Category Archives: ساینس

By Meredith WadmanSep. 24, 2020 , 2:00 PM

Science’s COVID-19 reporting is supported by the Pulitzer Center and the Heising-Simons Foundation.

From the first months of the COVID-19 pandemic, scientists baffled by the disease’s ferocity have wondered whether the body’s vanguard virus fighter, a molecular messenger called type I interferon, is missing in action in some severe cases. Two papers published online in Science this week confirm that suspicion. They reveal that in a significant minority of patients with serious COVID-19, the interferon response has been crippled by genetic flaws or by rogue antibodies that attack interferon itself.

“Together these two papers explain nearly 14% of severe COVID-19 cases. That is quite amazing,” says Qiang Pan- Hammarström, an immunologist at the Karolinska Institute.

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Tadatsugu Taniguchi, a pioneering interferon scientist and emeritus professor at the University of Tokyo, calls the discoveries “remarkable.” He says they highlight the “critical” role of type I interferons in SARS-CoV-2 infection and the development of potentially lethal COVID-19.

Co-author Isabelle Meyts, a pediatric immunologist at the University Hospitals Leuven, was struck by one paper’s finding that rogue antibodies underlie COVID-19 in 10% of gravely ill patients: “There has never been any infectious disease explained at this level by a factor in the human body. And it’s not an isolated cohort of Europeans. Patients are from all over the world, all ethnicities.” Another finding, that 94% of the patients with interferon-attacking antibodies were male, also helps explain why men face higher risk of severe disease.

The paired studies have immediate practical implications. Synthetic interferons, long used to treat other diseases, might help some at-risk patients, as might other therapies aimed at removing the damaging antibodies. A common kind of antibody test could be readily developed and return answers in hours. Those found to be at high risk of developing severe COVID- 19 could take precautions to avoid exposure or be prioritized for vaccination, says Elina Zuniga, an immunologist who studies interferons at the University of California, San Diego.

The findings also raise a red flag for plasma donations from recovered patients. Because it may be rich in antibodies to the virus, “convalescent plasma” is already given to some patients to fight the infection. But some donations could harbor the interferon-neutralizing antibodies. “You should eliminate these patients from the pool of donors,” Zuniga says. “You definitely don’t want to be transferring these autoantibodies into another person.”

Type I interferons are made by every cell in the body and are vital leaders of the antiviral battle early in infection. They launch an immediate, intense local response when a virus invades a cell, triggering infected cells to produce proteins that attack the virus. They also summon immune cells to the site and alert uninfected neighboring cells to prepare their own defenses.

In one study, Jean-Laurent Casanova, an infectious disease geneticist at Rockefeller University, and his team examined blood samples from 987 gravely ill patients from around the world. In 10.2% of the patients, the researchers identified antibodies that attacked and neutralized the patients’ own type I interferon. A subgroup of affected patients had extremely low or undetectable blood levels of this interferon. Lab studies confirmed the antibodies knocked the interferon out of action and cells exposed to the patients’ plasma failed to fend off invasion by the new coronavirus.

At least 10% of critical COVID-19 is an autoimmune attack.

None of the 663 people in a control group with mild or asymptomatic SARS-CoV-2 infection had those damaging antibodies. The antibodies were also scarce in the general population, showing up in only 0.33% of more than 1200 healthy people tested. “What this means is that at least 10% of critical COVID-19 is an autoimmune attack against the immune system itself,” Casanova says.

The preponderance of male patients was a surprise, because women have higher rates of autoimmune disease. “Our favorite hypothesis is that it is an X-linked recessive trait,” Casanova says. “Women with two X chromosomes are protected and men, with one, are not.” Supporting that suspicion, one woman with a rare condition that silences one X chromosome was among the severely ill patients with autoantibodies.

If these striking results hold up, they might also help explain the increased vulnerability of older people to severe COVID-19: Half the gravely ill patients with autoantibodies were older than 65.

The second paper found genetic flaws in patients that led to the same end result: a grossly inadequate interferon response to SARS-CoV-2 infection. The team sequenced DNA from 659 critically ill COVID-19 patients and from 534 controls with mild or asymptomatic disease. They examined 13 genes, chosen because flaws in them impair the body’s production or use of type I interferon; mutations in the genes underlie life-threatening influenza or other viral illnesses. The researchers found that 3.5% of the critically ill patients harbored rare mutations in eight of those genes. In patients for whom blood samples were available, interferon levels were vanishingly small. No members of the control group carried any of the mutations. “This is the first paper to pin down indisputably disease-causing mutations underlying severe COVID-19,” Pan-Hammarström says.

But it’s “probably the tip of the iceberg,” says Paul Hertzog, an interferon expert at the Hudson Institute of Medical Research. Many other damaging mutations, interferon related and not, may influence the development of severe COVID-19, he says.

Zuniga notes that none of the patients who made antibodies against interferon or had the mutations had a history of life-threatening viral illnesses requiring hospitalization. “This suggests that we are more reliant on type I interferons to protect ourselves against SARS-CoV-2 versus other viral infections,” she says. “That makes it important to try therapies aimed at boosting type I interferon responses.”

Dozens of randomized clinical trials are now deploying interferons against SARS-CoV-2. One, led by Tom Wilkinson at the University of Southampton, reported promising findings in a small group of hospitalized COVID-19 patients. But synthetic interferons won’t help patients who harbor mutations that prevent interferons from working, or those with antibodies that attack them.

Some researchers caution that the interferon-neutralizing antibodies could be a cause, rather than a consequence, of severe COVID-19. “It’s possible that they develop during the disease,” says Miriam Merad, an immunologist at the Icahn School of Medicine at Mount Sinai. That would explain why the patients hadn’t faced life-threatening viral infections before, she says.

But Casanova, who has made a career of discovering mutations that confer susceptibility to infectious diseases, says there is a strong case for causality. He points out that preexisting blood samples from a handful of patients showed they had the antibodies in their blood before contracting SARS-CoV-2. He argues that, in response to infection, it’s unlikely that the body could quickly generate the high levels of anti-interferon antibodies his team saw.

