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.”
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. 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.” 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. 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. 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. 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. 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. 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.”
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.
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.
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.
The massive Tonga eruption generated a set of planet-circling tsunamis that may have started out as a single mound of water roughly the height of the Statue of Liberty.
What’s more, the explosive eruption triggered an immense atmospheric shock wave that spawned a second set of especially fast-moving tsunamis, a rare phenomenon that can complicate early warnings for these oft-destructive waves, researchers report in the October Ocean Engineering.
As the Hunga Tonga–Hunga Ha’apai undersea volcano erupted in the South Pacific in January, it displaced a large volume of water upward, says Mohammad Heidarzadeh, a civil engineer at the University of Bath in England (SN: 1/21/22). The water in that colossal mound later “ran downhill,” as fluids tend to do, to generate the initial set of tsunamis. To estimate the original size of the mound, Heidarzadeh and his team used computer simulations, as well as data from deep-ocean instruments and coastal tide gauges within about 1,500 kilometers of the eruption, many of them in or near New Zealand. The arrival times of tsunami waves, as well as their sizes, at those locations were key pieces of data, Heidarzadeh says.
The team analyzed nine possibilities for the initial wave, each of which was shaped like a baseball pitcher’s mound and had a distinct height and diameter. The best fit to the real-world data came from a mound of water a whopping 90 meters tall and 12 kilometers in diameter, the researchers report.
That initial wave would have contained an estimated 6.6 cubic kilometers of water. “This was a really large tsunami,” Heidarzadeh says.
Despite starting out about nine times as tall as the tsunami that devastated the Tohoku region of Japan in 2011, the Tongan tsunamis killed only five people and caused about $90 million in damage, largely because of their remote source (SN: 2/10/12).
Another unusual aspect of the Tongan eruption is the second set of tsunamis generated by a strong atmospheric pressure wave.
That pressure pulse resulted from a steam explosion that occurred when a large volume of seawater infiltrated the hot magma chamber beneath the erupting volcano. As the pressure wave raced across the ocean’s surface at speeds exceeding 300 meters per second, it pushed water ahead of it, creating tsunamis, Heidarzadeh explains. Along many coastlines, including some in the Indian Ocean and Mediterranean Sea, these pressure wave–generated tsunamis arrived hours ahead of the gravity-driven waves spreading from the 90-meter-tall mound of water. Gravity-driven tsunami waves typically travel across the deepest parts of the ocean, far from continents, at speeds between 100 and 220 meters per second. When the waves reach shallow waters near shore, the waves slow, water stacks up and then strikes shore, where destruction occurs.
Pressure wave–generated tsunamis have been reported for only one other volcanic eruption: the 1883 eruption of Krakatau in Indonesia (SN: 8/27/83).
Those quicker-than-expected arrival times — plus the fact that the pressure-wave tsunamis for the Tongan eruption were comparable in size with the gravity-driven ones — could complicate early warnings for these tsunamis. That’s concerning, Heiderzadeh says.
One way to address the issue would be to install instruments that measure atmospheric pressure with the deep-sea equipment already in place to detect tsunamis, says Hermann Fritz, a tsunami scientist at Georgia Tech in Atlanta.
With that setup, scientists would be able to discern if a passing tsunami is associated with a pressure pulse, thus providing a clue in real time about how fast the tsunami wave might be traveling.
It was the juice that tipped him off. At lunch, Ícaro de A.T. Pires found the flavor of his grape juice muted, flattened into just water with sugar. There was no grape goodness. “I stopped eating lunch and went to the bathroom to try to smell the toothpaste and shampoo,” says Pires, an ear, nose and throat specialist at Hospital IPO in Curitiba, Brazil. “I realized then that I couldn’t smell anything.”
Pires was about three days into COVID-19 symptoms when his sense of smell vanished, an absence that left a mark on his days. On a trip to the beach two months later, he couldn’t smell the sea. “This was always a smell that brought me good memories and sensations,” Pires says. “The fact that I didn’t feel it made me realize how many things in my day weren’t as fun as before. Smell can connect to our emotions like no other sense can.”
