An unusual blast of radio waves from deep space had a sense of rhythm. Over the few seconds in December 2019 when the burst was detected, it kept a steady beat. That tempo holds clues to the potential origin of the mysterious outburst, one of a class of flares called fast radio bursts.
Of the hundreds of previously detected fast radio bursts, most last for mere milliseconds. But this one persisted for roughly three seconds, Daniele Michilli and colleagues report in the July 14 Nature. The burst consisted of multiple brief pulses, repeating about every two-tenths of a second. Scientists have previously observed fast radio bursts that repeat with a delay of minutes or days (SN: 3/2/16). “With this one it was a train of [pulses] one after the other, a heartbeat, like, ‘boom boom boom boom,’” says Michilli, an astronomer at MIT.
That makes this fast radio burst very special, says astrophysicist Bing Zhang of the University of Nevada, Las Vegas, who was not involved with the research. Compared with other fast radio bursts, “this is a different animal.”
Scientists still don’t know how fast radio bursts are generated, but evidence has been building that they are associated with ultradense, spinning dead stars called neutron stars and, in particular, highly magnetic neutron stars called magnetars (SN: 6/4/20).
The steady repetition rate hints at what may have caused this particular blast, discovered by the Canadian Hydrogen Intensity Mapping Experiment, a radio telescope in British Columbia.
Only certain types of cosmic processes produce such metronome-like signals. Neutron stars, for example, can appear to pulse as they spin, because they emit beams of radio waves that can sweep past Earth at regular intervals. Neutron stars tend to have tempos similar to that of the pulsating fast radio burst. But that burst was much more luminous than normal neutron star pulses, suggesting some unknown process would need to have amped up the emission.
Another idea is that large outbursts on magnetars could cause starquakes that jostle those stars’ solid crusts, generating regular barrages of radio waves. The rhythmic burst’s pulsing “is sort of consistent with a frequency with which we expect that magnetars could be shaking,” says astrophysicist Cecilia Chirenti of the University of Maryland in College Park, who was not involved with the new study.
Or the pulsing might result from two neutron stars that orbit one another. Outbursts could occur at regular points in that orbit, when the magnetic regions that surround each neutron star interact.
Scientists don’t know if all fast radio bursts are generated in the same way. An outlier like this one might have a different origin story than a more standard, one-off blast. That means it’s hard to make conclusions about other fast radio bursts, Zhang says. “Whatever we can derive from this one, I would not easily extrapolate to the other guys.”
Biologist Martin Dančák didn’t set out to find a plant species new to science. But on a hike through a rainforest in Borneo, he and colleagues stumbled on a subterranean surprise.
Hidden beneath the soil and inside dark, mossy pockets below tree roots, carnivorous pitcher plants dangled their deathtraps underground. The pitchers can look like hollow eggplants and probably lure unsuspecting prey into their sewer hole-like traps. Once an ant or a beetle steps in, the insect falls to its death, drowning in a stew of digestive juices (SN: 11/22/16). Until now, scientists had never observed pitcher plants with traps almost exclusively entombed in earth. “We were, of course, astonished as nobody would expect that a pitcher plant with underground traps could exist,” says Dančák, of Palacký University in Olomouc, Czech Republic.
That’s because pitchers tend to be fragile. But the new species’ hidden traps have fleshy walls that may help them push against soil as they grow underground, Dančák and colleagues report June 23 in PhytoKeys. Because the buried pitchers stay concealed from sight, the team named the species Nepenthes pudica, a nod to the Latin word for bashful.
The work “highlights how much biodiversity still exists that we haven’t fully discovered,” says Leonora Bittleston, a biologist at Boise State University in Idaho who was not involved with the study. It’s possible that other pitcher plant species may have traps lurking underground and scientists just haven’t noticed yet, she says. “I think a lot of people don’t really dig down.”
The next generation of dark matter detectors has arrived.
A massive new effort to detect the elusive substance has reported its first results. Following a time-honored tradition of dark matter hunters, the experiment, called LZ, didn’t find dark matter. But it has done that better than ever before, physicists report July 7 in a virtual webinar and a paper posted on LZ’s website. And with several additional years of data-taking planned from LZ and other experiments like it, physicists are hopeful they’ll finally get a glimpse of dark matter. “Dark matter remains one of the biggest mysteries in particle physics today,” LZ spokesperson Hugh Lippincott, a physicist at the University of California, Santa Barbara said during the webinar.
LZ, or LUX-ZEPLIN, aims to discover the unidentified particles that are thought to make up most of the universe’s matter. Although no one has ever conclusively detected a particle of dark matter, its influence on the universe can be seen in the motions of stars and galaxies, and via other cosmic observations (SN: 7/24/18).