Yanick Crow, a clinical geneticist at the University of Edinburgh who studies interferon signaling, calls the antibody paper “shocking,” in part because men were so much more likely than women to carry the rogue antibodies. Tests screening for the antibodies can and should be rapidly developed, he says, and will quickly reveal whether the new findings hold up. Given tens of millions of cases worldwide, he says, “10% is such a high figure and the implications are very important.”

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By Erik StokstadSep. 24, 2020 , 5:25 PM

Science’s COVID-19 reporting is supported by the Pulitzer Center and the Heising-Simons Foundation.

White-crowned sparrows are tough birds, able to survive the hustle and bustle of many North American cities. But growing noise pollution has forced males to sing louder, less effective songs in order to be heard by rivals and mates. During the pandemic lockdown this spring, the background din quieted. A new study shows that, in just a matter of weeks, the sparrows’ songs recovered the acoustic quality of songs sung decades ago, when city life was less noisy.

Elizabeth Derryberry, a behavioral ecologist at the University of Tennessee, Knoxville, and her colleagues have studied white-crowned sparrows in and around San Francisco for more than 2 decades, comparing their songs with recordings made in the 1970s. As traffic levels increased, the lowest frequencies of the sparrows’ songs rose, so as not to be drowned out by the background hum of vehicles. But their top frequencies remained about the same, narrowing the total bandwidth of their communication.

For many bird species, songs degraded in this way are less effective at deterring rivals and attracting females. Birds sing louder in noisy environments, and research has shown the resulting stress can speed aging and disrupt their metabolisms. Noise can also keep them from hearing their own chicks—or the warnings of fellow birds; it may even be driving down bird diversity in many cities.

When the pandemic lockdown began in mid-March, Derryberry remembers seeing a striking photo of the Golden Gate Bridge. “I was like, ‘Oh my God, it’s empty.’” And that made her wonder how the sparrows were responding to the quieter conditions.

Derryberry couldn’t travel to California, but her colleague, Jenny Phillips, a behavioral ecologist at California Polytechnic State University, recorded the birds in San Francisco and the surrounding areas (below). Her recordings revealed that the sparrows were singing 30% softer, on average, than before the lockdown. What’s more, they were singing songs with bandwidths typical of birds recorded in the 1970s. The combination of less background noise and the better signal from wider bandwidth meant the males could likely hear each other from twice as far away than before, they report today in Science.

The improved communication may have helped rival males avoid each other, meaning fewer fights. Phillips has previously found that urban birds are generally quicker to attack rivals. “I think that the aggression levels might have gone down so that everybody chilled out,” Derryberry says.

The new finding is “good news from the point of view of the birds,” says Sue Anne Zollinger, an ornithologist at Manchester Metropolitan University, who was not involved in the work. By showing the sparrows can adjust their songs to their environment, the study suggests species with more flexible behaviors can cope with aspects of changing environments. Reducing noise might allow other noise-sensitive bird species, such as California quail, to return to cities where they once sang. “If we can work to make things quieter, it will really have a big impact.”

But the respite provided by the pandemic has been short lived, as traffic and noise return to cities. When the birds start their springtime serenades next year, Derryberry and her colleagues plan to see whether their songs are suffering again.

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By Virginia MorellSep. 24, 2020 , 3:50 PM

Never before has “bird brain” been such a compliment: In recent years, birds have been found to make tools, understand abstract concepts, and even recognize paintings by Monet and Picasso. But their lack of a neocortex—the area of the mammalian brain where working memory, planning, and problem solving happen—has long puzzled scientists. Now, researchers have found a previously unknown arrangement of microcircuits in the avian brain that may be analogous to the mammalian neocortex. And in a separate study, other researchers have linked this same region to conscious thought.

The two papers are already being hailed as groundbreaking. “It’s often assumed that birds’ alien brain architecture limits thought, consciousness, and most advanced cognition,” says John Marzluff, a wildlife biologist and specialist on crows at the University of Washington, Seattle, who was not involved with either study. Researchers who have “demonstrated the cognitive abilities of birds won’t be surprised by these results,” he adds, “but they will be relieved.”

Indeed, it was because of birds’ and mammals’ similar cognitive abilities that Martin Stacho, a neuroanatomist at Ruhr-University Bochum, decided to investigate the avian forebrain, which controls perception. A gross comparison of mammalian and avian brains suggests “they have nothing in common,” he says. “Yet birds and mammals have many of the same cognitive skills.”

To find out how bird brains support these mental talents, Stacho and his colleagues examined microscopic slices of three homing pigeon brains using 3D polarized light imaging. This high-resolution technique let them analyze the circuitry of a forebrain region called the pallium, considered most similar to the mammalian neocortex. Although the pallium lacks the cortex’s six layers, it has distinctive structures connected by long fibers.

The scientists compared the images of the birds’ pallia with those of rat, monkey, and human cortices. Their analysis revealed the fibers in the birds’ pallia are organized in a manner strikingly similar to those of fibers in mammal cortexes.

Researchers also visualized the connections among neurons in the brains of two distantly related avian species: pigeons and owls. After removing the brains of deeply anesthetized birds, scientists injected crystals into the dissected brains and discovered circuits in the sensory regions that were similar to those found in the mammalian neocortex. It is this neuroarchitecture—the connections between structures, rather than the structures themselves—that explains why birds are as cognitively talented as mammals, they report today in Science.

“This research confirms the old adage that looks can be deceiving,” Marzluff says. Although bird and mammalian brains “look very different, this study shows us they are actually wired in very complementary ways.”

But do birds have conscious experiences? Are they aware of what they see and do? To find out, Andreas Nieder, a neurophysiologist at the University of Tübingen, observed the brains of carrion crows (Corvus corrone) as they responded to cues. Known as “feathered apes” for their intelligence, these crows and their cousins have even been shown to reason causally. But inferring consciousness from such experiments is challenging, Nieder says.

So, he and colleagues used a test similar to one that probes primates for signs of consciousness—a state of mind thought to arise with the sudden activation of certain neurons. They trained two lab-raised, 1-year-old carrion crows to move or stay still in response to a faint cue displayed on a monitor. When correct, the birds were rewarded. The scientists then implanted electrodes in the crows’ brains to record their neuronal signals as they responded. When the crows reacted, their neurons fired, suggesting they had consciously perceived the cue; but when they didn’t, their neurons were silent. The neurons that fired in agreement with the crows’ action were located in the pallia, the researchers report today, also in Science. Nieder calls this “an empirical marker of sensory consciousness in birds’ brains,” similar to that seen in primates.