As SARS-CoV-2, the virus responsible for COVID-19, ripped across the globe, it stole the sense of smell away from millions of people, leaving them with a condition called anosmia. Early in the pandemic, when Pires’ juice turned to water, that olfactory theft became one of the quickest ways to signal a COVID-19 infection. With time, most people who lost smell recover the sense. Pires, for one, has slowly regained a large part of his sense of smell. But that’s not the case for everyone. About 5.6 percent of people with post–COVID-19 smell loss (or the closely related taste loss) are still not able to smell or taste normally six months later, a recent analysis of 18 studies suggests. The number, reported in the July 30 British Medical Journal, seems small. But when considering the estimated 550 million cases and counting of COVID-19 around the world, it adds up.
Scientists are searching for ways to hasten olfactory healing. Three years into the COVID-19 pandemic, researchers have a better idea of how many people are affected and how long it seems to last. Yet when it comes to ways to rewire the sense of smell, the state of the science isn’t coming up roses.
A method called olfactory training, or smell training, has shown promise, but big questions remain about how it works and for whom. The technique has been around for a while; the coronavirus isn’t the first ailment to snatch away smell. But with newfound pressure from people affected by COVID-19, olfactory training and a host of other newer treatments are now getting a lot more attention.
The pandemic has brought increased attention to smell loss. “If we have to provide a silver lining, COVID is pushing the science at a speed that’s never happened before,” says Valentina Parma, an olfactory researcher and assistant director of the Monell Chemical Senses Center in Philadelphia. “But,” she cautions, “we are really far from a solution.”
Nasal attack Compared with sight or hearing, the sense of smell can seem like an afterthought. But losing it can affect people deeply. “Your world really changes if you lose the sense of smell, in ways that are usually worse,” Parma says. The smell of a baby’s head, a buttery curry or the sharp salty sea can all add emotional meaning to experiences. Smells can also warn of danger, such as the rotten egg stench that signals a natural gas leak.
As an ear, nose and throat doctor, Pires recalls a deaf patient who lost her sense of smell after COVID-19 and enrolled in a clinical trial that he and colleagues conducted on smell training. She worked in a perfumery company — her sense of smell was crucial to her job and her life. “At the first appointment, she said, with tears in her eyes, that it felt like she wasn’t living,” Pires recalls.
Unlike the cells that detect color or sound, the cells that sense smell can replenish themselves. Stem cells in the nose are constantly pumping out new smell-sensing cells. Called olfactory sensory neurons, these cells are dotted with molecular nets that snag specific odor molecules that waft into the nose. Once activated, these cells send messages through the skull and into the brain.
Because of their nasal neighborhood, olfactory sensory neurons are exposed to the hazards of the environment. “They may be covered with a little layer of mucus, but they’re sitting out there being constantly bombarded with bacteria and viruses and pollutants and who knows what else,” says Steven Munger, a chemosensory neuroscientist at the University of Florida College of Medicine in Gainesville.
Exactly how SARS-CoV-2 damages the smell system isn’t clear. But recent studies suggest the virus’s assault is indirect. The virus can infect and kill nose support cells called sustentacular cells, which are thought to help keep olfactory neurons happy and fed by delivering glucose and maintaining the right salt balance. That attack can inflame the olfactory epithelium, the layers of cells that line parts of the nasal cavity.
Once this tissue is riled up, the olfactory sensory neurons get wonky, even though the cells themselves haven’t been attacked. After an infection and ensuing inflammation, these neurons slow down the production of their odor-catching nets, a decrease that could blind themselves to odor molecules, scientists reported in the March 17 Cell.
With time, the inflammation settles down, and the olfactory sensory neurons can get back to their usual jobs, researchers suspect. “We do think that for post-viral smell disorders, the most common way to recover function is going to be spontaneous recovery,” Munger says. But in some people, this process doesn’t happen quickly, if ever.
That’s where smell training comes in.
A nose workout One of the only therapies that exists, smell training is quite simple — a good old-fashioned nose workout. It involves deeply smelling four scents (usually rose, eucalyptus, lemon and cloves) for 30 seconds apiece, twice a day for months.
In one study, 40 people who had smell disorders came away from the training with improved smelling abilities, on average, compared with 16 people who didn’t do the training, olfactory researcher Thomas Hummel and his colleagues reported in the March 2009 Laryngoscope.
Since then, the bulk of studies has shown that the method helps between 30 and 60 percent of the people who try it, says Hummel, of Technische Universität Dresden in Germany. His view is that the method can help some people, “but it does not work in everybody.”
One of the nice things is that there are no harmful side effects, Hummel says. That’s “the charming side of it.” But to do the training correctly takes discipline and stamina. “If you don’t do it regularly, and you give up after 14 days, this is futile,” he says.