Located about 1.5 kilometers underground at the Sanford Underground Research Facility in Lead, S.D., the detector is filled with 10 metric tons of liquid xenon. If dark matter particles crash into the nuclei of any of those xenon atoms, they would produce flashes of light that the detector would pick up.
The LZ experiment is one of a new generation of bigger, badder dark matter detectors based on liquid xenon, which also includes XENONnT in Gran Sasso National Laboratory in Italy and PandaX-4T in the China Jinping Underground Laboratory. The experiments aim to detect a theorized type of dark matter called Weakly Interacting Massive Particles, or WIMPs (SN: 12/13/16). Scientists scaled up the search to allow for a better chance of spying the particles, with each detector containing multiple tons of liquid xenon.
Using only about 60 days’ worth of data, LZ has already surpassed earlier efforts to pin down WIMPs (SN: 5/28/18). “It’s really impressive what they’ve been able to pull off; it’s a technological marvel,” says theoretical physicist Dan Hooper of Fermilab in Batavia, Ill, who was not involved with the study.
Although LZ’s search came up empty, “the way something’s going to be discovered is when you have multiple years in a row of running,” says LZ collaborator Matthew Szydagis, a physicist at the University at Albany in New York. LZ is expected to run for about five years, and data from that extended period may provide physicists’ best chance to find the particles.
Now that the detector has proven its potential, says LZ physicist Kevin Lesko of Lawrence Berkeley National Laboratory in California, “we’re excited about what we’re going to see.”
Tyrannosaurus rex’s tiny arms have launched a thousand sarcastic memes: I love you this much; can you pass the salt?; row, row, row your … oh.
But back off, snarky jokesters. A newfound species of big-headed carnivorous dinosaur with tiny forelimbs suggests those arms weren’t just an evolutionary punchline. Arm reduction — alongside giant heads — evolved independently in different dinosaur lineages, researchers report July 7 in Current Biology.
Meraxes gigas, named for a dragon in George R. R. Martin’s “A Song of Ice and Fire” book series, lived between 100 million and 90 million years ago in what’s now Argentina, says Juan Canale, a paleontologist with the country’s CONICET research network who is based in Buenos Aires. Despite the resemblance to T. rex, M. gigas wasn’t a tyrannosaur; it was a carcharodontosaur — a member of a distantly related, lesser-known group of predatory theropod dinosaurs. M. gigas went extinct nearly 20 million years before T. rex walked on Earth. The M. gigas individual described by Canale and colleagues was about 45 years old and weighed more than four metric tons when it died, they estimate. The fossilized specimen is about 11 meters long, and its skull is heavily ornamented with crests and bumps and tiny hornlets, ornamentations that probably helped attract mates.
Why these dinosaurs had such tiny arms is an enduring mystery. They weren’t for hunting: Both T. rex and M. gigas used their massive heads to hunt prey (SN: 10/22/18). The arms may have shrunk so they were out of the way during the frenzy of group feeding on carcasses.
But, Canale says, M. gigas’ arms were surprisingly muscular, suggesting they were more than just an inconvenient limb. One possibility is that the arms helped lift the animal from a reclining to a standing position. Another is that they aided in mating — perhaps showing a mate some love.
Getting a COVID-19 test has become a regular part of many college students’ lives. That ritual may protect not just those students’ classmates and professors but also their municipal bus drivers, neighbors and other members of the local community, a new study suggests.
Counties where colleges and universities did COVID-19 testing saw fewer COVID-19 cases and deaths than ones with schools that did not do any testing in the fall of 2020, researchers report June 23 in PLOS Digital Health. While previous analyses have shown that counties with colleges that brought students back to campus had more COVID-19 cases than those that continued online instruction, this is the first look at the impact of campus testing on those communities on a national scale (SN: 2/23/21). “It’s tough to think of universities as just silos within cities; it’s just much more permeable than that,” says Brennan Klein, a network scientist at Northeastern University in Boston.
Colleges that tested their students generally did not see significantly lower case counts than schools that didn’t do testing, Klein and his colleagues found. But the communities surrounding these schools did see fewer cases and deaths. That’s because towns with colleges conducting regular testing had a more accurate sense of how much COVID-19 was circulating in their communities, Klein says, which allowed those towns to understand the risk level and put masking policies and other mitigation strategies in place.
