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.”
We’ve now seen farther, deeper and more clearly into space than ever before.
A stellar birthplace, a nebula surrounding a dying star, a group of closely interacting galaxies, the first spectrum of an exoplanet’s light. These are some of the first images from the James Webb Space Telescope, released in a NASA news briefing on July 12. This quartet of cosmic scenes follows on the heels of the very first image released from the telescope, a vista of thousands of distant galaxies, presented in a White House briefing on July 11. “First of all, it’s really gorgeous. And it’s teeming with galaxies,” said JWST Operations Scientist Jane Rigby at the July 12 briefing. “That’s been true of every image we’ve taken with Webb. We can’t take [an image of] blank sky. Everywhere we look, there’s galaxies everywhere.”
Going deep The galaxies captured in the first released image lie behind a cluster of galaxies about 4.6 billion light-years away. The mass from those closer galaxies distorts spacetime in such a way that objects behind the cluster are magnified, giving astronomers a way to peer more than 13 billion years into the early universe.
Even with that celestial assist, other existing telescopes could never see so far. But the James Webb Space Telescope, also known as JWST, is incredibly large — at 6.5 meters across, its mirror is nearly three times as wide as that of the Hubble Space Telescope. It also sees in the infrared wavelengths of light where distant galaxies appear. Those features give it an edge over previous observatories.
“There’s a sharpness and a clarity we’ve never had,” said Rigby, of NASA’s Goddard Space Flight Center in Greenbelt, Md. “You can really zoom in and play around.” Although that first image represents the deepest view of the cosmos to date, “this is not a record that will stand for very long,” astronomer Klaus Pontoppidan of the Space Telescope Science Institute in Baltimore said in a June 29 news briefing. “Scientists will very quickly beat that record and go even deeper.”
But JWST wasn’t built only to peer deeper and farther back in time than ever before. The cache of first images and data showcases space scenes both near and far, glimpses of single stars and entire galaxies, and even a peek into the chemical composition of a far-off planet’s atmosphere.
“These are pictures just taken over a period of five days. Every five days, we’re getting more data,” European Space Agency science advisor Mark McCaughrean said at the July 12 briefing. (JWST is an international collaboration among NASA, ESA and the Canadian Space Agency.) “It’s a culmination of decades of work, but it’s just the beginning of decades. What we’ve seen today with these images is essentially that we’re ready now.” Cosmic cliffs This image shows the “Cosmic Cliffs,” part of the enormous Carina nebula, a region about 7,600 light-years from Earth where many massive stars are being born. Some of the most famous Hubble Space Telescope images feature this nebula in visible light, but JWST shows it in “infrared fireworks,” Pontoppidan says. JWST’s infrared detectors can see through dust, so the nebula appears especially spangled with stars. “We’re seeing brand new stars that were previously completely hidden from our view,” said NASA Goddard astrophysicist Amber Straughn.
But molecules in the dust itself are glowing too. Energetic winds from baby stars in the top of the image are pushing and sculpting the wall of gas and dust that runs across the middle. “We see examples of bubbles and cavities and jets that are being blown out from newborn stars,” Straughn said. And gas and dust are the raw material for new stars — and new planets.
“It reminds me that our sun and our planets, and ultimately us, were formed out of this same stuff that we see here,” Straughn said. “We humans really are connected to the universe. We’re made out of the same stuff.” Foamy nebula The Southern Ring nebula is an expanding cloud of gas that surrounds a dying star about 2,000 light-years from Earth. In previous Hubble images, the nebula looks like an oblong swimming pool with a fuzzy orange deck and a bright diamond, a white dwarf star, in the middle. JWST expands the view far beyond that, showing more tendrils and structures in the gas than previous telescopes could see. “You see this bubbly, almost foamy appearance,” said JWST astronomer Karl Gordon, of the Space Telescope Science Institute. In the left hand image, which captures near-infrared light from JWST’s NIRCam instrument, the foaminess traces molecular hydrogen that formed as dust expanded away from the center. The center appears blue due to hot ionized gas heated by the leftover core of the star. Rays of light escape the nebula like the sun peeking through patchy clouds.