Pires in his recent trial had hoped to speed up the process, which usually takes three months, by adding four more odors to the regimen. For four weeks, 80 participants received either four or eight smells. Both groups improved, but there was no difference between the two groups, the researchers reported July 21 in the American Journal of Rhinology & Allergy.
It’s not known how the technique works in the people it seems to help. It could be that it focuses people’s attention on faint smells; it could be stimulating the growth of replacement cells; it could be strengthening some pathways in the brain. Data from other animals suggest that such training can increase the number of olfactory sensory neurons, Hummel says.
Overall, this nose boot camp may be a possible approach for people to try, but big questions remain about how it works and for whom, Munger says. “In my view, it’s very important to be up front with patients about the very real possibility this therapy may not lead to a restoration of smell, even if they and their doctor feel it is worth trying,” he says. “I am not trying to discourage people here, but I also think we need to be very careful not to give unwarranted promises.”
Smell training doesn’t come with harmful biological side effects, but it can induce frustration if it doesn’t work, Parma says. In her practice, “I have been talking to a lot of people who say, ‘I did it every day for six months, twice a day for 10 minutes. I met in groups with other people, so we kept each other accountable, and I did that for six months. And it didn’t work for me.’” She adds, “I would want to address the frustration that this induces in patients.”
Beyond training Other potential treatments are coming under scrutiny, such as steroids, omega-3 supplements, growth factors and vitamins A and E, all of which might encourage the recovery of the nasal epithelium.
More futuristic remedies are also in early stages of research. These include epithelial transplants designed to boost olfactory stem cells, treatments with platelet-rich plasma to curb inflammation and promote healing, and even an “electronic nose” that would detect odor molecules and stimulate the brain directly. This cyborg-smelling system takes inspiration from cochlear implants for hearing and retinal implants for vision. For many people, the sense of smell is appreciated only after it’s gone, Parma says, an apathy that’s illustrated in stark terms by a recent study of about 400 people. The vast majority of respondents — nearly 85 percent — would rather give up their sense of smell than sight or hearing. About 19 percent of respondents said they would prefer to give up their sense of smell than their cell phone. The survey results “dramatically illustrate the negligible value people place on their sense of smell,” researchers wrote in the March Brain Sciences.
Even as a doctor who treats people with smell loss, Pires has a newfound fondness for a good whiff. “Having lost it for a while made me appreciate it even more.”
Giant honeybees send waves rippling across their open nests by flipping their abdomens upward in coordination, a sight that approaching predators seem to shy away from. A new study is revealing details about what triggers the behavior, known as shimmering.
That shimmering is strongest when the bees are shown a dark object that moves against a light background under bright ambient light, researchers report in the September Journal of Experimental Biology. The experimental setup simulates animals such as hornets, one of the bees’ main predators, flying against the bright sky, and shows what visual cues set off the behavior, the researchers say. The behavior “is intriguing as this is possibly one way in which a species of animal communicates with another to warn that they are capable of defending themselves,” says Kavitha Kannan, a neurobiologist at the University of Konstanz in Germany who was not involved in the study.
Giant honeybees, including Apis dorsata, typically form open nests uncovered by other materials in areas like tree branches and window ledges. In the new study, the researchers worked with two A. dorsata nests in roof rafters. Standing near the hives, behavioral ecologist Sajesh Vijayan moved circular cardboard pieces of different sizes in shades of gray and black against either a gray or a black background. The bees shimmered when a black object moved against the gray backdrop, but not when the contrast was flipped.
That’s probably because the black-on-gray setup “resembles a natural predator or a natural condition,” says Sajesh, who goes by his first name, as is common in many parts of southern India. “These are open-nesting colonies, so they are always exposed to a bright sky.”
The team observed little shimmering during the dim twilight periods of dawn and dusk. Since shimmering is a response meant to be perceived by a predator or other unwelcome visitor, such as a bee from another colony, the researchers think that other defensive behaviors might be at play during dim conditions. “We also think that shimmering is a specialized response towards hornets because it has not really been reported in cases of birds attacking or birds flying past these colonies,” Sajesh says. Birds, instead, “elicit a mass stinging response.” That could be because approaching birds loom comparatively large in the bees’ visual field, and at that point, the bees’ attitude may be “let’s not take any more chances, just sting,” Sajesh says.