The results highlight the crucial role testing can continue to play as students return to campus this fall, says Sam Scarpino, vice president of pathogen surveillance at the Rockefeller Foundation’s Pandemic Prevention Institute in Washington, D.C. Testing “may not be optional in the fall if we want to keep colleges and universities open safely,” he says. Finding a flight path As SARS-CoV-2, the virus that causes COVID-19 rapidly spread around the world in the spring of 2020, it had a swift impact on U.S. college students. Most were abruptly sent home from their dorm rooms, lecture halls, study abroad programs and even spring break outings to spend what would be the remainder of the semester online. And with the start of the fall semester just months away, schools were “flying blind” as to how to bring students back to campus safely, Klein says.
That fall, Klein, Scarpino and their collaborators began to put together a potential flight path for schools by collecting data from COVID-19 dashboards created by universities and the counties surrounding those schools to track cases. The researchers classified schools based on whether they had opted for entirely online learning or in-person teaching. They then divided the schools with in-person learning based on whether they did any testing.
It’s not a perfect comparison, Klein says, because this method groups schools that did one round of testing with those that did consistent surveillance testing. But the team’s analyses still generally show how colleges’ pandemic response impacted their local communities.
Overall, counties with colleges saw more cases and deaths than counties without schools. However, testing helped minimize the increase in cases and deaths. During the fall semester, from August to December, counties with colleges that did testing saw on average 14 fewer deaths per 100,000 people than counties with colleges that brought students back with no testing — 56 deaths per 100,000 versus about 70. The University of Massachusetts Amherst, with nearly 30,000 undergraduate and graduate students in 2020, is one case study of the value of the testing, Klein says. Throughout the fall semester, the school tested students twice a week. That meant that three times as many tests occurred in the city of Amherst than in neighboring cities, he says. For much of the fall and winter, Amherst had fewer COVID-19 cases per 1,000 residents than its neighboring counties and statewide averages.
Once students left for winter break, campus testing stopped – so overall local testing dropped. When students returned for spring semester in February 2021, area cases spiked — possibly driven by students bringing the coronavirus back from their travels and by being exposed to local residents whose cases may have been missed due to the drop in local testing. Students returned “to a town that has more COVID than they realize” Klein says.
Renewed campus testing not only picked up the spike but quickly prompted mitigation strategies. The university moved classes to Zoom and asked students to remain in their rooms, at one point even telling them that they should not go on walks outdoors. By mid-March, the university reduced the spread of cases on campus and the town once again had a lower COVID-19 case rate than its neighbors for the remainder of the semester, the team found.
The value of testing It’s helpful to know that testing overall helped protect local communities, says David Paltiel, a public health researcher at the Yale School of Public Health who was not involved with the study. Paltiel was one of the first researchers to call for routine testing on college campuses, regardless of whether students had symptoms.
“I believe that testing and masking and all those things probably were really useful, because in the fall of 2020 we didn’t have a vaccine yet,” he says. Quickly identifying cases and isolating affected students, he adds, was key at the time. But each school is unique, he says, and the benefit of testing probably varied between schools. And today, two and a half years into the pandemic, the cost-benefit calculation is different now that vaccines are widely available and schools are faced with newer variants of SARS-CoV-2. Some of those variants spread so quickly that even testing twice a week may not catch all cases on campus quickly enough to stop their spread, he says.
As colleges and universities prepare for the fall 2022 semester, he would recommend schools consider testing students as they return to campus with less frequent follow-up surveillance testing to “make sure things aren’t spinning crazy out of control.”
Still, the study shows that regular campus testing can benefit the broader community, Scarpino says. In fact, he hopes to capitalize on the interest in testing for COVID-19 to roll out more expansive public health testing for multiple respiratory viruses, including the flu, in places like college campuses. In addition to PCR tests — the kind that involve sticking a swab up your nose — such efforts might also analyze wastewater and air within buildings for pathogens (SN: 05/28/20).
Unchecked coronavirus transmission continues to disrupt lives — in the United States and globally — and new variants will continue to emerge, he says. “We need to be prepared for another surge of SARS-CoV-2 in the fall when the schools reopen, and we’re back in respiratory season.”
Demond “Dom” Mullins’ days as a student at Lehman College in New York were interrupted in 2004 when his National Guard unit was deployed to Baghdad. A year later, he returned home but struggled with depression and rage. Immersing himself in his studies helped him make sense of the world and his experiences. After completing degrees in Africana studies and political science, Mullins earned a Ph.D. in sociology, focusing his research on a subject he knew firsthand: how returning veterans reintegrate into society.
In 2015, the avid climber and adventure sportsman joined six other veterans and a journalist on a monthlong excursion to climb Alaska’s Denali, the highest peak in North America. To understand the health benefits of high-risk outdoor adventuring outside the clinical therapy framework, Mullins interviewed each participant and collected data about group cohesion and the impact of such high-risk activities on social bonds for his study “Veterans Expeditions: Tapping the great outdoors.”