In the right-hand image, taken by the MIRI mid-infrared camera, the outer rings look blue and trace hydrocarbons forming on the surface of dust grains. The MIRI image also reveals a second star in the nebula’s core.
“We knew this was a binary star, but we didn’t see much of the actual star that produced this nebula,” Gordon said. “Now in MIRI this star glows red.” A galactic quintet Stephan’s Quintet is a group of galaxies about 290 million light-years away that was discovered in 1877. Four of the galaxies are engaged in an intimate gravitational dance, with one member of the group passing through the core of the cluster. (The fifth galaxy is actually much closer to Earth and just appears in a similar spot on the sky.) JWST’s images show off more structure within the galaxies than previous observations did, revealing where stars are being born.
“This is a very important image and area to study,” because it shows the sort of interactions that drive the evolution of galaxies, said JWST scientist Giovanna Giardino of the European Space Agency.
In an image from the MIRI instrument alone, the galaxies look like wispy skeletons reaching towards each other. Two galaxies are clearly close to merging. And in the top galaxy, evidence of a supermassive black hole comes to light. Material swirling around the black hole is heated to extremely high temperatures and glows in infrared light as it falls into the black hole. An exoplanet’s sky This “image” is clearly different from the others, but it’s no less scientifically exciting. It shows the spectrum of light from the star WASP 96 as it passes through the atmosphere of its gas giant planet, WASP 96b.
“You get a bunch of what looks like bumps and wiggles to some people but it’s actually full of information content,” said NASA exoplanet scientist Knicole Colón. “You’re actually seeing bumps and wiggles that indicate the presence of water vapor in the atmosphere of this exoplanet.” The planet is about half the mass of Jupiter and orbits its star every 3.4 days. Previously astronomers thought it had no clouds in its sky, but the new data from JWST show signs of clouds and haze. “There is evidence of clouds and hazes because the water features are not quite as large as we predicted,” Colón said. A long time coming These first images and data have been a very long time coming. The telescope that would become JWST was first dreamed up in the 1980s, and the planning and construction suffered years of budget issues and delays (SN: 10/6/21).
The telescope finally launched on December 25. It then had to unfold and assemble itself in space, travel to a gravitationally stable spot about 1.5 million kilometers from Earth, align its insectlike primary mirror made of 18 hexagonal segments and calibrate its science instruments (SN: 1/24/22). There were hundreds of possible points of failure in that process, but the telescope unfurled successfully and got to work.
“We are so thrilled that it works because there’s so much at risk,” says JWST senior project scientist John Mather of NASA’s Goddard Space Flight Center. “The world has trusted us to put our billions into this and make it go, and it works. So it’s an immense relief.” In the months following, the telescope team released teasers of imagery from calibration, which already showed hundreds of distant, never-before-seen galaxies. But the images now being released are the first full-color pictures made from the data scientists will use to start unraveling mysteries of the universe.
“It sees things that I never dreamed were out there,” Mather says.
For the telescope team, the relief in finally seeing the first images was palpable. “It was like, ‘Oh my god, we made it!’” says image processor Alyssa Pagan, also of Space Telescope Science Institute. “It seems impossible. It’s like the impossible happened.”
In light of the expected anticipation surrounding the first batch of images, the imaging team was sworn to secrecy. “I couldn’t even share it with my wife,” says Pontoppidan, leader of the team that produced the first color science images.
“You’re looking at the deepest image of the universe yet, and you’re the only one who’s seen that,” he says, of the first picture released July 11. “It’s profoundly lonely.” Soon, though, the team of scientists, image processors and science writers was seeing something new every day for weeks as the telescope downloaded the first images. “It’s a crazy experience,” Pontoppidan says. “Once in a lifetime.”
