predictions with experimental techniques to understand how the pieces fit together, researchers reported in the June 10 Science.

Now that AlphaFold has pretty much solved how to fold single proteins, this year CASP organizers are asking teams to work on the next challenges: Predict the structures of RNA molecules and model how proteins interact with each other and with other molecules.

For those sorts of tasks, Moult says, deep-learning AI methods “look promising but have not yet delivered the goods.”

Where AI falls short

Being able to model protein interactions would be a big advantage because most proteins don’t operate in isolation. They work with other proteins or other molecules in cells. But AlphaFold’s accuracy at predicting how the shapes of two proteins might change when the proteins interact are “nowhere near” that of its spot-on projections for a slew of single proteins, says Forman-Kay, the University of Toronto protein biophysicist. That’s something AlphaFold’s creators acknowledge too.

The AI trained to fold proteins by examining the contours of known structures. And many fewer multiprotein complexes than single proteins have been solved experimentally.

Gametocyte surface antigen 48/45

Source organism: 

Malaria parasite (Plasmodium falciparum)

Importance:

Allows the parasite’s male and female gametes to fuse. It is being developed as a potential vaccine.

Forman-Kay studies proteins that refuse to be confined to any particular shape. These intrinsically disordered proteins are typically as floppy as wet noodles (SN: 2/9/13, p. 26). Some will fold into defined forms when they interact with other proteins or molecules. And they can fold into new shapes when paired with different proteins or molecules to do various jobs.

AlphaFold’s predicted shapes reach a high confidence level for about 60 percent of wiggly proteins that Forman-Kay and colleagues examined, the team reported in a preliminary study posted in February at bioRxiv.org. Often the program depicts the shapeshifters as long corkscrews called alpha helices.

Forman-Kay’s group compared AlphaFold’s predictions for three disordered proteins with experimental data. The structure that the AI assigned to a protein called alpha-synuclein resembles the shape that the protein takes when it interacts with lipids, the team found. But that’s not the way the protein looks all the time.

For another protein, called eukaryotic translation initiation factor 4E-binding protein 2, AlphaFold predicted a mishmash of the protein’s two shapes when working with two different partners. That Frankenstein structure, which doesn’t exist in actual organisms, could mislead researchers about how the protein works, Forman-Kay and colleagues say.

Eukaryotic translation initiation factor 4E-binding protein 2

Source organism:

Human

Importance:

Helps control production of other proteins and may be involved in learning and memory. Despite AlphaFold’s high confidence (blue) in its predictions of the lower coiled area and the ribbon structure just above it, the two would never appear at the same time.

AlphaFold may also be a little too rigid in its predictions. A static “structure doesn’t tell you everything about how a protein works,” says Jane Dyson, a structural biologist at the Scripps Research Institute in La Jolla, Calif. Even single proteins with generally well-defined structures aren’t frozen in space. Enzymes, for example, undergo small shape changes when shepherding chemical reactions.

If you ask AlphaFold to predict the structure of an enzyme, it will show a fixed image that may closely resemble what scientists have determined by X-ray crystallography, Dyson says. “But [it will] not show you any of the subtleties that are changing as the different partners” interact with the enzyme.

“The dynamics are what Mr. AlphaFold can’t give you,” Dyson says.

A revolution in the making

The computer renderings do give biologists a head start on solving problems such as how a drug might interact with a protein. But scientists should remember one thing: “These are models,” not experimentally deciphered structures, says Gonen, at UCLA.

He uses AlphaFold’s protein predictions to help make sense of experimental data, but he worries that researchers will accept the AI’s predictions as gospel. If that happens, “the risk is that it will become harder and harder and harder to justify why you need to solve an experimental structure.” That could lead to reduced funding, talent and other resources for the types of experiments needed to check the computer’s work and forge new ground, he says.

Vitellogenin

Source organism:

Honeybee (Apis mellifera)

Importance:

Helps protect against bacterial infections.

Harvard Medical School’s Bouatta is more optimistic. He thinks that researchers probably don’t need to invest experimental resources in the types of proteins that AlphaFold does a good job of predicting, which should help structural biologists triage where to put their time and money.

“There are proteins for which AlphaFold is still struggling,” Bouatta agrees. Researchers should spend their capital there, he says. “Maybe if we generate more [experimental] data for those challenging proteins, we could use them for retraining another AI system” that could make even better predictions.

He and colleagues have already reverse engineered AlphaFold to make a version called OpenFold that researchers can train to solve other problems, such as those gnarly but important protein complexes.

Massive amounts of DNA generated by the Human Genome Project have made a wide range of biological discoveries possible and opened up new fields of research (SN: 2/12/22, p. 22). Having structural information on 200 million proteins could be similarly revolutionary, Bouatta says.

In the future, thanks to AlphaFold and its AI kin, he says, “we don’t even know what sorts of questions we might be asking.”

in Science News on 2022-09-23 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

The UK Is Rejoining the Space Race

in WIRED Science on 2022-09-23 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

The Wild Plan to Export Sun From the Sahara to the UK

in WIRED Science on 2022-09-23 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

BS 200 Embodied Cognition in Education with Sheila Macrine and Jennifer Fugate

This month's episode is a discussion with the editors of a fascinating new book Movement Matters: How Embodied Cognition Informs Teaching and Learning. We explore how embodied cognition challenges long standing dualist approaches to both cognition and learning. Sheila Macrine and Jennifer Fugate also share some of the innovative approaches that improve both how we teach and how we learn.

Links and References:

• Movement Matters: How Embodied Cognition Informs Teaching and Learning edited by Sheila L. Macrine and Jennifer M.B. Fugate
• Recent episodes about Embodied Cognition:
  • BS 193 What does it mean to say the Mind is Embodied?
  • BS 198 Encore of interview with Evan Thompson
• Please visit http://brainsciencepodcast.com for additional references and episode transcripts.

• TextEpander at textexpander.com/podcast
• BetterHelp at betterhelp.com/ginger

Announcements:

Please take a few minutes to complete this audience survey.