Formerly an adjunct assistant professor at the Cooper Union for the Advancement of Science and Art in New York City, Mullins has climbed Kilimanjaro and Mount Kenya. In May, he tackled his biggest climbing challenge yet: summiting Mount Everest, the world’s tallest mountain. He and seven other members of Full Circle Everest, an all-Black mountaineering team, set out to make history. Seven of them reached the summit, coming very close to doubling the number of Black people who have achieved that feat. Science News asked Mullins, while he was preparing for the climb, about his research and why he wants more Black people in outdoor spaces. This interview was edited for clarity and length.
SN: When you returned home from Iraq, you cut yourself off from others and contemplated ending your life. What helped you get through the worst times?
Mullins: Education. I was grappling with the discontents of coming home and struggling with what I had experienced in the Iraq War. Education allowed me to explore aspects of my experience intellectually through things that really engaged me — history and social theory.
SN: Did the war change what you envisioned for yourself academically?
Mullins: It influenced my trajectory. Graduate school was not even on my radar before. When I came home, I had this great urgency to improve my future, learn more about global politics and understand how history could produce such a moment. I also wanted to know how all of that might influence veterans’ reintegration.
SN: How did the Denali research expedition follow on your work on veteran reintegration?
I became an avid mountaineer, rock and ice climber and began training with Veterans Expeditions [a nonprofit that works to enhance the life of U.S. veterans]. By the time the Denali expedition came about in May 2015, the cofounder [Nick Watson] asked me to be a part of it. I wanted to tell the story of veterans summiting Denali in a way that makes sense, was scientifically rigorous and could contribute to the research. I wanted to answer certain questions about how interventions like hiking and climbing might come into play. Ethnography [the study of people in their environment] was the best way to do that.
SN: What did you learn about veterans and outdoor adventuring?
Mullins: Much more than in the past, my generation of veterans is more willing to talk about their experiences with each other to find affinity and solidarity. After leaving the service, some lose their identity, partly because there is no space reserved for them to perform the identities they have cultivated through military training, socialization and performance. I learned that they engage in these kinds of high-risk sporting events to support their identities. The outdoors is sort of a theater to perform the heroic identities they’ve developed in a way that can be conducive to greater physical and communal health. One veteran said to me, “The rock and the ice don’t lie to me.” He was reasserting that he is a warrior. SN: How did you become a part of Full Circle Everest?
Mullins: Through Veterans Expeditions, I developed a relationship with [world-famous mountaineer] Conrad Anker. Conrad had this idea about putting together an all-Black expedition to Everest. He introduced me to [Full Circle expedition leader and organizer] Philip Henderson, who had been considering this for a long time. I met Phil and knew right away that I wanted to be a part of that expedition and help find other athletes.
SN: What, if anything, about your experience on Denali do you believe will benefit your attempt to summit Mount Everest?
Mullins: Everest is 9,000 feet taller than Denali. It’s a longer pursuit and a longer expedition, but the conditions will be similar. We got snowed in on Denali for 17 days, which I believe has prepared me for my expedition with Full Circle.
This pursuit is about developing relationships with people who have common experiences. It’s having someone who gets your drift, who understands what you mean without you needing to explain everything. It’s about building community and feeling like you belong. People want to feel like the group is better as a result of their participation. It’s all about social cohesion.
SN: Will you be conducting research on this expedition?
Mullins: This time, I’ll be studying myself — doing an autoethnography. I took time off from work to do this climb, so I don’t have any pressing job to get back to. I plan to take some time to reflect and write about this once it’s over, to help people understand the value of it for me. SN: The Full Circle team spent a few weeks together in January at the Khumbu Climbing Center in Nepal. Your teammates went home, then came back in April to start the climb, but you stayed in Nepal. Why?
Mullins: It gives me an edge in so many different ways: having time for my body to properly acclimate to the elevation, understanding how to keep myself safe and comfortable in the elements. Also developing relationships with the locals, the Sherpas and the other Nepalese persons who are supporting the expedition.
SN: What do you want people to take away from your Full Circle Everest expedition?
Mullins: Diversity in the outdoors matters. The military completely introduced me to outdoor sports. When I was a kid, I never went camping or even hiking. I thought [Brooklyn’s] Prospect Park was the wilderness. These activities have benefits for all people. Hopefully, Full Circle will help African Americans of all ages get outside to hike, camp and explore.
Pig hearts beat for three days inside the chests of two brain-dead patients who were kept alive using ventilators. The feat helps researchers prepare for future clinical trials of pig-to-human transplants, surgeons at the NYU Langone Health in New York City announced at a news conference on July 12.