In both hives, shimmering completely vanished when the bees were presented with the smallest objects, in this case a circle four centimeters in diameter. The result suggests that there is a minimum size threshold that triggers the ripples.
Shimmering strength did not wane even when the bees were exposed to the artificial setup repeatedly, perhaps because it’s advantageous to stay vigilant against predators like hornets that make persistent attacks.
How exactly the bees are perceiving the objects in the study is not yet known. “They could be actually seeing this object moving, or they could just be responding to a reduction in their visual field,” Sajesh says.
The researchers plan to explore that question further. They are also designing experiments with LED screens to tweak the background colors and patterns and object shapes to figure out what types of shapes and even motions might matter to the bees.
After receiving an experimental treatment to stop the body from attacking itself, five people no longer have any symptoms of lupus.
That treatment, called CAR-T cell therapy, seems to have reset the patients’ immune systems, sending their autoimmune disease into remission, researchers report September 15 in Nature Medicine. It’s not yet clear how long the relief will last or whether the therapy will work for all patients.
Even so, the results could be “revolutionary,” says immunologist Linrong Lu of the Shanghai Immune Therapy Institute at the Shanghai Jiao Tong University School of Medicine, who was not involved in the study. CAR-T cell therapy has been used for various types of cancer, but it’s still in testing for autoimmune diseases (SN: 2/2/22). In the new study, all five participants went into remission without needing additional drugs beyond the genetically engineered CAR-T cells. The target of those engineered cells — immune cells key for fighting off infections — returned a few months after being wiped out. Some of those cells are primed to attack viruses and bacteria but not the study participants’ healthy cells.
It’s unknown how many people worldwide have lupus, a painful disease in which some immune proteins called antibodies attack healthy tissue and organs (SN: 4/25/19). An estimated 161,000 to 322,000 people in the United States live with the most common form called systemic lupus erythematosus. While there are effective therapies, those treatments don’t work for everyone.
The five people in the study had this common form with symptoms resistant to multiple commonly used lupus drugs, such as hydroxychloroquine. But laboratory studies in mice hinted that CAR-T cells might help. So immunologist Georg Schett and colleagues took T cells from each patient and genetically modified the cells to track down and kill all antibody-producing cells. All five participants — four female and one male ages 18 to 24 — were in remission three months after being treated with the altered cells.
The antibody-producing cells, called B cells, disappeared from blood samples as the CAR-T cells killed them off. But B cells are an important defense against infectious diseases such as measles. Luckily, the immune cells weren’t gone permanently, says Schett, of Friedrich-Alexander-Universität Erlangen-Nürnberg in Germany. A few months later, the patients’ bone marrow had made more. The B cells were back; the lupus was not.
“Which means, in a way, that we have a reset of the immune system in these young individuals,” Schett says.
Typically, the immune system has checkpoints that eliminate cells that attack the body instead of a foreign invader. Autoimmune diseases such as lupus occur when these cells that recognize and attack “self” escape scrutiny. For lupus to come back, Schett says, the same mistake may need to happen twice. “So far we think the disease is gone.”
To know for sure, the team needs more time to follow the participants. In August 2021, the researchers reported in the New England Journal of Medicine that the first treated participant, a 20-year-old woman, was in remission three months after receiving the drug. Now, that patient has been healthy for a year and a half, Schett says. The other four have been healthy for six months to a year. Time will tell how long these people will stay lupus-free.
Which people might benefit most from CAR-T cell therapy is not yet clear either. Lupus symptoms and severity vary from person to person. The treatment could, for instance, be most useful for patients who are in earlier stages of the disease before it becomes too severe, Lu says. Still, if future clinical trials prove effective, CAR-T cell therapy could be another way to offer hope to patients with the disease.
On the fringe of Kenya’s Gazi village, 50 kilometers south of Mombasa, Mwatime Hamadi walks barefoot on a path of scorching-hot sand toward a thicket of trees that seem to float where the land meets the Indian Ocean. Behind her moves village life: Mothers carry babies on their backs while they hang laundry between palm trees, women sweep the floors of huts thatched with palm fronds and old men chat idly about bygone days under the shade of mango trees.