• Contact Dr. Campbell if you are interested a listener meet-up or sponsoring a talk by Dr. Campbell during her trip to Europe in April 2023.
• Get free gift "5 Things You Need to Know about YOUR Brain when you sign up for the free Brain ScienceNewsletter to get show notes automatically every month. You can also text brainscience to 55444 to sign up.
• Check out the Brain Science podcast channel on YouTube
• Support Brain Science by buying Are You Sure? The Unconscious Origins of Certainty by Virginia "Ginger" Campbell, MD. (Autographed copies are available)
• Check out the free Brain Science Mobile app for iOS, Android, and Windows. (It's a great way to get both new episodes and premium content.)
• Learn more ways to support Brain Science at http://brainsciencepodcast.com/donations

Connect on Social Media:

• Twitter: @docartemis
• Facebook page: http://www.facebook.com/brainsciencepodcast

Contact Dr. Campbell:

• Email: brainsciencepodcast@gmail.com

in Brain Science with Ginger Campbell, MD: Neuroscience for Everyone on 2022-09-23 09:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Schneider Shorts 23.09.2022 – Elsevier apologises

in For Better Science on 2022-09-23 05:27:54 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Fired postdoc faked recommendation letters from supervisor, OSU alleges

in Retraction watch on 2022-09-22 20:52:36 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

How ghostly neutrinos could explain the universe’s matter mystery

The answer to one of the greatest mysteries of the universe may come down to one of the smallest, and spookiest, particles.

Matter is common in the cosmos. Everything around us — from planets to stars to puppies —  is made up of matter. But matter has a flip side: antimatter. Protons, electrons and other particles all have antimatter counterparts: antiprotons, positrons, etc. Yet for some reason antimatter is much rarer than matter — and no one knows why.

Physicists believe the universe was born with equal amounts of matter and antimatter. Since matter and antimatter counterparts annihilate on contact, that suggests the universe should have ended up with nothing but energy. Something must have tipped the balance.

Some physicists think lightweight subatomic particles called neutrinos could point to an answer. These particles are exceedingly tiny, with less than a millionth the mass of an electron (SN: 4/21/21). They’re produced in radioactive decays and in the sun and other cosmic environments. Known for their ethereal tendency to evade detection, neutrinos have earned the nickname “ghost particles.”  These spooky particles, originally thought to have no mass at all, have a healthy track record of producing scientific surprises (SN: 10/6/15).

Now researchers are building enormous detectors to find out if neutrinos could help solve the mystery of the universe’s matter. The Hyper-Kamiokande experiment in Hida City, Japan, and the Deep Underground Neutrino Experiment in Lead, S.D., will study neutrinos and their antimatter counterparts, antineutrinos. A difference in neutrinos’ and antineutrinos’ behavior might hint at the origins of the matter-antimatter imbalance, scientists suspect.

Watch the video below to find out how neutrinos might reveal why the universe contains, well, anything at all.

in Science News on 2022-09-22 14:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

There’s New Proof Crispr Can Edit Genes Inside Human Bodies

in WIRED Science on 2022-09-22 13:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Lawns Are Dumb. But Ripping Them Out May Come With a Catch

in WIRED Science on 2022-09-22 12:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

This face mask can sense the presence of an airborne virus

Face masks — the unofficial symbol of the COVID-19 pandemic — are leveling up.

A mask outfitted with special electronics can detect SARS-CoV-2, the virus that causes COVID-19, and other airborne viruses within 10 minutes of exposure, materials researcher Yin Fang and colleagues report September 19 in Matter.

“The lightness and wearability of this face mask allows users to wear it anytime, anywhere,” says Fang, of Tongji University in Shanghai. “It’s expected to serve as an early warning system to prevent large outbreaks of respiratory infectious diseases.”

Airborne viruses can hitch a ride between hosts in the air droplets that people breathe in and out. People infected with a respiratory illness can expel thousands of virus-containing droplets by talking, coughing and sneezing. Even those with no signs of being sick can sometimes pass on these viruses; people who are infected with SARS-CoV-2 can start infecting others at least two to three days before showing symptoms (SN: 3/13/20). So viruses often have a head start when it comes to infecting new people. 

Fang and his colleagues designed a special sensor that reacts to the presence of certain viral proteins in the air and attached it to a face mask. The team then spritzed droplets containing proteins produced by the viruses that cause COVID-19, bird flu or swine flu into a chamber with the mask.

The sensor could detect just a fraction of a microliter of these proteins — a cough might contain 10 to 80 times as much. Once a pathogen was detected, the sensor-mask combo sent a signal to the researchers informing them of the virus’s presence. Ultimately, the researchers plan for such signals to be sent to a wearer’s phone or other devices. By combining this technology with more conventional testing, the team says, health care providers and public health officials might be able to better contain future pandemics.

in Science News on 2022-09-22 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Europe’s Heat Waves Offer a Grim Vision of the Future

in WIRED Science on 2022-09-22 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

A journal did nothing about plagiarism allegations for a year. Then the tweets (and an email from Retraction Watch) came.

in Retraction watch on 2022-09-22 10:11:18 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

A Better Birth Is Possible

in WIRED Science on 2022-09-22 10:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Celebrating Peer Review Week at BMC: What’s next for Research Integrity and the Reproducibility Crisis?

John Ioannidis’ 2005 article Why Most Published Research Findings Are False was an uncomfortable wake-up call for many in the scientific community. The paper has led many to take a more critical eye to published research, leading to a wave of high-profile retractions and several major studies warning of a reproducibility crisis in science. So great is this concern that it has moved out of the academic sphere with governments and regulators taking an interest, such as the 2021 call from the UK House of Commons Science and Technology Committee for evidence on reproducibility and research integrity across research institutions.

Alongside the reproducibility crisis the meaning of the term ‘Research Integrity’ has evolved. Originally used to define a governing ethos for best practice in scientific research and the practices it encompasses, Research Integrity has become a research field in its own right spanning sociology, philosophy, statistics, science education and meta-research. BMC Research Notes recently closed its collection on Reproducibility and Research Integrity, launched in collaboration with the UK Reproducibility Network. The submissions reflect how this field has matured, shifting focus from identifying problems – to offering solutions.

Education

A popular solution to improving research integrity is to educate aspiring researchers on the importance of robust, reproducible scientific practice. Andreas Meid describes a pilot lecture series created to equip their students with this understanding and gives an honest account of what worked and what did not. Dr Meid’s lectures placed focus on developing statistical skills, an approach supported by Penny Reynolds. In her commentary, she lays out her case for better statistical education for all investigators as a solution to the pervasive reproducibility issues found in translating pre-clinical research stating “Properly designed and analyzed experiments are a matter of ethics as much as procedure…reducing the numbers of animals wasted in non-informative experiments and increasing overall scientific quality and value of published research.”

“Properly designed and analyzed experiments are a matter of ethics as much as procedure…reducing the numbers of animals wasted in non-informative experiments and increasing overall scientific quality and value of published research.”