In mid-June, surgeons transplanted a heart from a genetically modified pig into Lawrence Kelly — a 72-year-old Vietnam veteran with a history of heart problems. A second patient received a porcine heart on July 6. The team monitored both patients for 72 hours before taking them off life support.
For those three days, the hearts kept the recently deceased patients’ blood flowing. “We learned a tremendous amount from the first operation,” surgeon Nader Moazami said at the news conference. The new heart was too small for Kelly’s chest. So surgeons had to adjust blood vessels to account for the size mismatch and blood flow wasn’t perfect. Last year, another team at NYU Langone Health transplanted a pig kidney into a brain-dead woman (SN: 10/22/21). The first pig-to-human heart transplant happened in a living patient in January: 57-year-old David Bennet survived two months with a pig heart before dying of heart failure (SN: 1/31/22). All the organs had been genetically modified to avoid immediate rejection by the body and make them safe for people.
It’s unclear why Bennet’s new heart ultimately failed. Transplanting organs into brain-dead people allows for in-depth analyses that aren’t possible in living patients, NYU Langone surgeon Robert Montgomery said. Researchers can take tissue samples and pictures of the organ immediately following the procedure, while the focus for living people is on keeping them alive and comfortable.
Next, the team plans to do longer-term transplants in more brain-dead patients to determine how long pig hearts might last.
Modern mammals are known for their big brains. But new analyses of mammal skulls from creatures that lived shortly after the dinosaur mass extinction show that those brains weren’t always a foregone conclusion. For at least 10 million years after the dinosaurs disappeared, mammals got a lot brawnier but not brainier, researchers report in the April 1 Science.
That bucks conventional wisdom, to put it mildly. “I thought, it’s not possible, there must be something that I did wrong,” says Ornella Bertrand, a mammal paleontologist at the University of Edinburgh. “It really threw me off. How am I going to explain that they were not smart?”
Modern mammals have the largest brains in the animal kingdom relative to their body size. How and when that brain evolution happened is a mystery. One idea has been that the disappearance of all nonbird dinosaurs following an asteroid impact at the end of the Mesozoic Era 66 million years ago left a vacuum for mammals to fill (SN: 1/25/17). Recent discoveries of fossils dating to the Paleocene — the immediately post-extinction epoch spanning 66 million to 56 million years ago — does reveal a flourishing menagerie of weird and wonderful mammal species, many much bigger than their Mesozoic predecessors (SN: 10/24/19). It was the dawn of the Age of Mammals. Before those fossil finds, the prevailing wisdom was that in the wake of the mass dino extinction, mammals’ brains most likely grew apace with their bodies, everything increasing together like an expanding balloon, Bertrand says. But those discoveries of Paleocene fossil troves in Colorado and New Mexico, as well as reexaminations of fossils previously found in France, are now unraveling that story, by offering scientists the chance to actually measure the size of mammals’ brains over time.
Bertrand and her colleagues used CT scanning to create 3-D images of the skulls of different types of ancient mammals from both before and after the extinction event. Those specimens included mammals from 17 groups dating to the Paleocene and 17 to the Eocene, the epoch that spanned 56 million to 34 million years ago.
What the team found was a shock: Relative to their body sizes, Paleocene mammal brains were relatively smaller than those of Mesozoic mammals. It wasn’t until the Eocene that mammal brains began to grow, particularly in certain sensory regions, the team reports.
To assess how the sizes and shapes of those sensory regions also changed over time, Bertrand looked for the edges of different parts of the brains within the 3-D skull models, tracing them like a sculptor working with clay. The size of mammals’ olfactory bulbs, responsible for sense of smell, didn’t change over time, the researchers found — and that makes sense, because even Mesozoic mammals were good sniffers, she says.
The really big brain changes were to come in the neocortex, which is responsible for visual processing, memory and motor control, among other skills. But those kinds of changes are metabolically costly, Bertrand says. “To have a big brain, you need to sleep and eat, and if you don’t do that you get cranky, and your brain just doesn’t function.” So, the team proposes, as the world shook off the dust of the mass extinction, brawn was the priority for mammals, helping them swiftly spread out into newly available ecological niches. But after 10 million years or so, the metabolic calculations had changed, and competition within those niches was ramping up. As a result, mammals began to develop new sets of skills that could help them snag hard-to-reach fruit from a branch, escape a predator or catch prey.
Other factors — such as social behavior or parental care — have been important to the overall evolution of mammals’ big brains. But these new finds suggest that, at least at the dawn of the Age of Mammals, ecology — and competition between species — gave a big push to brain evolution, wrote biologist Felisa Smith of the University of New Mexico in Albuquerque in a commentary in the same issue of Science. “An exciting aspect of these findings is that they raise a new question: Why did large brains evolve independently and concurrently in many mammal groups?” says evolutionary biologist David Grossnickle of the University of Washington in Seattle.