Hamadi is on her way to Gazi Forest, a dense patch of mangroves along Gazi Bay that coastal residents see as vital to their future. Mangroves “play a crucial role in safeguarding the marine ecosystem, which in turn is important for fisheries we depend on for our livelihood,” she says as she reaches a boardwalk that snakes through the coastal wetland. Hamadi is a tour guide with Gazi Ecotourism Ventures, a group dedicated to empowering women and their community through mangrove conservation. This group is part of a larger carbon offset project called Mikoko Pamoja that has taken root and is now being copied farther south on Kenya’s coastline and in Mozambique and Madagascar.
Through Mikoko Pamoja, residents of Gazi and nearby Makongeni are cultivating an economic ecosystem that relies on efforts to preserve and restore the mangrove forests. Revenue from carbon credits sold plus the money Hamadi and others earn from ecotourism are split between salaries, project costs and village improvements to health care, sanitation, schools and more.
Mikoko Pamoja, launched in 2013, is the world’s first mangrove-driven carbon credit initiative. It earned the United Nations’ Equator Prize in 2017, awarded for innovative solutions to poverty that involve conservation and sustainable use of biodiversity.
“The mangrove vegetation was a thriving, healthy ecosystem in precolonial times,” says Ismail Barua, Mikoko Pamoja’s chairperson. During British rule, which stretched from the 1890s to 1963, the colonial government issued licenses to private companies to export mangrove wood. They did this without community involvement, which led to poaching of trees. Even after Kenya gained independence, mangroves were an important source of timber and fuel for industrial processes, main drivers of extensive destruction of the forests.
Today, mangrove restoration is helping the region enter a new chapter, one where labor and resources are well-managed by local communities instead of being exploited. “The community is now able to run its own affairs,” Barua notes. Through innovative solutions and hard work, he says, “we’re trying to bring back a semblance of that ecosystem.” A fragile carbon sponge The dominant mangrove species in Gazi Forest is Rhizophora murcronata. With oval, leathery leaves about the size of a child’s palm and spindly branches that reach to the sun, the trees can grow up to 27 meters tall. Their interlaced roots, which grow from the base of the trunk into the saltwater, make these evergreen trees unique.
Salt kills most plants, but mangrove roots separate freshwater from salt for the tree to use. At low tide, the looping roots act like stilts and buttresses, keeping trunks and branches above the waterline and dry. Speckling these roots are thousands of specialized pores, or lenticels. The lenticels open to absorb gases from the atmosphere when exposed, but seal tight at high tide, keeping the mangrove from drowning.
The thickets of roots also prevent soil erosion and buffer coastlines against tropical storms. Within these roots and branches, shorebirds and fish — and in some places, manatees and dolphins — thrive.
Mangrove roots support an ecosystem that stores four times as much carbon as inland forests. That’s because the saltwater slows decomposition of organic matter, says Kipkorir Lang’at, a principal scientist at the Kenya Marine and Fisheries Research Institute, or KMFRI. So when mangrove plants and animals die, their carbon gets trapped in thick soils. As long as mangroves stay standing, the carbon stays in the soil.
Robust estimates of mangrove forest area in Kenya before 1980 are not available, Lang’at says. However, with the clear-cutting of mangrove forests in Gazi Bay in the 1970s, he says, the area was left with vast expanses of bare, sandy coast.
Other parts of the country experienced similar losses: Kenya lost up to 20 percent of its mangrove forests between 1985 and 2009 because no mechanism existed for their protection. The losses had a steep price: Just as mangroves absorb more carbon than inland forests, when destroyed, they release more carbon than other forests. And since the mangroves provided habitat and shelter for fish, their destruction meant that fishers were catching less. Recognizing this high cost, as well as the ecosystem’s other benefits, Kenya’s government ratified the Forest Conservation and Management Act of 2016, a law protecting mangroves and inland forests. Cutting down mangroves is now banned throughout the country, except in very specific areas under very specific circumstances.
Available data suggest that Kenya’s rate of mangrove loss has declined in the last two decades. The country is now losing about 0.65 percent of its mangrove forest annually, according to unpublished evaluations conducted in 2020 by KMFRI. Since the turn of the millennium, global mangrove deforestation has slowed as well, hovering between a loss of 0.2 and 0.7 percent per year, says a 2020 study in Scientific Reports.
Mikoko Pamoja offers hope for turning around those declines. The project, whose Swahili name means “mangroves together,” has its roots in a small mangrove restoration effort that started in 1991 in Gazi Bay, spearheaded by KMFRI. The effort evolved into a scientific experiment to see what it would take to restore a degraded ecosystem. It attracted collaborators from Edinburgh Napier University, Europe’s Earthwatch Institute and other organizations across Europe.