Technical education alone is not enough, argue Ilinca Ciubotariu and Gundula Bosch. They highlight the importance of science-communication to ratify research quality and promote trust in researchers. In their commentary, they showcase the framework of responsible science communication taught to students at Johns Hopkins Bloomberg School of Public Health. They hope fostering this ethos will promote more transparent and accountable science in the future. Daniel Pizzolato and Kris Dierickx also consider ways to stimulate responsible research practices across the hierarchies of academic institutions. They advocate turning traditional ideas of pedagogy on their head through reverse mentoring, where a junior academic shares their scientific insights with a senior colleague. Such approaches are well established across many other industries; it seems high time for academia to catch up.

Institutions

Across the collection, many call for change at the institutional level. Olivia Kowalczyk describes how institute heads can cultivate an environment of reproducible, open research by changing funding and hiring criteria to align with such principles. Sweeping changes in how we value research are called for by Stephen Bradley. He argues that funders should stop using citations and impact factors to assess research and instead make judgements based on quality, reproducibility, and societal value. Scientific publishers must also play their part in the pursuit of better science. Patrick Diaba-Nuhoho and Michael Amponsah-Offeh call for journals to promote the publication of unexpected results and null findings to help dispel the distinctly unscientific taboo of publishing null and negative data*.

Peer Review

Peer review also comes under critique. Robert Schultz ponders the potential of automated screening tools to aid manuscript assessment, hoping it might help to screen a growing influx of new submissions more quickly, allowing reviewers more time to consider the papers they receive. Alexandru Marcoci advocates a total overall to the traditional peer review system. He proposes it be treated like an expert elicitation process, applying methods from mathematics, psychology, and decision theory to mitigate biases and enhance the transparency, accuracy, and defensibility of the resulting judgment. In this way, he argues, peer review will become an intrinsically more transparent and reliable process. An ambitious initiative but perhaps it is time to think big.

Collaboration

I contacted two contributors to the collection with the question, ‘If money were no object – what one initiative would about the greatest improvement in research integrity? One wanted the methods section to be mandated as open access across all journals, believing that transparent methods can lead to better science. The other wished to begin a longitudinal study of academic supervisors and their students to identify the best means to promote reproducible science across generations of researchers. Clearly, potential solutions to the reproducibility crisis are manifold, transcending fields and institutions. In a sentiment echoed across the collection, Andrew Stewart of the UK Reproducibility Network argues that the only way to improve research integrity is to drive systematic change across the key scientific stakeholders: academic institutions, research organizations, funders, publishers, and the government. In agreement, Natasha Drude emphasizes that the research community should “view initiatives that promote reproducibility not as a one-size-fits-all undertaking, but rather as an opportunity to unite stakeholders and customize drivers of cultural change.”

Overall the view of the collection seems cautiously optimistic. Now that we have established the issues of reproducibility and research integrity, perhaps we have a chance to change science for the better. An attitude well summarized in the title of Guest Editor Marcus Munafò’s article –

“The reproducibility debate is an opportunity, not a crisis”.

My sincere thanks to my predecessor Dr. Tamara Hughes for instigating this collection and to Professor. Marcus Munafò for putting it together.

*I feel I must note that BMC Research Notes welcomes submissions presenting null and negative results.

The post Celebrating Peer Review Week at BMC: What’s next for Research Integrity and the Reproducibility Crisis? appeared first on BMC Series blog.

in BMC Series blog on 2022-09-21 15:43:03 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

After eons of isolation, these desert fish flub social cues

Getting out into society after a long isolation gets awkward. Ask the Pahrump poolfish, loners in a desert for some 10,000 years.

This hold-in-your-hand-size fish (Empetrichthys latos) has a chubby, torpedo shape and a mouth that looks as if it’s almost smiling. Until the 1950s, this species had three forms, each evolving in its own spring. Now only one survives, which developed in a spring-fed oasis in the Mojave Desert’s Pahrump Valley, about an hour’s drive west of Las Vegas.

Fish in a desert are not that weird when you take the long view (SN: 1/26/16). In a former life, some desert valleys were ancient lakes. As the region’s lakes dried up, fish got stuck in the remaining puddles. Various stranded species over time adapted to quirks of their private microlakes, and a desert-fish version of the Galapagos Islands’ diverse finches arose.

“We like to say that Darwin, if he had a different travel agent, could have come to the same conclusions just from the desert,” says evolutionary biologist Craig Stockwell of North Dakota State University in Fargo.

The desert “island” where E. latos evolved was Manse Spring on a private ranch. From a distance, the spring looked “just like a little clump of trees,” remembers ecologist Shawn Goodchild, who is now based in Lake Park, Minn. The spot of desert greenery surrounded the Pahrump poolfish’s entire native range, about the length of an Olympic swimming pool.

By the 1960s, biologists feared the fish were doomed. The spring’s flow rate had dropped some 70 percent as irrigation for farms in the desert sucked away water. And disastrous predators arrived: a kid’s discarded goldfish. Conservation managers fought back, but neither poison nor dynamite wiped out the newcomers. And then in August of 1975, Manse Spring dried up.

Conservation managers had moved some poolfish to other springs, but the long-isolated species just didn’t seem to get the dangers of living with other kinds of fishes. The poolfish were easily picked off by predators in their new home.

Lab tests of fake fish-murder scenes may help explain why. For instance, researchers tainted aquarium water with pureed fish bits. In an expected reaction, fathead minnows (Pimephales promelas) freaked at traces of dead minnow drifting through the water and huddled low in the tank. The Pahrump poolfish in water tainted with blender-whizzed skin of their kind just kept swimming around the upper waters as if corpse taint were no scarier than tap water. Literally. Stockwell and colleagues can say that because they ran a fear test with nonscary dechlorinated tap water. Poolfish didn’t huddle then either, the team reports in the Aug. 31 Proceedings of the Royal Society B.

Then, however, Stockwell and a colleague were musing about some rescued poolfish in cattle tanks when nearby dragonflies caught the researchers’ attention.

Before dragonflies mature into shimmering aerial marvels, the young prowl underwater as violent predators. In moves worthy of scary aliens in a sci-fi movie, many dragonfly nymphs can shoot their jaws out from their head to scoop up prey, including fish eggs and fish larvae. With young dragonflies prowling a pool’s bottom and plants, poolfish moving up the water column “would be a good way to reduce their risk,” Stockwell says. Testing of that idea has begun.