That’s certain to stir debate, as “some researchers argue that consciousness is uniquely human,” says Irene Pepperberg, a comparative psychologist at Harvard University known for her work with Alex, an African gray parrot who communicated in English about abstract concepts. Pepperberg was not involved in these new studies but finds them “really exciting.”

Stacho and Nieder add that the building blocks for mammalian and avian cognition may have been present in their last common ancestor, some 320 million years ago. “Of course, mammal and bird brains evolved differently,” Stacho says. “What is surprising is how similar they still are in their perceptual and cognitive abilities.”

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By Ann GibbonsSep. 24, 2020 , 2:00 PM

Neanderthals have long been seen as uber-masculine hunks, at least compared with their lightweight human cousins, with whom they competed for food, territory, and mates. But a new study finds Homo sapiens men essentially emasculated their brawny brethren when they mated with Neanderthal women more than 100,000 years ago. Those unions caused the modern Y chromosomes to sweep through future generations of Neanderthal boys, eventually replacing the Neanderthal Y.

The new finding may solve the decade-old mystery of why researchers have been unable to find a Neanderthal Y chromosome. Part of the problem was the dearth of DNA from men: Of the dozen Neanderthals whose DNA has been sequenced so far, most is from women, as the DNA in male Neanderthal fossils happened to be poorly preserved or contaminated with bacteria. “We began to wonder if there were any male Neanderthals,” jokes Janet Kelso, a computational biologist at the Max Planck Institute for Evolutionary Anthropology and senior author of the new study.

But in a technical breakthrough, Max Planck graduate student Martin Petr designed a set of probes that used the DNA sequence from small chunks of modern men’s Y chromosomes to “fish out” and bind with DNA from archaic men’s Y chromosomes. The new method works because the Neanderthal and modern human chromosomes are mostly similar; the DNA probes also reel in the few basepairs that differ.

The researchers probed the fragmentary Y chromosomes of three Neanderthal men from Belgium, Spain, and Russia who lived about 38,000 to 53,000 years ago, and two male Denisovans, close cousins of Neanderthals who lived in Siberia’s Denisova Cave about 46,000 to 130,000 ago. When the researchers sequenced the DNA, they got a surprise: The Neanderthal Y “looked more like modern humans’ than Denisovans’,” Kelso says.

This was a “puzzle,” Petr says, as earlier studies showed the rest of the Neanderthal nuclear genome is a closer match for Denisovans. That suggests the two groups diverged from modern humans about 600,000 years ago. But the appearance of the unusual Y chromosome parallels another genetic takeover: Neanderthal remains dating from 38,000 to 100,000 years ago contain the maternally inherited mitochondrial DNA (mtDNA) of a modern human woman, instead of the ancient Neanderthal mtDNA found in earlier fossils. In that case, an early H. sapiens woman likely interbred with a Neanderthal man more than 220,000 years ago and their descendants carried the modern mtDNA.

The best scenario to explain the Y pattern is that early modern human men mated with Neanderthal women more than 100,000 but less than 370,000 years ago, according to the team’s computational models. Their sons would have carried the modern human Y chromosome, which is paternally inherited. The modern Y then rapidly spread through their offspring to the small populations of Neanderthals in Europe and Asia, replacing the Neanderthal Y, the researchers report today in Science. Interestingly, the modern human mates were not ancestors to today’s H. sapiens—but were likely part of a population that migrated early out of Africa and then went extinct. Traces of Neanderthal DNA in living humans were inherited from a separate mixing event between 50,000 and 70,000 years ago.

Researchers aren’t sure exactly why the replacement happened. Natural selection may have favored the H. sapiens Y chromosome, because Neanderthals had more deleterious mutations across their genomes, Kelso says. Neanderthals had smaller populations than moderns, and small populations tend to accumulate deleterious mutations, especially on the X and Y sex chromosomes. Modern humans, with their bigger, more genetically diverse ancestral populations, may have had a genetic advantage. Another possibility is that once Neanderthals had inherited a modern human mtDNA, their cells might have favored interaction with the modern human Y, says computational biologist Adam Siepel of Cold Spring Harbor Laboratory, who was not part of the study.

The best way to test this scenario is to get DNA from early Neanderthals to see whether their Y chromosome looked more like the one in Denisovans. In the meantime, the study shows the admixture between modern humans and Neanderthals was “a defining feature of hominin history,” says population geneticist Josh Akey of Princeton University, not part of the study. Not only did it give modern humans Neanderthal DNA, but it also changed Neanderthals in fundamental ways.

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By Lizzie WadeSep. 24, 2020 , 12:20 PM

Science’s COVID-19 reporting is supported by the Pulitzer Center and the Heising-Simons Foundation.

Abigail Echo-Hawk can’t even count how many times she’s been called a troublemaker. It’s happened at conferences, workshops, and even after she testified before Congress—all places where she has advocated for the full and ethical inclusion of American Indians and Alaska Natives in public health data. “I didn’t used to know what to say,” she says. “Now, my answer is, ‘Is calling for justice making trouble?’”

As the director of the Urban Indian Health Institute (UIHI) and the chief research officer for the Seattle Indian Health Board, Echo-Hawk has been working for years with Indigenous people, mostly in cities, across the United States to collect data about their communities. She has also advised the Centers for Disease Control and Prevention (CDC), the National Institutes of Health, and many universities on best practices for analyzing data about American Indian and Alaska Native communities. Now, the COVID-19 pandemic has given Echo-Hawk’s work even more urgency.

Voices of the pandemic

The virus has taken a disproportionate toll on many Indigenous communities in the United States. But its full impact is unclear because of problems Echo-Hawk has long fought to correct, including racial misclassification and the exclusion of Indigenous communities from data sets and analyses used to make health policy decisions.

“Abigail has highlighted the inadequacy of, the restricted access to, and the delays in receiving data” about how COVID-19 is affecting Indigenous people in the United States, says Spero Manson, director of the Centers for American Indian and Alaska Native Health at the Colorado School of Public Health, who is Pembina Chippewa. “But it all builds on her prior work.”