Now, Gazi Forest boasts 615 hectares of mangrove forest, including 56,000 individual seedlings planted by the community. Plans to plant more mangrove trees — at least 2,000 per year — are in the works. Creating carbon credits Gazi Forest siphons carbon from the atmosphere at a rate of 3,000 metric tons per year, says Rahma Kivugo, the outgoing project coordinator for Mikoko Pamoja. These aren’t merely ballpark numbers: To sell the carbon offsets collected by Mikoko Pamoja, forest managers must calculate the amount of carbon stored by mangroves.
Volunteers venture into the forest twice a year, checking on 10 selected 10-square-meter plots in the wild forest and five plots in planted forest. Workers measure the diameter of mature trees at an adult’s chest height. They then estimate the trees’ height. Finally, they classify young trees as knee-height, waist-height, chest-height and higher.
From these observations, researchers estimate the volume of mangrove material above ground in each plot and extrapolate for the whole forest area.
Once they have an idea of the volume of plant material above ground, team members can estimate root volume below ground using a standardized factor specific to mangrove forests, says Mbatha Anthony, a research assistant at KMFRI in charge of carbon accounting. Even though mangrove forests store a lot of soil carbon, the project calculates carbon stored only by the tree itself because “calculating soil carbon is a resource-intensive undertaking for a small project like Mikoko Pamoja,” Anthony says.
With an estimate of the total volume of biomass in the forest in hand, “we can then translate that into tons of carbon,” says environmental biologist Mark Huxham of Edinburgh Napier University, who helps Mikoko Pamoja with its calculations. In general, 50 percent of aboveground biomass is carbon. Below ground, 39 percent of biomass is carbon.
The amount of carbon stored by Gazi Forest is then relayed to the Plan Vivo Foundation, a group based in Scotland that certifies carbon calculations. Once its calculations are certified, Mikoko Pamoja receives Plan Vivo Certificates, or PVCs.
One PVC is equivalent to one metric ton of carbon dioxide emission reductions. These PVCs are submitted to the Association for Coastal Ecosystem Services — an organization that markets carbon credits for Mikoko Pamoja and similar projects. Through ACES, Mikoko Pamoja’s PVCs can then be purchased by anyone who wishes to offset their carbon emissions.
Roughly 117 hectares of Gazi Forest have been demarcated for the sale of carbon credits. “Mikoko Pamoja generates approximately $15,000 annually from the sale of carbon credits,” Anthony says. From 2014 to 2018, the project generated 9,880 credits — 9,880 tons of avoided carbon dioxide emissions. A community at work Mikoko Pamoja sells carbon credits at more than $7 per ton. Revenues get split in a clearly defined manner, according to what residents decide are pressing needs of Makongeni and Gazi villages. Around 21 percent pays wages of residents involved with Mikoko Pamoja. And “more than half of what is earned goes toward community projects,” Kivugo says.
In total, about $117,000 has gone to community projects since Mikoko Pamoja was founded. These projects include donating medicine to health clinics and textbooks to schools and digging clean water wells. Plans are under way to revive a windmill in Gazi for pumping water and renovate Makongeni’s primary school.
“The need in the community is great. So carbon trading is unlikely to meet all the needs,” Huxham says. But the funds make a significant contribution to local livelihoods, which primes the community to support conservation, he says.
The approach seems to be working. On a winding path into the forest, visitors encounter a signboard, with large letters in Swahili declaring, “Take note! This is a Mikoko Pamoja area protected by the community. Littering is prohibited! Trimming trees is prohibited!” Active community participation is central to Mikoko Pamoja’s success. Not only do community members plant mangrove seedlings and survey trees to gauge carbon storage, community scouts monitor the health of this ecosystem.
Scouts clean up litter within the forests and survey the forest’s biodiversity. From a wooden watchtower above the forest, scouts also track and report illegal logging.
“Should we spot suspicious activities in the forest, we will call the Kenya Forest Service rangers, who have the authority to detain and arrest any trespasser,” says local scout Shaban Jambia.
Back at the boardwalk, Hamadi leads a small knot of visitors through the mangroves, pausing occasionally to touch a tree’s waxy leaves. She plucks a propagule — a dark-brown pod longer than her hand — from a tree belonging to the mangrove species Bruguiera gymnorhiza.