Fish that people thought were foolishly naïve may just be savvy in a different way. Especially after isolation in a desert with dragons.

in Science News on 2022-09-21 15:39:49 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Open Access Doesn’t Need APCs: Our Progress To-Date

Author: Sara Rouhi, Director of Strategic Partnerships, PLOS

Earlier this year I outlined three ways PLOS is working to eliminate author fees through new business models. The models we introduced in 2020 began as an experiment to systemically address the barriers publications fees pose for many researchers and prove that APCs are not the only way to support Open Access. More sustainable–and equitable–models exist and we’re grateful to have partnered with so many institutions that are ready to flip the system.

Change is coming

Though we still have more work ahead of us and many more conversations to be had with research stakeholders around the world, I am super gratified to report that as of today, 181 institutions in 26 countries have partnered with us., that’s up from 93 and 6, respectively from last year.

Here’s a look back at the road to get here so far:

The new era of Open Access

PLOS was founded in 2001 with a mission to transform science communication. PLOS journals were some of the earliest Open Access titles in biology and medicine, and a key driver in proving all readers can and should have access to research without barriers. Today, many research funders, institutions, and governments now require research to be made available under Open Access licensing and provide funds that can be applied to authors’ Open Access publication costs. But the ways in which Open Access is supported varies across different fields and global regions. There are gaps that leave many researchers who want to publish in Open Access journals without funding for APCs.

That’s why we embarked on this journey nearly three years ago. We were the vanguard of publishers who demonstrated that Open Access publishing could be sustainable, but we only had half the equation right. In short, we weren’t fulfilling our entire vision for an open and inclusive research ecosystem that facilitated the exchange of free and unrestricted knowledge. Anyone could read the research we published, but the cost of publishing in an Open venue was–and continues to be–a barrier for many authors.

Progress towards fee-free publishing

This year, we have signed three large consortia deals. Bibsam, CSAL, and IReL. They join a growing list of institutions including the Sachsen Consortia led by the Saxon State and University Library, the Big Ten Academic Alliance, the University of California system, CRL and NERL, Jisc (including University College London, Imperial College London, University of Manchester) and the Canadian Research Knowledge Network among others

At PLOS we are committed to co-creating pathways to Open Access and Open Science as we carry our mission forward. A piece of that is ensuring our approach to Open Access solutions are not one-size-fits-all. It’s the reason we don’t have just one institutional partnership model for all of our journals, but several that cater to the needs of the journal research communities, and the bodies who financially support researchers’ work. These include CAP, which keeps costs low for selective journals (and was recently honored with an ALPSP award);  Global Equity, which reflects regional economic differences; and our Flat Fee model that aims to make Open Access publishing easier and more accessible for researchers.

The uptake of these models is incredible. Doubling the number of institutions is gratifying, but, on a personal note, I take greater pride in spreading Open Access publishing worldwide. This is great for institutions and PLOS, but even better for researchers. We are as eager as any author to see open-to-publish frameworks become the norm, just as Open Access has taken hold over the past two decades. I’m just excited to be playing a part in making that happen. Watch this space for more updates!

The post Open Access Doesn’t Need APCs: Our Progress To-Date appeared first on The Official PLOS Blog.

in The Official PLOS Blog on 2022-09-21 14:27:38 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

A protogalaxy in the Milky Way may be our galaxy’s original nucleus

The Milky Way left its “poor old heart” in and around the constellation Sagittarius, astronomers report. New data from the Gaia spacecraft reveal the full extent of what seems to be the galaxy’s original nucleus — the ancient stellar population that the rest of the Milky Way grew around — which came together more than 12.5 billion years ago.

“People have long speculated that such a vast population [of old stars] should exist in the center of our Milky Way, and Gaia now shows that there they are,” says astronomer Hans-Walter Rix of the Max Planck Institute for Astronomy in Heidelberg, Germany.

The Milky Way’s ancient heart is a round protogalaxy that spans nearly 18,000 light-years and possesses roughly 100 million times the mass of the sun in stars, or about 0.2 percent of the Milky Way’s current stellar mass, Rix and colleagues report in a study posted September 7 at arXiv.org.

“This study really helps to firm up our understanding of this very, very, very young stage in the Milky Way’s life,” says Vasily Belokurov, an astronomer at the University of Cambridge who was not involved in the work. “Not much is really known about this period of the Milky Way’s life,” he says. “We’ve seen glimpses of this population before,” but the new study gives “a bird’s-eye view of the whole structure.”

Most stars in the Milky Way’s central region abound with metals, because the stars originated in a crowded metropolis that earlier stellar generations had enriched with those metals through supernova explosions. But Rix and his colleagues wanted to find the exceptions to the rule, stars so metal-poor they must have been born well before the rest of the galaxy’s stellar denizens came along — what Rix calls “a needle-in-a-haystack exercise.”

His team turned to data from the Gaia spacecraft, which launched in 2013 on a mission to chart the Milky Way (SN: 6/13/22). The astronomers searched about 2 million stars within a broad region around the galaxy’s center, which lies in the constellation Sagittarius, looking for stars with metal-to-hydrogen ratios no more than 3 percent of the sun’s.

The astronomers then examined how those stars move through space, retaining only the ones that don’t dart off into the vast halo of metal-poor stars engulfing the Milky Way’s disk. The end result: a sample of 18,000 ancient stars that represents the kernel around which the entire galaxy blossomed, the researchers say. By accounting for stars obscured by dust, Rix estimates that the protogalaxy is between 50 million and 200 million times as massive as the sun.

“That’s the original core,” Rix says, and it harbors the Milky Way’s oldest stars, which he says probably have ages exceeding 12.5 billion years. The protogalaxy formed when several large clumps of stars and gas conglomerated long ago, before the Milky Way’s first disk — the so-called thick disk — arose (SN: 3/23/22).

The protogalaxy is compact, which means little has disturbed it since its formation. Smaller galaxies have crashed into the Milky Way, augmenting its mass, but “we didn’t have any later mergers that deeply penetrated into the core and shook it up, because then the core would be larger now,” Rix says.

The new data on the protogalaxy even capture the Milky Way’s initial spin-up — its transition from an object that didn’t rotate into one that now does. The oldest stars in the proto–Milky Way barely revolve around the galaxy’s center but dive in and out of it instead, whereas slightly younger stars show more and more movement around the galactic center. “This is the Milky Way trying to become a disk galaxy,” says Belokurov, who saw the same spin-up in research that he and a colleague reported in July.