Echo-Hawk, who is a citizen of the Pawnee Nation of Oklahoma, grew up in rural Alaska. She credits her interest in public health to the values she saw modeled by the leaders and members of her tribal communities. “They think about the health and well-being of an entire community in a very holistic way,” Echo-Hawk says.

She had a different experience after moving to Seattle for college and seeking prenatal care for her first pregnancy at a local hospital. When a medical assistant found out that Echo-Hawk was Indigenous, she began to aggressively question her about drinking and drug use. (Echo-Hawk was doing neither.) “That was very traumatic for me … I was treated in a way that a lot of people of color are, and that is with disdain, discrimination, and outright racism. And it inhibited my care,” she says.

She didn’t see a doctor again until her second trimester, when she went to the Seattle Indian Health Board. There she was welcomed, trusted, and treated with respect. That experience set Echo-Hawk on a path that eventually led to studying health policy at the University of Washington, Bothell, and working at the research program Partnerships for Native Health, now at Washington State University. She became director of UIHI in 2016.

“The system of colonialism in the United States has created, and continues to increase risk factors for, poor health outcomes in Native communities,” Echo-Hawk says. The U.S. government removed many Indigenous communities from their lands and confined them to reservations. Many didn’t have access to medical care and were cut off from their traditional diets and lifestyles, including spiritual practices that were tied to their homelands. Today, American Indians and Alaska Natives have higher rates of obesity, diabetes, asthma, and heart disease than white Americans, as well as higher rates of suicide. The system of oppression in the United States, Echo-Hawk says, “has built a perfect environment to kill us in a pandemic.”

But data showing the pandemic’s full impact on Indigenous communities across the country have not been collected, and accessing the information that does exist can be an uphill battle. Citing privacy concerns, for example, CDC initially denied tribal epidemiology centers, including UIHI, access to data about testing and confirmed COVID-19 cases, even though it was making those data available to states. What’s more, data collected by tribes, local and state health departments, and national agencies are often wildly inconsistent, says Desi Rodriguez-Lonebear, a social demographer at the University of California, Los Angeles, and a citizen of the Northern Cheyenne Nation. “I cannot tell you with any sort of certainty the number of positive cases of COVID-19 on my reservation right now,” she says. “It’s shocking.”

It also reflects an old pattern, Rodriguez-Lonebear says. “For so long, data has been used against our people.” For example, the U.S. census, which began in 1790, excluded all American Indians until 1860, and didn’t count those living on reservations until 1900. The census data were then used to justify the invasion and settlement of supposedly empty land, Rodriguez-Lonebear says.

Today, American Indians and Alaska Natives make up about 2% of the U.S. population but are often left out of national data analyses or marked as statistically insignificant. “I see being eliminated in the data as an ongoing part of the continuing genocide of American Indians and Alaska Natives. If you eliminate us in the data, we no longer exist,” Echo-Hawk says.

One way this erasure happens is through racial misclassification, Echo-Hawk says. Documents such as hospital intake forms might not give people the option to identify as American Indian or Alaska Native, lumping them into an “other” category. Similarly, CDC reports maternal mortality data by three racial categories: white, Black, and Hispanic. All other races are classified as “other.” When UIHI did its own analysis of maternal mortality, it found that urban American Indian mothers were 4.2 times more likely to die during or shortly after pregnancy than non-Hispanic white mothers.

Echo-Hawk is pushing for similar detail on COVID-19 cases. Before the pandemic, she traveled the country working with Indigenous communities and training scientists at universities and other institutions to change their data collection and analysis practices. Now, she can’t leave Seattle because of the pandemic, but she’s working up to 15 hours a day, 7 days a week. “This is probably the most troubling time ever in my career,” she says. Echo-Hawk and others pushed CDC to give tribal health authorities access to COVID-19 cases—with some success. Still, the data are “a sliver” of what she asked for, she says. “The federal government is failing to uphold their end of the bargain,” Rodriguez-Lonebear agrees. CDC did not respond to a request for comment.

Echo-Hawk is a co-author on a recent article in the Morbidity and Mortality Weekly Report that found American Indians and Alaska Natives were 3.5 times more likely to be diagnosed with COVID-19 than non-Hispanic white people. “That is a gross underreporting,” she says, because the study could only analyze data from the 23 states that reported patients’ race and ethnicity over 70% of the time. “The data is a national disgrace,” and the gaps affect all communities of color, Echo-Hawk says. “How can decisions be made in the United States to prevent, intervene, and treat COVID-19, when you can’t even truly tell what populations are most affected?”

“Data can be used as a weapon to further marginalize and harm communities of color,” especially Indigenous communities, agrees Kelly Gonzales, a citizen of the Cherokee Nation who studies the effects of systemic racism and colonialism on health at the Oregon Health & Science University–Portland State University School of Public Health. As a founding member of the independent Black, Indigenous, and People of Color (BIPOC) Decolonizing Research and Data Council, she draws on Echo-Hawk’s work to design and teach methods of data collection and analysis that advance racial justice. “On days where doing this work in the context of ongoing white supremacy and colonial violence feels really challenging and impossible, I remember her doing this work, and I remember I’m not alone.”

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By Jocelyn KaiserSep. 24, 2020 , 11:50 AM

MOUNT CHIRRIPÓ IN COSTA RICA—Framed by drifting clouds, ecologist Andrea Vincent surveyed the hot tub–size dome her students had erected here at nearly 3800 meters, on Costa Rica’s highest peak. “We did it!” she exulted. Vincent’s team from the University of Costa Rica (UCR) had made the steep 15-kilometer hike up to this tropical alpine landscape—known as a páramo—in a bid to understand how global warming might affect the mosaic of shrubs and grasses. The team had built 20 of the open-topped domes, which block the winds that buffet the slopes, thus slightly warming the plants inside and mimicking conditions they might experience in the future. “There are interesting questions here,” Vincent says. One is whether the páramo will be overrun by the oak trees now restricted to lower, warmer elevations, threatening its biodiversity.