Most modern mammals have relatively large brains, so studies that examine only modern species might conclude that large brains evolved once in mammal ancestors, Grossnickle says. But what this study uncovered is a “much more interesting and nuanced story,” that these brains evolved separately in many different groups, he says. And that shows just how important fossils can be to stitching together an accurate tapestry of evolutionary history.
Researchers have finally deciphered a complete human genetic instruction book from cover to cover.
The completion of the human genome has been announced a couple of times in the past, but those were actually incomplete drafts. “We really mean it this time,” says Evan Eichler, a human geneticist and Howard Hughes Medical Institute investigator at the University of Washington in Seattle.
The completed genome is presented in a series of papers published online March 31 in Science and Nature Methods.
An international team of researchers, including Eichler, used new DNA sequencing technology to untangle repetitive stretches of DNA that were redacted from an earlier version of the genome, widely used as a reference for guiding biomedical research.
Deciphering those tricky stretches adds about 200 million DNA bases, about 8 percent of the genome, to the instruction book, researchers report in Science. That’s essentially an entire chapter. And it’s a juicy one, containing the first-ever looks at the short arms of some chromosomes, long-lost genes and important parts of chromosomes called centromeres — where machinery responsible for divvying up DNA grips the chromosome.
“Some of the regions that were missing actually turn out to be the most interesting,” says Rajiv McCoy, a human geneticist at Johns Hopkins University, who was part of the team known as the Telomere-to-Telomere (T2T) Consortium assembling the complete genome. “It’s exciting because we get to take the first look inside these regions and see what we can find.” Telomeres are repetitive stretches of DNA found at the ends of chromosomes. Like aglets on shoelaces, they may help keep chromosomes from unraveling.
Data from the effort are already available for other researchers to explore. And some, like geneticist Ting Wang of Washington University School of Medicine in St. Louis, have already delved in. “Having a complete genome reference definitely improves biomedical studies.… It’s an extremely useful resource,” he says. “There’s no question that this is an important achievement.”
But, Wang says, “the human genome isn’t quite complete yet.”
To understand why and what this new volume of the human genetic encyclopedia tells us, here’s a closer look at the milestone. What did the researchers do? Eichler is careful to point out that “this is the completion of a human genome. There is no such thing as the human genome.” Any two people will have large portions of their genomes that range from very similar to virtually identical and “smaller portions that are wildly different.” A reference genome can help researchers see where people differ, which can point to genes that may be involved in diseases. Having a view of the entire genome, with no gaps or hidden DNA, may give scientists a better understanding of human health, disease and evolution.
The newly complete genome doesn’t have gaps like the previous human reference genome. But it still has limitations, Wang says. The old reference genome is a conglomerate of more than 60 people’s DNA (SN: 3/4/21). “Not a single individual, or single cell on this planet, has that genome.” That goes for the new, complete genome, too. “It’s a quote-unquote fake genome,” says Wang, who was not involved with the project.
The new genome doesn’t come from a person either. It’s the genome of a complete hydatidiform mole, a sort of tumor that arises when a sperm fertilizes an empty egg and the father’s chromosomes are duplicated. The researchers chose to decipher the complete genome from a cell line called CHM13 made from one of these unusual tumors.
That decision was made for a technical reason, says geneticist Karen Miga of the University of California, Santa Cruz. Usually, people get one set of chromosomes from their mother and another set from their father. So “we all have two genomes in every cell.”
If putting together a genome is like assembling a puzzle, “you essentially have two puzzles in the same box that look very similar to each other,” says Miga, borrowing an analogy from a colleague. Researchers would have to sort the two puzzles before piecing them together. “Genomes from hydatidiform moles don’t present that same challenge. It’s just one puzzle in the box.”
The researchers did have to add the Y chromosome from another person, because the sperm that created the hydatidiform mole carried an X chromosome.
Even putting one puzzle together is a Herculean task. But new technologies that allow researchers to put DNA bases — represented by the letters A, T, C and G — in order, can spit out stretches up to more than 100,000 bases long. Just as children’s puzzles are easier to solve because of larger and fewer pieces, these “long reads” made assembling the bits of the genome easier, especially in repetitive parts where just a few bases might distinguish one copy from another. The bigger pieces also allowed researchers to correct some mistakes in the old reference genome.
What did they find? For starters, the newly deciphered DNA contains the short arms of chromosomes 13, 14, 15, 21 and 22. These “acrocentric chromosomes” don’t resemble nice, neat X’s the way the rest of the chromosomes do. Instead, they have a set of long arms and one of nubby short arms.