Today, the Milky Way is a giant galaxy that spins rapidly — each hour our solar system speeds through 900,000 kilometers of space as we race around the galaxy’s center. But the new study shows that the Milky Way got its start as a modest protogalaxy whose stars still shine today, stars that astronomers can now scrutinize for further clues to the galaxy’s birth and early evolution.

in Science News on 2022-09-21 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

It’s Time for Cities to Ditch Delivery Trucks—for Cargo Bikes

in WIRED Science on 2022-09-21 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

C Ronald Kahn and The Problem of Irreproducible Bioscience Research

in For Better Science on 2022-09-21 06:49:35 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Former Iranian government official up to two retractions, five corrections

in Retraction watch on 2022-09-21 02:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Drumming woodpeckers use similar brain regions as songbirds

Songbirds get a lot of love for their dulcet tones, but drummers may start to steal some of that spotlight.

Woodpeckers, which don’t sing but do drum on trees, have brain regions that are similar to those of songbirds, researchers report September 20 in PLOS Biology. The finding is surprising because songbirds use these regions to learn their songs at an early age, yet it’s not clear if woodpeckers learn their drum beats (SN: 9/16/21). Whether woodpeckers do or not, the result suggests a shared evolutionary origin for both singing and drumming.

The ability to learn vocalizations by listening to them, just like humans do when learning to speak, is a rare trait in the animal kingdom. Vocal learners, such as songbirds, hummingbirds and parrots, have independently evolved certain clusters of nerve cells called nuclei in their forebrains that control the ability. Animals that don’t learn vocally are thought to lack these brain features.

While it’s commonly assumed that other birds don’t have these nuclei, “there’s thousands of birds in the world,” says Matthew Fuxjager, a biologist at Brown University in Providence, R.I. “While we say these brain regions only exist in these small groups of species, nobody’s really looked in a lot of these other taxa.”

Fuxjager and his colleagues examined the noggins of several birds that don’t learn vocally to check if they really did lack these brain nuclei. Using molecular probes, the team checked the bird brains for activity of a gene called parvalbumin, a known marker of the vocal learning nuclei. Many of the birds, including penguins and flamingos, came up short, but there was one exception — male and female woodpeckers, which had three spots in their brains with high parvalbumin activity.

Though woodpeckers don’t sing, they do perform a rapid drumming on trees and house gutters to defend their territories or find mates. This drumming is different from the drilling the birds do to find food. When the team found brain nuclei similar to songbirds in woodpeckers, Fuxjager was immediately intrigued. “I thought right away it’s probably related to drumming,” he says.

The researchers subjected downy woodpeckers (Dryobates pubescens) in the wild to audio recordings of drumming from other woodpeckers. This faux territorial invasion sparked an aggressive drumming response from the birds, which were then captured and euthanized to have their recent brain activity analyzed. Sure enough, the same regions identified by earlier lab tests had been activated in the drummers.

The brains of bird vocalists and drummers evolved separately, but the similarity of the analyzed regions hints at a common origin. “It suggests that there are common themes about how you develop these complex behaviors,” says Bradley Colquitt, a biologist at the University of California, Santa Cruz who was not involved in the study. The neural circuitry formed by these nuclei most likely developed from an ancestral circuit controlling movement, Colquitt says.

“Birdsong is basically the brain controlling muscles in a vocal organ called the syrinx,” Fuxjager says. These sophisticated movements are not unlike the swift head-and-neck motions involved in drumming.

Whether drumming is learned like birdsong remains an open question that the team is now exploring. Future work will also look at how woodpeckers’ brains are wired, how these nuclei control drumming and how the brain regions’ role in drumming evolved across woodpecker species, Fuxjager says.

This new study “uncovers another species that we can add to our comparative efforts” to better understand how complex behaviors evolve, Colquitt says. “It is a preview into potentially exciting evolutionary neurobiology.” Now that woodpeckers have joined the band of important musical birds, it looks like the drummers may soon get their chance to shine.

in Science News on 2022-09-20 18:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

The Fungus That Killed Frogs—and Led to a Surge in Malaria

in WIRED Science on 2022-09-20 16:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Fossil finds put gibbons in Asia as early as 8 million years ago

Small-bodied, long-armed apes called gibbons swing rapidly through the trees, far outpacing scientists’ attempts to decipher these creatures’ evolutionary story.

Now, a partial upper jaw and seven isolated teeth found near a southwestern Chinese village have added bite to a suggestion that the earliest known gibbons hung out there about 7 million to 8 million years ago, researchers report in the October Journal of Human Evolution.

Those fossils, as well as 14 teeth previously found at the same site and a nearby site, belong to an ancient hylobatid species called Yuanmoupithecus xiaoyuan, say paleoanthropologist Xueping Ji of the Kunming Natural History Museum of Zoology in China and colleagues. Hylobatids, a family of apes that includes about 20 species of living gibbons and a black-furred gibbon called the siamang, inhabit tropical forests from northeastern India to Indonesia.

Ji’s group has presumed that Y. xiaoyuan was an ancient gibbon since introducing the species in a 2006 Chinese publication. But additional fossils were needed to check that suspicion.

The newly discovered upper jaw piece — found by a local villager and given to Ji during fieldwork around a decade ago — contains four teeth, including a partly erupted molar that helped researchers identify it as the remains of an infant that died before reaching age 2.

Comparisons with modern apes and fossils of ancient primates peg Y. xiaoyuan as the oldest known gibbon and cast doubt on a two-year-old report that a roughly 13-million-year-old molar tooth found in northern India came from a hylobatid, the team says (SN: 9/8/20). The fossil found in India, assigned to a species dubbed Kapi ragnagarensis, represents an extinct group of South Asian primates that were not closely related to present-day apes, the scientists say.

Prior DNA analyses of living primates suggested that hylobatids diverged from other apes in Africa between 22 million and 17 million years ago. But it’s a mystery when gibbon ancestors arrived in Eurasia, says paleoanthropologist and study coauthor Terry Harrison of New York University. A gap in the fossil record of about 10 million years exists between the estimated time when hylobatids emerged in or near Africa and evidence of Y. xiaoyuan in Asia.

Genetic evidence also indicates that gibbon species today shared a common ancestor around 8 million years ago, when Y. xiaoyuan was alive. “It could be that [Y. xiaoyuan] is the ancestor of all later gibbons,” Harrison says. If not, Y. xiaoyuan was closely related to a modern gibbon ancestor, he suspects.