Setting up the experiment in February marked a professional milestone for the 39-year-old Vincent: It was her first major project as a principal investigator on a grant from Costa Rica’s government, after years of working as a collaborator with other scientists, often from the United States. “It’s really cool when it’s your intellectual child,” she says. And she’s pleased that her project is part of a network of similar studies taking place in Ecuador and Colombia. “It’s ciencia criolla,” she boasts—a term of pride for projects led by scientists from Latin America.

Costa Rica’s renowned biodiversity has made it a go-to destination for field biologists from around the world. But despite its relatively small population of just 5 million, the country has also been successful at nurturing its scientific talent in recent decades. And Vincent, who grew up mostly in the capital of San José and trained in Europe, is one of a growing number of Costa Rican scientists who have returned home to launch their careers. It’s a trend the government has encouraged, in part by filling open slots at universities with Ph.D.-level scholars, including some promised jobs before they were sent abroad for advanced schooling.

The result, Vincent says, is a new generation of Costa Rican scientists that is better trained and more ambitious, especially in her field of tropical biology. They are no longer satisfied playing support roles for visiting researchers. “A lot of people are hungry to do research that is competitive at the international level,” Vincent says.

The blossoming has a downside, however: Although Vincent and other Costa Rican biologists have managed to build careers at home, the country is struggling to absorb all of the researchers it is producing. “There is no room in Costa Rica’s universities for the number of scientists who are coming back,” says plant ecologist Oscar Rocha, a Costa Rican working at Kent State University in Ohio. “A lot of well-trained scientists are now working for field stations or programs that are training undergraduates,” he says, instead of leading projects.

Granted, researchers in many nations face a scarcity of faculty jobs. But it’s an especially painful paradox given the natural riches beckoning scientists in Costa Rica. “A lot of us were pushed [to excel] in a good sense,” says insect ecologist Fernando Soley Guardia, who earned a Ph.D. in Australia and is now teaching courses at UCR and the Organization for Tropical Studies (OTS), a nonprofit research and education organization based in the United States and Costa Rica (see sidebar, below). “Now, a lot of us want to be back here, to do research where we learned from the environment. But there’s not enough space.”

Although definitive statistics aren’t available, observers say it’s clear that Costa Rica’s growing pool of Ph.D. tropical biologists marks a departure from 30 years ago. Then, for example, just 13 of 32 faculty at the UCR School of Biology had a doctorate. Now, 80% hold that degree, and a Ph.D. is mandatory for new hires.

Rocha, who is 62, experienced that transformation firsthand. While earning a master’s degree at UCR in the 1980s, he worked as a manager at La Selva, a research station some 80 kilometers north of San José run by OTS. The exposure to visiting scientists helped inspire Rocha to go abroad; he earned a Ph.D. from Pennsylvania State University in the United States in 1990. He then returned to Costa Rica and later became chair of UCR’s School of Biology.

In that job, Rocha promoted efforts to send Costa Rican students abroad to Ph.D. programs—to avoid “inbreeding,” he says—and then lure them back. His department bolstered training in the analytical skills students needed to qualify for foreign programs. Faculty worked to place them with colleagues in the United States and Europe, and helped students win funding from foreign sources. Under a system called reserva de plaza, Costa Rican universities also directly funded graduate studies abroad for some students, if they agreed to return to a reserved university job. “The ball started rolling,” Rocha says.

Many of the biologists who have emerged from such efforts have moved beyond the taxonomy and descriptive science that has long been a tradition in Costa Rica. Vincent, for example, pursues broader, hypothesis-driven research as UCR’s first ecosystem ecologist, working to reveal how physical processes like geochemical cycles shape organisms and ecosystems. “There was a sense long ago that we were more like passionate technicians,” says forest ecologist Roberto Cordero, of the National University of Costa Rica, who at 58 is part of Rocha’s generation. “Now, we are demanding more and providing more insights.”

Microbial ecologist Adrián Pinto, 42, is one member of this new generation. Earlier this year, he stood in his lab on the UCR campus in San José peering into glass boxes housing leafcutter ants that he uses to educate schoolchildren. Some of the busy ants carried leaf fragments, others tended a brown fungal structure. Pinto’s graduate research at the University of Wisconsin (UW), Madison, showed how bacteria in the ants’ fungal gardens fix nitrogen, or convert it from the air into a biologically usable form; the work was published in Science in 2009. He then returned to Costa Rica, where he had a job awaiting at UCR because of the reserva system.

Pinto has shifted his focus from the nitrogen-fixing role of such bacteria toward mining them for useful chemicals. “Here basic research is very hard to fund,” he says. He and two co-investigators now lead a 22-person team devoted, in large part, to probing Costa Rica’s insect ecosystems for compounds that might be useful in medicine. (Biologists found one promising antibiotic, dubbed selvamicin, in a leafcutter ant garden at La Selva.) “It’s a great country for microbial ecology,” Pinto says.

Pinto is a rarity in Costa Rica: He’s also a co–principal investigator on a U.S. National Institutes of Health grant with researchers at UW. His lab screens bacteria for antimicrobial activity, then ships promising leads to UW for expensive animal studies. Pinto “has created a really good model for how to be successful” in Costa Rica, says UW evolutionary biologist Cameron Currie.

Other returning biologists have focused on conserving Costa Rica’s vulnerable species. Gilbert Alvarado, 37, a wildlife pathologist who studies threatened tropical frogs, earned his Ph.D. in Brazil. Now at UCR, Alvarado has helped rediscover several populations, and one entire species, of frogs in Costa Rica that were thought to have been wiped out in the 1980s and 1990s by a fungus called chytrid, which has killed amphibians worldwide. He and U.S. collaborators recently used Costa Rican museum specimens to show chytrid was present in the nation’s frogs a half-century ago, suggesting it spread slowly or evolved to become more lethal. He is now raising chytrid-resistant frogs in the lab that will be released to shore up vulnerable populations.

UCR evolutionary biologist Beatriz Willink, 32, who came back to Costa Rica 2 years ago after a Ph.D. in Sweden, is pursuing more fundamental research. She has studied why damselflies evolved certain colors to attract mates. She returned home not only because Costa Rica’s ecology abounds “with questions,” but also because she feels a moral obligation to teach here, attracted by “the idea that people from all backgrounds in this small Latin American country can have this great publicly funded education.”