The length of the short arms belies their importance. These arms are home to rDNA genes, which encode rRNAs, which are key components of complex molecular machines called ribosomes. Ribosomes read genetic instructions and build all the proteins needed to make cells and bodies work. There are hundreds of copies of these rDNA regions in every person’s genome, an average of 315, but some people have more and some fewer. They’re important for making sure cells have protein-building factories at the ready.
“We didn’t know what to expect in these regions,” Miga says. “We found that every acrocentric chromosome, and every rDNA on that acrocentric chromosome, had variants, changes to the repeat unit that was private to that particular chromosome.”
By using fluorescent tags, Eichler and colleagues discovered that repetitive DNA next to the rDNA regions — and perhaps the rDNA too — sometimes switches places to land on another chromosome, the team reports in Science. “It’s like musical chairs,” he says. Why and how that happens is still a mystery.
The complete genome also contains 3,604 genes, including 140 that encode proteins, that weren’t present in the old, incomplete genome. Many of those genes are slightly different copies of previously known genes, including some that have been implicated in brain evolution and development, autism, immune responses, cancer and cardiovascular disease. Having a map of where all these genes lie may lead to a better understanding of what they do, and perhaps even of what makes humans human.
One of the biggest finds may be the structure of all of the human centromeres. Centromeres, the pinched portions which give most chromosomes their characteristic X shape, are the assembly points for kinetochores, the cellular machinery that divvies up DNA during cell division. That’s one of the most important jobs in a cell. When it goes wrong, birth defects, cancer or death can result. Researchers had already deciphered the centromeres of fruit flies and the human 8, X and Y chromosomes (SN: 5/17/19), but this is the first time that researchers got a glimpse of the rest of the human centromeres.
The structures are mostly head-to-tail repeats of about 171 base pairs of DNA known as alpha satellites. But those repeats are nestled within other repeats, creating complex patterns that distinguish each chromosome’s individual centromere, Miga and colleagues describe in Science. Knowing the structures will help researchers learn more about how chromosomes are divvied up and what sometimes throws off the process. Researchers also now have a more complete map of epigenetic marks — chemical tags on DNA or associated proteins that may change how genes are regulated. One type of epigenetic mark, known as DNA methylation, is fairly abundant across the centromeres, except for one spot in each chromosome called the centromeric dip region, Winston Timp, a biomedical engineer at Johns Hopkins University and colleagues report in Science.
Those dips are where kinetochores grab the DNA, the researchers discovered. But it’s not yet clear whether the dip in methylation causes the cellular machinery to assemble in that spot or if assembly of the machinery leads to lower levels of methylation.
Examining DNA methylation patterns in multiple people’s DNA and comparing them with the new reference revealed that the dips occur at different spots in each person’s centromeres, though the consequences of that aren’t known.
About half of genes implicated in the evolution of humans’ large, wrinkly brains are found in multiple copies in the newly uncovered repetitive parts of the genome (SN: 2/26/15). Overlaying the epigenetic maps on the reference allowed researchers to figure out which of many copies of those genes were turned on and off, says Ariel Gershman, a geneticist at Johns Hopkins University School of Medicine.
“That gives us a little bit more insight into which of them are actually important and playing a functional role in the development of the human brain,” Gershman says. “That was exciting for us, because there’s never been a reference that was accurate enough in these [repetitive] regions to tell which gene was which, and which ones are turned on or off.”
What is next? One criticism of genetics research is that it has relied too heavily on DNA from people of European descent. CHM13 also has European heritage. But researchers have used the new reference to discover new patterns of genetic diversity. Using DNA data collected from thousands of people of diverse backgrounds who participated in earlier research projects compared with the T2T reference, researchers more easily and accurately found places where people differ, McCoy and colleagues report in Science.
The Telomere-to-Telomere Consortium has now teamed up with Wang and his colleagues to make complete genomes of 350 people from diverse backgrounds (SN: 2/22/21). That effort, known as the pangenome project, is poised to reveal some of its first findings later this year, Wang says.
McCoy and Timp say that it may take some time, but eventually, researchers may switch from using the old reference genome to the more complete and accurate T2T reference. “It’s like upgrading to a new version of software,” Timp says. “Not everyone is going to want to do it right away.”
The completed human genome will also be useful for researchers studying other organisms, says Amanda Larracuente, an evolutionary geneticist at the University of Rochester in New York who was not involved in the project. “What I’m excited about is the techniques and tools this team has developed, and being able to apply those to study other species.”