Bumps and depressions on chewing surfaces and other tooth and jaw features of Y. xiaoyuan look much like those of living gibbons, Ji’s team says. Some traits of the fossil species were precursors of slightly different traits in modern gibbons, the researchers suggest.

Based on molar sizes, they estimate that Y. xiaoyuan weighed about six kilograms, similar to gibbons today. Molar structure indicates that Y. xiaoyuan focused on eating fruits, like most gibbon species today, Harrison says.

Ji’s group “makes a very good case that [Y. xiaoyuan] is a hylobatid,” says paleoanthropologist David Alba of Institut Català de Paleontologia Miquel Crusafont in Barcelona.

But the evolutionary status of K. ragnagarensis remains unsettled because only a single tooth from that species has been found, says Alba, who did not participate in the new study.

in Science News on 2022-09-20 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

The US Is Measuring Extreme Heat Wrong

in WIRED Science on 2022-09-20 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Research Revealed

You never know how a discovery may affect future research—and as much as they try to anticipate the contribution or future application of a paper, neither do editors.

When journals only focus on significance of advance and priority of discovery, valuable information is excluded from the scientific record. Rigorous research that adds supporting evidence, re-examines and broadens our understanding leads to a stronger foundation of knowledge. But without the right ways to share it, many important insights could remain hidden from public view, buried in filing drawers and hard drives. 

At PLOS, we’re committed to helping researchers share more of their science—including contributions that might otherwise be excluded from the scientific record. We use journal policy, specialized articles types, and unique editorial selection criteria to help ensure that important advances receive the respect and attention they deserve. Here’s how:

1. The PLOS-wide Complementary Research (or “Scooping”) Policy

Sometimes, two research groups independently achieve similar results around the same time. When that happens, it can be difficult for the second group to publish their work, because it may no longer meet the novelty requirements for selective journals.

At PLOS, we see complementary findings as a positive, reinforcing the validity of both studies. That’s why all of our journals—even the most selective—offer scooping protection to ensure that complementary results will not be rejected for novelty within six months of a similar preprint or publication by another group.

Read more about the PLOS Complementary Research Policy.

“I’m delighted to support PLOS Biology’s mission for open science by acting as an Academic Editor. The editorial process is a collaboration between the academic and professional editors – the best of both worlds! The no-scoop policy for manuscripts under consideration reflects the emphasis on quality.”

Emma Rawlins, Cambridge University UK, Academic Editor, PLOS Biology

2. Registered Reports and Preregistered Research Articles

Preregistration is the practice of formally depositing a study design in a repository and submitting it for peer review at a journal prior to conducting experiments, data collection or analysis. Evaluating study designs supports a strong methodological approach, increases the credibility and reproducibility of results, and helps address publication bias. Accepted study design protocols receive a provisional acceptance for the future research article reporting the results—so researchers can proceed with the study knowing that the work will be publishable, no matter the outcome. Preregistration can be especially beneficial for Early Career Researchers, and anyone conducting high risk/high reward research. PLOS offers two options for researchers seeking to preregister their work: Registered Reports (PLOS ONE) and Preregistered Research Articles (PLOS Biology). 

Read more about the value of preregistered research.

“Preregistering the analysis that you’re going to do beforehand doesn’t mean that you can’t do exploratory analysis later, but it does mean that people know what you’re actually going to do before you do it. And it means that you’ve had to think through that process.”

Mark Williams, Macaquarie University, Academic Editor, PLOS ONE

3. Incremental advances, negative, and null results

With all the pressure to publish exciting and impactful new results, incremental advances, negative and null outcomes can get left behind—and left out of the scientific record. Over the long term, this creates knowledge gaps in the literature that can undermine credibility, slow progress, and waste resources.

Small advances, negative outcomes, and inconclusive results do matter. Seemingly minor findings can have major impacts down the line. Small discoveries can plant the seeds for future investigations. In demonstrating what doesn’t work, negative and null results can point the way toward alternative solutions which may prove more effective—not to mention saving other research groups time and resources.

All PLOS journals will consider meaningful negative and null outcomes if the research question they answer is sufficiently relevant to the field—but we also publish several journals that make incremental, negative and null results essential to their mission and editorial vision: PLOS ONE, PLOS Global Public Health, PLOS Climate, and PLOS Water.  Each of these journals is built on the editorial philosophy that all rigorous, well-conducted research has value, and should be preserved as a part of the permanent scientific record—including replication studies, as well as negative, and inconclusive results.

Read more about PLOS’s approach to negative and null results.

“Very frequently, journals will not accept negative results …publishing that negative data helps move science forward so that another lab shouldn’t spend money and time repeating the same experiments only to come out with negative data.”

Yvonne Fondufe-Mittendorf, University of Kentucky

4. That hard-to-place research article

Interdisciplinary research and studies from emerging fields can be difficult to place in many field-specific journals. Small or specialized editorial boards may lack the expertise necessary to evaluate the work from different angles, scope may rule some excellent research out if it is perceived to be on the edge of the field. PLOS ONE ensures this research finds a home and is discoverable to readers everywhere. Because of the journal’s inclusive scope, commitment to rigor instead of novelty or impact, and our broad network of editorial board members with expertise in more than 200 disciplines, all research in the sciences and related disciplines can be evaluated and shared with readers around the world.

Read more about PLOS ONE’s scope.

“My questions are often much bigger than I can answer. Our PLOS ONE article …  required molecular geneticists, population ecologists in Eurasia and North America, geographical statisticians, climate ecologists, and worldwide citizen scientists. True interdisciplinary research is rare. Few reviewers are available with the proper mindset, but reviewers and editors with these views are critical to the success of these papers. “

Beth Middleton, US Geological Survey, Wetland and Aquatic Research Center

Bonus: Ensuring research reaches the broadest audience

Even when published, research may remain out of view from audiences who need it. Broadly, Open Access licensing, article promotion and indexing all help ensure published (or preprinted!) research is available to as many people as possible. But where and how research is shared still shapes who sees it.

Many journals are built with a specific community in mind, catering to researchers in a specific field as both authors and readers eager to stay up-to-date on progress from their peers or dive deeper into discoveries and techniques that directly impact their own research. These journals are helpful spaces for building networks and sparking discussions that accelerate progress in a given field—but some topics are too big to tackle from within just one discipline or have far-reaching implications beyond a single field of study.