Although Vincent, Pinto, Alvarado, and Willink have secured tenure-track positions, many other Costa Rican researchers are finding it difficult to land satisfying jobs. “I know people who are extremely qualified and have published lots of good papers who are just waiting in line,” Willink says.

One obstacle, several scientists say, is Costa Rica’s reserva system. Its intent, to lure back and retain talent by assuring doctoral candidates a job, once made sense, they say. (Only Vincent did not get her job this way.) But now, with an abundance of researchers trained overseas who are ready to compete for academic jobs, the reserva seems a bit “outdated,” says evolutionary biologist Marcelo Araya-Salas, a non-reserva Ph.D. who is job hunting in Costa Rica.

In a bid to stay active while waiting for a job to open up, some Ph.D.-level scientists are working for conservation organizations or teaching, in some cases squeezing in research part time. For instance, Jimena Samper-Villareal teaches and works on seagrass ecology and restoration at UCR’s marine science center in a staff scientist position that hovers between one-quarter and three-quarter time each year. She came back in 2016 after her Ph.D. in Australia so her two young kids could be close to family. But there are “very limited opportunities in Costa Rica,” Samper-Villareal says, and she’s “trying to keep my publications up” while watching for an opening.

Some researchers have opted to try to wait things out in postdoctoral positions abroad. Other have joined Costa Rica’s science diaspora, taking faculty positions in the United States or elsewhere instead of trying to return, Rocha notes.

Whether the job crunch will ease in the future is unclear. A shortage of funding has reduced the number of Costa Ricans receiving scholarships to pursue doctoral degrees; at UCR they dropped from nearly 50 a year in 2016 to just 22 last year. That could reduce the competition for jobs. But the same funding shortage could limit jobs at home. The country now spends about 0.4% of its gross domestic product on science, down slightly from previous years when its economy was stronger.

Another factor is a university pension system that appears to be discouraging older faculty from retiring and creating new openings, says geneticist Gabriel Macaya, a former UCR rector. One solution would be for research universities to set aside more funds to hire scientists for nontenured, fulltime positions, Macaya says.

Some senior scientists who have mentored this next generation are dismayed. “It is troubling to see good young people with good training not being able to employ their talents,” says William Eberhard, a leading U.S. evolutionary biologist who joined the UCR faculty in 1979 and retired about 5 years ago. “And it is especially frustrating when one has invested time and effort in helping them get to where they are.”

Among Eberhard’s undergraduate students was Soley Guardia, who went on to study how assassin bugs use clever strategies to catch web-weaving spiders for his Ph.D. in Australia. Soley Guardia now wants to do comparative research with Costa Rican species of these aggressive predators, but hasn’t yet found a tenure-track position. He says his twin brother Mariano, a biogeographer, is in the same situation.

Soley Guardia speaks wistfully of the prominent scientists, some from outside Costa Rica, who influenced him. “It was good to have that exposure,” he says. “Now we’re kind of self-sustaining in a good way. We come up with our own ideas.”

But he fears he won’t be able to follow through on them if he stays in his homeland. “The bad thing,” he says, “is we’re aspiring to do science at the level of developed countries without the money to pay for it.”

Travel for this story was supported by the International Center for Journalists in Washington, D.C.

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By Gabriel PopkinSep. 23, 2020 , 12:25 PM

Forests are having their moment. Because trees can vacuum carbon from the atmosphere and lock it away in wood and soil, governments and businesses are embracing efforts to fight climate change using trees.

Nations have pledged to plant or restore forests over a combined area larger than India. One corporate-backed initiative has secured pledges to conserve or restore 855 million trees by 2030. Even President Donald Trump, an ardent climate change skeptic, endorsed a trillion-tree planting initiative at the World Economic Forum in January; a companion bill was introduced in the U.S. House of Representatives in February.

Scientists agree that new trees and forests can, in theory, cool the planet. But many have warned that the enthusiasm and money flowing to forest-based climate solutions threaten to outpace the science.

Two papers published this week seek to put such efforts on a firmer footing. One study quantifies how much carbon might be absorbed globally by allowing forests cleared for farming or other purposes to regrow. The other calculates how much carbon could be sequestered by forests in the United States if they were fully “stocked” with newly planted trees. Each strategy has promise, the studies suggest, but also faces perils.

To get a worldwide perspective on the potential of second-growth forests, an international team led by ecologist Susan Cook-Patton of the Nature Conservancy (TNC) assembled data from more than 13,000 previously deforested sites where researchers had measured regrowth rates of young trees. The team then trained a machine-learning algorithm on those data and dozens of variables, such as climate and soil type, to predict and map how fast trees could grow on other cleared sites where it didn’t have data.

In 2017, a TNC-led team had calculated that some 678 million hectares, an area nearly the size of Australia, could support second-growth forests. (The total excludes land where trees might not be desirable, such as farmland and ecologically valuable grasslands.) New forests growing throughout that area could soak up one-quarter of the world’s fossil fuel emissions over the next 30 years, Cook-Patton and colleagues report today in Nature. That absorption rate is 32% higher than a previous estimate, based on coarser data, produced by the Intergovernmental Panel on Climate Change. But the total carbon drawdown is 11% lower than the 2017 estimate.

Can the forest regenerate naturally, or can we do something to help?

The study highlights “what nature can do all on its own,” Cook-Patton says. Although reforesting the full area of opportunity is unrealistic, she says, reforestation planners can use her team’s results to estimate how much carbon sequestration to expect.

The study represents “a lightning step forward” in precision compared with earlier studies, says geographer Matthew Fagan of the University of Maryland, Baltimore County, who was not involved in the work.

But, Fagan adds, “Natural regrowth is not going to save the planet.” Young forests are easier to cut down or burn than old ones, Fagan cautions, making them frequent targets for farmers and ranchers. Second-growth forests in the Amazon typically last only 5 to 8 years, according to studies, though trees on slopes or near streams often survive longer. Even in Costa Rica, renowned as a reforestation champion that has doubled its forest cover in recent decades, half of regrowing forests fall within 20 years.

In many places, grazing cattle or growing crops is simply more profitable than allowing trees to come back, notes Pedro Brancalion, a forest expert at the University of São Paulo in Piracicaba, Brazil. Policies that promote reforestation and better markets for both carbon and forest products are needed, he says, to give trees a boost. Right now, “Nobody will abandon cattle ranching or agriculture for growing carbon.”