Eichler and others already have plans to make complete genomes of chimpanzees, bonobos and other great apes to learn more about how humans evolved differently than apes did. “No one should see this as the end,” Eichler says, “but a transformation, not only for genomic research but for clinical medicine, though that will take years to achieve.”
With soils rich for cultivation, most land in the Midwestern United States has been converted from tallgrass prairie to agricultural fields. Less than 0.1 percent of the original prairie remains.
This shift over the last 160 years has resulted in staggering — and unsustainable — soil erosion rates for the region, researchers report in the March Earth’s Future. The erosion is estimated to be double the rate that the U.S. Department of Agriculture says is sustainable. If it continues unabated, it could significantly limit future crop production, the scientists say.
In the new study, the team focused on erosional escarpments — tiny cliffs formed through erosion — lying at boundaries between prairie and agricultural fields (SN: 1/20/96). “These rare prairie remnants that are scattered across the Midwest are sort of a preservation of the pre-European-American settlement land surface,” says Isaac Larsen, a geologist at the University of Massachusetts Amherst.
At 20 sites in nine Midwestern states, with most sites located in Iowa, Larsen and colleagues used a specialized GPS system to survey the altitude of the prairie and farm fields. That GPS system “tells you where you are within about a centimeter on Earth’s surface,” Larsen says. This enables the researchers to detect even small differences between the height of the prairie and the farmland.
At each site, the researchers took these measurements at 10 or more spots. The team then measured erosion by comparing the elevation differences of the farmed and prairie land. The researchers found that the agricultural fields were 0.37 meters below the prairie areas, on average. This corresponds to the loss of roughly 1.9 millimeters of soil per year from agricultural fields since the estimated start of traditional farming at these sites more than a century and a half ago, the researchers calculate. That rate is nearly double the maximum of one millimeter per year that the USDA considers sustainable for these locations.
There are two main ways that the USDA currently estimates the erosion rate in the region. One way estimates the rate to be about one-third of that reported by the researchers. The other estimates the rate to be just one-eighth of the researchers’ rate. Those USDA estimates do not include tillage, a conventional farming process in which machinery is used to turn the soil and prepare it for planting. By disrupting the soil structure, tilling increases surface runoff and erosion due to soil moving downslope.
Larsen and colleagues say that they would like to see tillage incorporated into the USDA’s erosion estimates. Then, the USDA numbers might better align with the whopping 57.6 billion metric tons of soil that the researchers estimate has been lost across the entire region in the last 160 years.
This massive “soil loss is already causing food production to decline,” Larsen says. As soil thickness decreases, the amount of corn successfully grown in Iowa is reduced, research shows. And disruption to the food supply could continue or worsen if the estimated rate of erosion persists.
Not everyone is convinced that the average amount of soil lost each year has remained steady since farming in the region started. Much of the erosion that the researchers measured could have been caused in the earlier histories of these sites, dating back to when farmers “began to break prairies and/or forests and clear things,” says agronomist Michael Kucera.
Perhaps current erosion rates have slowed, says Kucera, who is the steward of the National Erosion Database at the USDA’s National Soil Survey Center in Lincoln, Neb. To help reduce future erosion, farmers can use no-till farming and plant cover crops, the researchers note. By planting cover crops during off-seasons, farmers reduce the amount of time the soil is bare, making it less vulnerable to wind and water erosion.
In the United States, no-till and similar practices to help limit erosion have been implemented at least sometimes by 51 percent of corn, cotton, soybean and wheat farmers, according to the USDA. But cover crops are only used in about 5 percent of cases where they could be, says Bruno Basso, a sustainable agriculture researcher at Michigan State University in East Lansing who wasn’t involved with the study. “It costs $40 to $50 per acre to plant a cover crop,” he says. Though some government grant funding is available, “the costs of cover crops are not supported,” and there is a need for additional incentives, he says.
To implement no-till strategies, “the farmer has to be a better manager,” says Keith Berns, a farmer who co-owns and operates Green Cover Seed, which is headquartered in Bladen, Neb. His company provides cover crop seeds and custom seed mixtures. He has also been using no-till practices for decades.
To succeed, farmers must decide what particular cover crops are most suitable for their land, when to grow them and when to kill them. Following these regimens, which can be more complicated than traditional farming, can be “difficult to do on large scales,” Berns says.
Cover crops can confer benefits such as helping farmers repair erosion and control weeds within the first year of planting. But it can take multiple years for the crops’ financial benefits to exceed their cost. Some farmers don’t even own the land they work, making it even less lucrative for them to invest in cover crops, Berns notes.
Building soil health can take half a decade, Basso says. “Agriculture is really always facing this dilemma [of] short-sighted, economically driven decisions versus longer-term sustainability of the whole enterprise.”