Multidisciplinary journals bring different viewpoints, skillsets and analytical approaches together, encouraging collaboration and conversation amongst research groups and decision-makers working to solve similar challenges. Many of our journals consider multi- or inter- disciplinary research in order to present a robust view of the field and it is a centerpiece of the mission for PLOS Climate, PLOS Global Public Health, and PLOS Water. These journals bridge gaps between related fields, consider social, economic, and behavioral factors that affect these issues, and bring regional perspectives together to address global challenges. By bringing together this work in a single venue, readers get a more holistic view of the topics and challenges in these areas, and how they might inform each other to foster more creative solutions, robust decision-making, or deepen existing knowledge.

What other aspects of scientific research should be uncovered and preserved?

Are there more ways PLOS could help to facilitate the sharing of high quality research that would ordinarily remain hidden? Share your thoughts in the comments.

The post Research Revealed appeared first on The Official PLOS Blog.

in The Official PLOS Blog on 2022-09-19 16:57:42 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Video shows the first fox known to fish for food

The fox froze. Inches from his paws, frenzied, spawning carp writhed in the shallow water along a reservoir’s shore. In a sudden flash of movement, the fox dove nose-first into the water, emerging with a large carp wriggling in his mouth. 

In March 2016, two researchers in Spain watched as a male red fox (Vulpes vulpes) stalked and caught 10 carp over a couple of hours. The event, described in a study published August 18 in Ecology, seems to be the first recorded instance of a fox fishing, the researchers say. The discovery makes red foxes just the second type of canid — the group that includes wolves and dogs — known to hunt fish.

“Seeing the fox hunting carp one after another was incredible,” says ecologist Jorge Tobajas of the University of Córdoba. “We have been studying this species for years, but we never expected something like this.” 

Tobajas and his colleague Francisco Díaz-Ruiz of the University of Málaga stumbled across the fishing fox while surveying a site for a different project. The fox first caught their attention because it didn’t immediately flee when it spotted the researchers. Seizing the opportunity, Tobajas and Díaz-Ruiz decided to hide nearby and see what the fox was up to.

Their curiosity turned into excitement after the fox caught its first fish. “The most surprising thing was to see how the fox hunted many carp without making any mistakes,” Tobajas says. “This made us realize that it was surely not the first time he had done it.”

Instead of immediately guzzling down all of the fish, the fox hid most of its catch and appeared to share at least one fish with a female fox, possibly its mate.

Fish remains have been spotted in the scat of foxes before. But scientists weren’t sure whether foxes had caught the fish themselves or were simply scavenging dead fish. This research confirms that some foxes fish for their food, says Thomas Gable, a wildlife ecologist at the University of Minnesota in Minneapolis who wasn’t involved in the research.

“I would be shocked if this was the only fox to have learned how to fish,” Gable says.

Wolves living on the Pacific coast of North America and in Minnesota are the only other canids known to fish (SN: 2/11/20). The fact that two canid species living on separate continents both fish opens the possibility that the behavior might be more common than previously thought, Gable says.

For Tobajas, the fishing fox is an example of how much scientists still don’t know about the natural world, even for species that live fairly close with humans. “The red fox is a very common species and is in many cases a bit hated,” he says. Foxes sometimes attack pets or livestock and are considered a pest in many places. But “observations like this show us that it a fascinating and very intelligent animal.”

in Science News on 2022-09-19 13:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

To Understand Brain Disorders, Consider the Astrocyte

in WIRED Science on 2022-09-19 12:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

This environmentally friendly quantum sensor runs on sunlight

Quantum tech is going green.

A new take on highly sensitive magnetic field sensors ditches the power-hungry lasers that previous devices have relied on to make their measurements and replaces them with sunlight. Lasers can gobble 100 watts or so of power — like keeping a bright lightbulb burning. The innovation potentially untethers quantum sensors from that energy need. The result is an environmentally friendly prototype on the forefront of technology, researchers report in an upcoming issue of Physical Review X Energy.

The big twist is in how the device uses sunlight. It doesn’t use solar cells to convert light into electricity. Instead, the sunlight does the job of the laser’s light, says Jiangfeng Du, a physicist at the University of Science and Technology of China in Hefei.   

Quantum magnetometers often include a powerful green laser to measure magnetic fields. The laser shines on a diamond that contains atomic defects (SN: 2/26/08). The defects result when nitrogen atoms replace some of the carbon atoms that pure diamonds are made of. The green laser causes the nitrogen defects to fluoresce, emitting red light with an intensity that depends on the strength of the surrounding magnetic fields.

The new quantum sensor needs green light too. There’s plenty of that in sunlight, as seen in the green wavelengths reflected from tree leaves and grass. To collect enough of it to run their magnetometer, Du and colleagues replaced the laser with a lens 15 centimeters across to gather sunlight. They then filtered the light to remove all colors but green and focused it on a diamond with nitrogen atom defects. The result is red fluorescence that reveals magnetic field strengths just as laser-equipped magnetometers do.

Changing energy from one type to another, as happens when solar cells collect light and produce electricity, is an inherently inefficient process (SN: 7/26/17). The researchers claim that avoiding the conversion of sunlight to electricity to run lasers makes their approach three times more efficient than would be possible with solar cells powering lasers.

“I’ve never seen any other reports that connect solar research to quantum technologies,” says Yen-Hung Lin, a physicist at the University of Oxford who was not involved with the study. “It might well ignite a spark of interest in this unexplored direction, and we could see more interdisciplinary research in the field of energy.”

Quantum devices sensitive to other things, like electric fields or pressure, could also benefit from the sunlight-driven approach, the researchers say. In particular, space-based quantum technology might use the intense sunlight available outside Earth’s atmosphere to provide light tailored for quantum sensors. The remaining light, in wavelengths that the quantum sensors don’t use, could be relegated to solar cells that power electronics to process the quantum signals.

The sunlight-driven magnetometer is just a first step in the melding of quantum and environmentally sustainable technology. “In the current state, this device is primarily for developmental purposes,” Du says. “We expect that the devices will be used for practical purposes. But there [is] lots of work to be done.”

in Science News on 2022-09-19 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Electric Vehicles Could Rescue the US Power Grid

in WIRED Science on 2022-09-19 11:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Journal says ivermectin study met standard for ‘credible science’

in Retraction watch on 2022-09-19 10:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

ORI Fail

in For Better Science on 2022-09-19 04:47:46 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Epigenetic ‘Clocks’ Predict Animals’ True Biological Age

in WIRED Science on 2022-09-18 12:00:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

Readers discuss colors and spikes in the James Webb Space Telescope’s images and more

Space palettes

The stunning first pictures from the James Webb Space Telescope provide the deepest and clearest look yet into outer space, Lisa Grossman reported in “Postcards from a new space telescope” (SN: 8/13/22, p. 30).