Robin Chazdon, a University of Connecticut, Storrs, ecologist and study co-author, urges conservationists to help farmers grow both trees and crops or cattle—a concept, she notes, that has a long history of success. “If you look at the history of Indigenous peoples, you will find many, many examples of how they managed and modified the forest for their own uses,” she says. “It doesn’t have to be completely left alone.”

Some advocates promote expanding tree planting in existing forests. To boost that concept, a team of researchers at the U.S. Forest Service (USFS) quantified how many additional trees U.S. forests could hold. Drawing on a federal inventory, they found that more than 16% of forests in the continental United States are “understocked”—holding fewer than 35% of the trees they could support. Fully stocking these 33 million hectares of forest would ultimately enable U.S. forests to sequester about 18% of national carbon emissions each year, up from 15% today, the team reported this week in the Proceedings of the National Academy of Sciences. But for that to happen, the United States would have to “massively” expand its annual tree-planting efforts, from about 1 billion to 16 billion trees, says lead author Grant Domke, a USFS research forester in St. Paul, Minnesota.

Planting trees might make sense in some places, Cook-Patton says. But she cautions that adding trees in fire-prone areas could increase fire risk. And although tree planting often gets the hype, cheaper natural regeneration usually results in a more diverse mix of species and provides more carbon bang for the buck. “For any given site,” she says, “we should always ask ourselves first: ‘Can the forest regenerate naturally, or can we do something to help?’”

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By Lucy HicksSep. 23, 2020 , 11:40 AM

Cells have places to be, and they have all evolved different ways to get there: Red blood cells change their shape, and bacteria use whiplike appendages to propel themselves forward. Now, new research suggests white blood cells have their own special way of swimming, which biologists have dubbed “molecular paddling.”

For years, scientists thought white bloods cells could move across 2D surfaces, like blood vessels or skin layers, only by attaching to and crawling along them. They also knew certain human and mouse white blood cells could swim in liquids, but they weren’t sure how.

To find out, researchers recorded how human white blood cells, or leukocytes, moved in liquids and on solid surfaces. Videos suggested the cells swam by changing their shape and using a breaststrokelike motion. But such movement wasn’t enough to explain the speeds clocked by the cells. So the scientists came up with a new proposal: The cells’ membranes are packed with protein “paddles” that give them a speed boost.

As the leukocytes swam, researchers saw protruding proteins migrate from the front to the back the cell, as if on a treadmill (above). According to their hypothesis, as the cell membrane moves backward, these proteins contract and propel the cell forward. Then, when the proteins reach the back of the cell, they migrate inside the membrane and move back out to the front to start the process over again.

And because the proposed paddling proteins moved internally from the rear to the front of the cell as it swam, the researchers suspect the proteins are “recycled,” allowing the cell to continuously paddle, they reported online last month in Biophysical Journal. Don’t expect a speedy journey, though. This novel paddling mechanism is about four times slower than crawling.

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By Elizabeth PennisiSep. 23, 2020 , 12:10 PM

An exotic metallic green beetle is eating its way through North American forests, leaving dead ash trees in its wake. In the 20 years since this Asian pest, the emerald ash borer (Agrilus planipennis), was first discovered in Michigan, it has killed tens of millions of trees and spread to 35 U.S. states and parts of Canada. Now, a new analysis predicts ash populations might not recover, because the beetle also attacks young trees that sprout after older trees are gone, blocking long-term reproduction.

In some places, ash may disappear completely, says forest ecologist Isabelle Aubin of Natural Resources Canada, who was not involved with the work. “Losing key species like ash is weakening forest ecosystems.”

Known as the Venus of the woods, ash trees are valued in both forests and urban landscapes. Tough yet elastic ash wood is quite versatile, and has been used to make skis, baseball bats, guitars, and office furniture. In the forest, the trees provide a home and food for numerous birds, insects, and squirrels.

The staple-size emerald ash borer is believed to have reached North America in wood used to pack freight. As its name implies, its larvae bore into trunks, where they chew through the water—and nutrient-conducting tissues. They can kill a tree in as little as 2 years.

The distribution of ash logs as firewood helped spread the pest, as did the transport of nursery trees from infected areas. The invader is considered the most destructive forest pest in North America, according to the Emerald Ash Borer Information Network, at times killing more than 99% of ash trees in a forest.

To evaluate the extent of the borer’s destruction, Purdue University forest ecologist Songlin Fei and his colleagues turned to the U.S Forest Inventory and Analysis. The federal survey of public and private forest plots in 40,000 locations across the United States periodically records the number, health, and growth of each tree species in a plot.

The data go back to 1930, but Fei’s postdoc Samuel Ward focused on those data collected since the borer was discovered. He divided the data into three time periods: 2002–06, 2007–12 and 2013–18. Fei, Ward, and their colleagues then counted the number of ash trees, saplings, and seedlings and noted which ashes had died between surveys.

Ash makes a quick comeback, the team reports this month in Forest Ecology and Management. Where the borer had taken its toll in the early 2000s, ash seedlings and saplings were thriving, sometimes reaching densities of more than 1200 per hectare within the subsequent decade.

But the data also showed those youngsters were mostly gone by 2018. “Ash recruitment is not keeping up with mortality, and few seedlings appear to reach reproductive age,” says Juliann Aukema, an ecologist the U.S. Agency for International Development who was not involved with the research. With no mature trees to produce new seeds, eventually there will be no seeds left in the soil to replace the dead trees, she says. The ash, Aukema fears, could virtually disappear, just as the chestnut, once the dominant tree in eastern U.S. forests, did during the past century after the introduction of a deadly fungus.

Until now, such long-term analyses of ash populations had been done only in individual forests. They had shown similar outcomes for young ash trees. But, “This paper is providing evidence that what we were observing locally was in fact a global trend,” Aubin says.

Ian Boyd, a systems scientist at the University of St. Andrews, thinks the future of the ash may be less dire than this analysis indicates, however. For one, the ash “doesn’t just roll over and succumb,” Boyd says—also not involved with the work—and lots of seedlings provide a potential way for ash species to bounce back. He also doesn’t think enough time has passed to know the ash’s future. “It will likely take decades for the dynamics of the relationship between the borer and ash to settle down,” he says. This work is “the first chapter of a long story of how a new balance will eventually emerge between it and ash trees.”