She drops the propagule over the boardwalk’s handrail, into the soft marsh soil about 1.5 meters below. It lands, sticking almost perfectly perpendicular in the ground. “This will soon take root and germinate into a new plant,” she explains to the visitors. “That’s how this species propagates.”
Hamadi, the tour guide, is one of 27 members of the Gazi Women Mangrove Boardwalk group. Members offer interpretive services to visitors for a fee. The women also prepare Swahili cuisine for sale to groups visiting the area.
“A dish of coconut rice served with snapper fish is particularly popular, washed down with flavored black tea or tamarind juice,” says Mwanahamisi Bakari, the group’s treasurer.
These ecotourism efforts have attracted international support. The World Wide Fund for Nature Kenya, for instance, constructed a conference facility, which the women’s group rents to those who want to use the location as a backdrop to discuss sustainability efforts.
A template for others Mikoko Pamoja’s success is spurring conservation efforts throughout Kenya and beyond. For instance, on southern Kenya’s coast is the Vanga Blue Forest, a swath of mangroves five times as large as Gazi Forest. Of Vanga Blue’s more than 3,000 hectares of mangrove forest, a little more than 15 percent — 460 hectares — has been set aside for the sale of carbon credits following Mikoko Pamoja’s example.
In 2020, with help from KFMRI, a network of scientists from countries along the western Indian Ocean published a blueprint for mangrove restoration. These guidelines are now being customized to suit the restoration plans of individual countries, says Lang’at. The group is also using Mikoko Pamoja’s carbon credit example to set up projects of its own.
Madagascar’s first community-led mangrove carbon project, known as Tahiry Honko (which means “preserving mangroves” in the local Vezo dialect), was introduced in 2013 and then certified for carbon sale by Plan Vivo in 2019. With Mikoko Pamoja as a guide, Tahiry Honko “is helping tackle climate breakdown and build community resilience by preserving and restoring mangrove forests,” says Lalao Aigrette, an adviser at Blue Ventures, the conservation group coordinating the preservation effort.
Tahiry Honko is generating carbon credits through the conservation and restoration of over 1,200 hectares of mangroves surrounding the Bay of Assassins on Madagascar’s southwest coast.
In Mozambique, studies are under way to gauge how much mangrove preservation can protect communities against cyclones, says Célia Macamo, a marine biologist at Eduardo Mondlane University in Maputo, Mozambique.
In the meantime, the Limpopo estuary and other locations along the Mozambican coast are sites of mangrove restoration efforts. KMFRI is helping local organizers structure their efforts. “We also hope they will assist us when we start working with carbon credits,” Macamo adds. Blue economies Less than 1 percent of Earth’s surface is covered by mangroves, equivalent to 14.8 million hectares. “Because this area is minuscule compared to terrestrial forests, mangroves have been neglected throughout the world,” says James Kairo, chief scientist at KMFRI.
At Gazi Bay, a 2011 assessment by the United Nations Environment Programme estimated that the mangrove forests are worth about $1,092 per hectare per year, thanks in part to the potential of fisheries, aquaculture, carbon sequestration and damages averted by the coastal protection that mangroves provide. Assuming that numbers in Gazi Bay hold for the rest of the world, mangroves could provide more than $16 billion in economic benefits planetwide.
Toward the end of 2020, Kenya’s government included mangroves and seagrasses for the first time in its Nationally Determined Contributions, or NDCs — the greenhouse gas emission reduction commitments for countries that ratified the Paris Agreement. The agreement seeks to limit global warming to below 2 degrees Celsius above preindustrial levels.
This inclusion commits Kenya to conserving mangroves to balance its emissions. Kenya’s government now “recognizes the potential and importance of the mangrove and seagrass resources that Kenya has,” Huxham says.
“This is a great commitment on the part of the government. The next challenge is the implementation of these commitments,” says Kairo, who sits on the advisory board of the U.N. Decade of Ocean Science for Sustainable Development (2021–2030), which aims to support efforts to reverse the cycle of decline in ocean health.
Now, scientists and community managers for that effort need to determine how mangroves can adapt to rising sea levels. “How can communities next to the sea live in harmony with this system, without impacting on their resiliency and productivity?” Kairo asks.
Mikoko Pamoja is helping provide answers, Kairo adds. Thanks in large part to that small project that began in a secluded corner on the Kenya coast, those answers are now spreading to the rest of the world.