JWST observes space using infrared, a form of light not visible to the human eye. To visualize the images, scientists colorize them. Reader John Dohrmann wondered how that colorizing is done.

JWST’s images are colorized by senior data imaging developer Joseph DePasquale and science visuals developer Alyssa Pagan, both of the Space Telescope Science Institute in Baltimore, Grossman says. Their basic rule of thumb is to paint the pictures using wavelengths of light as a guide. The light emitted in the longest wavelength in an image is assigned the color red, and the shortest blue, she says. Wavelengths in between are assigned a spectrum of greens and yellows (SN: 3/17/18, p. 4). But there are also other considerations, such as data on the chemical compositions of stuff in the image. How to colorize those elements can be more of an art than a science, Grossman says. “There’s a subjective artistry to it too.”

Reader Stu Kantor asked why some stars in the JWST images appear to have eight spikes — six large ones and two smaller ones (see “Out of this world,” below).

Those are called diffraction spikes, Grossman says, and they’re an artifact of the telescope’s optical setup. JWST has two mirrors: a primary hexagonal mirror and a smaller secondary mirror that sits in front of the primary mirror and is held up by three support beams. When it hits the telescope, light bends at the two edges of each of the secondary mirror’s supports, producing six diffraction spikes. The six edges of the primary mirror also create six spikes. Scientists designed the telescope so that four of the spikes from the secondary supports overlap with four of the primary mirror’s spikes, Grossman says, so though there are 12 spikes, we see only eight.

Diffraction spikes are not unique to JWST. “Images from the Hubble Space Telescope have these too, but they only have four,” Grossman says. “The eight points are a distinctive feature of JWST, like an artist’s signature.”

Out of this world

The James Webb Space Telescope’s first mind-blowing images, including one of the “Cosmic Cliffs” (shown below), thrilled many readers. On Facebook, reader Jeff Reynolds marveled at the great achievement: “A magic day when super science mingles with the bright stuff of dreams.”

On the nose

Scientists discovered a neural link in the dog brain that connects the olfactory system to vision, which may help explain why humankind’s best friend is such a good sniffer, Laura Sanders reported in “New nose-to-brain link ID’d in dogs” (SN: 8/13/22, p. 9).

The story inspired several readers to reflect on the behavior of their own furry friends.

“I now know why my German shepherd could not play the simplest version of the shell game,” Ed Hughes wrote. “Using a small piece of dog food and two Dixie cups … one shift in the location of the cup hiding the dog food completely confused her. I could watch her eyes follow the cup, but she never picked the cup with the dog food. She had prelocated it with her nose, and anything her eyes detected was completely ignored.”

Reader Roy R. Ferguson shared his fascination with dogs’ sniffing abilities, having worked with the animals in search and rescue efforts for the last 20 years with his wife.

“We have learned to allow the K-9s to do their work with as little super​vision as possible,” Ferguson wrote. “They constantly make decisions that seem unusual at the time but make sense once the full story is known.”

“Our K-9s have located drops of blood in light rain and human decomposition in various vehicles. Live finds include one man who wandered over 10 miles after a head wound and a 6-year-old who had been out all night …. The child find was notable due to the large amount of scent contamination in the area,” Ferguson added.

“We have no idea how these amazing creatures do such marvelous feats. They work their hearts out for nothing more than praise and a toy reward,” Ferguson wrote. “It has occurred to [us] that we are there to provide them support, drive and work the radio. In return, they make us look as though we know what we’re doing.”

in Science News on 2022-09-18 11:15:00 UTC.

- Wallabag.it! - Save to Instapaper - Save to Pocket -

So much of science is looking and seeing

One of my great joys in life is one of the simplest: looking at the world around me. I often walk along the C&O Canal, a defunct marvel of 19th century transportation engineering that reaches west from Washington, D.C. As I walk, I look. And even though I have strolled the towpath so many times before, I always see something new.

Last Saturday, I saw a native persimmon tree with fruit the size of Ping-Pong balls just starting to turn color. I spied two beaver dams spanning the canal, marvels of rodent engineering. And I saw how the September sunlight was softening into fall, giving everything a glow that an Impressionist painter might envy.

So much of science is looking and seeing. On September 1, the astronomy world went bonkers when news broke that the James Webb Space Telescope had taken its first direct image of a planet outside our solar system. Scientists’ Twitter feeds erupted in exclamation points and comments like “thrilled” and “amazing.” Taking pictures of very distant planets is exceedingly difficult, but the new megatelescope, which released its first images in July, has made seeing better than any other telescope look easy-peasy (SN: 8/13/22, p. 30). Or as associate news editor Christopher Crockett commented wryly in one of our internal Slack channels: “OK JWST, now you’re just showing off.”

The telescope has also captured the light spectrum of a probable brown dwarf and confirmed the existence of carbon dioxide in the atmosphere of another exoplanet, as astronomy writer Lisa Grossman explains. This raises hopes that the telescope might someday spot Earthlike planets capable of sustaining life. That hope may never be fulfilled, but it’s clear that if the telescope keeps performing at this level, many extraordinary sights are headed our way.

Serendipitously, this issue of the magazine chronicles another scientific achievement in looking and seeing, using artificial intelligence systems to visualize the 3-D structures of proteins. These molecules are the building blocks of biological life, and their shapes define their purpose. But proteins twist and fold themselves into complex tangles, and scientists’ labors to decipher them using electron microscopes and other technologies have been painfully slow.

Enter an AI system called AlphaFold that evaluates already-mapped proteins and uses that information to predict the structures of others. As molecular biology senior writer Tina Hesman Saey reports on, this should speed up efforts to study life on Earth, whether to develop new medical treatments or learn more about human evolution. Some of AlphaFold’s predictions are less accurate than others, as Saey points out, and the AI system so far can’t cope with the challenges of decoding how protein structures interact with each other, and with other molecules. That’s where a deeper understanding of protein structures will really pay off, scientists say. But even without that capacity, the system is helping scientists skip much of the scut work and move forward to tackling big questions across the life sciences.

These new technologies and the scientists who created and use them let me see things I never imagined possible. And like those happy astronomers, I am thrilled and amazed.

in Science News on 2022-09-18 11:00:00 UTC.