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By Adrian ChoSep. 23, 2020 , 1:35 PM

You might call Jeffrey Shapiro the reluctant godfather of quantum radar. Twelve years ago, the electrical engineer at the Massachusetts Institute of Technology (MIT) helped develop the key concept underlying this scheme to dramatically increase radar’s sensitivity. But even he doesn’t think the technology will work. “There’s just a lot of problems that make it hard for me to believe that this system is going to be of any use,” Shapiro says. So he is both bemused and dismayed by the attention other researchers and funding agencies continue to lavish on it.

A mini–arms race is unfolding in the supposed field, initiated by press reports in 2016 that China had built a quantum radar—potentially threatening the ability of stealthy military aircraft to hide in plain sight from conventional radars. “I started working on this because there were government people coming to me and saying, ‘There are reports of quantum radar coming out of China. Is this real?’” says Christopher Wilson, a physicist at the University of Waterloo in Canada. His group and others have demonstrated elements of a quantum radar scheme, but only in limited experiments that a nonquantum system can still match.

The quantum radar story began in 2008, when Seth Lloyd, a quantum engineer at MIT, unveiled his concept of quantum illumination. Lloyd argued that you could more easily detect an object against a bright background if, instead of merely reflecting light off it, you exploited a quantum connection between particles called entanglement. Every photon has a frequency that determines its energy. Quantum theory says, weirdly, that a photon can have multiple frequencies at once—until it’s measured and “collapses” randomly to one frequency or another. Even weirder, two such photons can then be entangled so that their frequencies, although uncertain, are correlated: They are sure to be identical whenever they’re measured.

Lloyd calculated that an observer could more easily pick out an object by generating entangled pairs, shining one photon toward the object, keeping the other, and then measuring the retained and returning photons together in a particular way. Essentially, the entanglement correlations would make it harder to mistake a background photon for one reflected off a target. The signal to noise ratio would scale with the amount of entanglement: The more frequencies spanned by each photon in an entangled pair, the stronger the signal.

Lloyd’s calculation relied on a highly idealized form of entanglement. So that same year, he, Shapiro, and colleagues redid it for the real entangled light pulses that experimenters can generate with a special crystal that converts a single higher frequency pulse to two entangled pulses at lower frequencies. The pulses have no definite number of photons—just an average number—and they are “noisy,” like radio static. But thanks to the entanglement, the noise in the two pulses is highly correlated.

The researchers compared the sensitivity of a detector relying on the entangled pulses with a conventional one sending out single pulses of laser light, also known as coherent states. They found that the quantum effects boosted the signal-to-noise ratio by just a factor of four, less than they hoped for. “We were slightly disappointed,” says Si-Hui Tan, now a quantum information theorist at Horizon Quantum Computing. “Coherent states, they’re just so damned good!” she says.

A visionary scheme

Still, the calculation gave experimenters a target. In 2015, researchers at MIT demonstrated quantum illumination at optical frequencies, realizing a 20% increase in signal to noise. But that experiment had a major limitation. The whole idea was to detect an object against a bright background, but there’s very little optical background at room temperature—your surroundings don’t glow visibly. So the MIT team had to generate artificial background light.

Things are different in the microwave band, where radar works, says Johannes Fink, an experimental physicist at the Institute of Science and Technology Austria. At room temperature, microwaves stream from everything, even the air. “People are interested in the microwave because the background is always present,” he says. Stealth technologies hide military planes by suppressing their reflectivity at microwave frequencies so that the glow of the surroundings masks the plane’s reflections.

Quantum illumination seemed to promise a way to defeat stealth technologies. However, demonstrating the scheme with microwaves has proved daunting. Physicists can generate pairs of entangled microwave pulses from single ones using, instead of a crystal, a gizmo called a Josephson parametric converter. But that device only works at temperatures near absolute zero, which requires working within cryostats cooled with liquid helium.

Still, in 2019 Wilson and colleagues demonstrated that they could generate entangled microwaves and use them to detect an object within the same cryostat, as they reported in March 2019 in Applied Physics Letters. Fink; Shabir Barzanjeh, a physicist now at the University of Calgary; and colleagues performed a similar experiment, but amplified the signal pulse and ferried it out of the cryostat to detect a room temperature object, as they reported on 8 May in Science Advances.

But to really make the scheme work, physicists must also preserve the retained microwave pulse until the reflected pulse (or the background replacing it) returns. Then, both pulses can be measured together in a way that enables the quantum waves to interfere. So far, however, nobody has done that. Instead, they’ve measured the retained pulse immediately and the returning pulse later, which in the experiments wipes out any gain from the quantum correlations.

Even if experimenters can overcome the technical hurdles, quantum radar would still suffer from a fatal weakness, researchers say. The entangled pulses of microwaves provide an advantage only when the broadcast pulses are extremely faint. The extra quantum correlations fade from prominence if pulses contain significantly more than one photon—which is overwhelmingly the case in real radar. “If you crank up the power, you won’t see any difference between the quantum and the classical,” Barzanjeh says. And cranking up the power is a much easier way to improve the sensitivity.

Such considerations suggest quantum radar will never be deployed for long-range uses such as tracking airplanes, says Fabrice Boust, a physicist at France’s aerospace agency, ONERA, who specializes in radar. And whatever system China may have developed, it almost certainly isn’t a quantum radar as commonly conceived, he says. “I am convinced that when they announced their quantum radar it was not working,” Boust says. “But they knew they would get a reaction.”

Fink says his personal goal remains scientific: demonstrating in the laboratory the true advantage—however small it may be—of entanglement for detecting objects hidden by glare. But the dream of fielding a quantum radar to detect stealth aircraft will likely fade away, says Giacomo Sorelli, a theorist at the Sorbonne University. “Taking out the long-range application of the technology will surely take out a lot of the interest of funding agencies,” he says.

Shapiro is less sure. This week, he notes, researchers again discussed quantum radar in a special session of the online Radar Conference of the Institute of Electrical and Electronics Engineers.

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