For Pagan, the timing is perfect. “It’s a very unifying thing,” she says. “The world is so polarized right now. I think it could use something that’s a little bit more universal and connecting. It’s a good perspective, to be reminded that we’re part of something so much greater and beautiful.”
JWST is just getting started as it now begins its first round of full science operations. “There’s lots more science to be done,” Mather says. “The mysteries of the universe will not come to an end anytime soon.”
As a journalist covering COVID-19, I’ve had a front-row seat to the pandemic. I’ve been overwhelmed with despair over the death and suffering. I’ve been numb, trying to keep up with the deluge of COVID-19 studies. One balm has been the understanding of colleagues who also report on COVID-19.
I found solace too in Virology, microbiologist Joseph Osmundson’s book of 11 wide-ranging essays, in which he writes of the pandemic and calls for “a new rhetoric of care.” Osmundson includes journal entries from the pandemic, and some of his experiences are similar to mine. He dreams he’s at a gathering where no one is masked. He too felt the “density” of the pandemic: “Emotionally dense, with loss and struggle and even sometimes joy,” he writes. “Scientifically dense, with papers and pre-prints out every day that need reading and some analysis.”
Osmundson doesn’t just focus on the coronavirus. He jumps from other viruses and the immune system to illness and metaphors for illness, to sex and HIV, to archiving history and whose stories get told. Parts of the book feel like an anthology, with quotes from many writers who have weighed in on these topics. Parts are a call to care for everyone, regardless of race, ethnicity, wealth or who one loves. Overall, Osmundson questions how society thinks about viruses. “Viruses … are not evil, they don’t invade. They just are,” he writes. “The meaning we give a virus affects how we live with it.” When we describe viruses as enemies and illness as a war, it “assumes the necessity of casualties.” He argues instead to focus resources on caring for one another.
Born in the early 1980s, Osmundson, a gay man, is acutely aware of the messages that come with viruses. “Our generation of gay men came after the plague,” he writes. “HIV didn’t just kill bodies. It killed a type of sex as well, a type of pleasure.” But new therapies have saved lives and altered perceptions. Pre-exposure prophylaxis can prevent infection, while treatment can render HIV untransmissible (SN: 11/15/19). These advances changed our relationship with the virus, Osmundson writes. “I used to think that HIV would make it harder to find love and sex. Now we know that HIV-positive and undetectable is safe. It’s sexy.”
But the biomedicine that can change our relationship with viruses has not been wielded equitably, Osmundson observes. He returns throughout the book to our common humanity. “That fact of all our bodies, vulnerable together, necessitates mutual care.”
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.”
The nucleus of a comet discovered in 2014 is the largest ever spotted.
The “dirty snowball” at the center of comet C/2014 UN271 is about 120 kilometers across, researchers report in the April 10 Astrophysical Journal Letters. That makes this comet — also known as Bernardinelli-Bernstein, after its discoverers — about twice as wide as Rhode Island, says David Jewitt, an astronomer at UCLA.
Though the comet is big — and vastly larger than Halley’s comet, which measures a little more than 11 kilometers across — it will never be visible to the naked eye from Earth because it’s too far away, Jewitt says (SN: 12/14/15). The object is now about 3 billion kilometers from Earth. At its closest approach in 2031, the comet will come no closer to the sun than 1.6 billion kilometers, about the same distance as Saturn. Jewitt and colleagues sized up the comet with the help of new images from the Hubble Space Telescope, combined with images taken by another team at far-infrared wavelengths. The analysis also revealed that the comet’s nucleus reflects only about 3 percent of the light that strikes it. That makes the object “blacker than coal,” Jewitt says.
Comet Bernardinelli-Bernstein takes about 3 million years to circle the sun in a highly elliptical orbit. At its farthest, the comet may reach about half a light-year from the sun — about one-eighth of the distance to the next nearest star.
The comet is likely “just the tip of the iceberg” as far as undiscovered comets of this size go, Jewitt says. And for every comet this size, he suggests, there could be tens of thousands of smaller objects circling the sun undetected.
A massive urban landscape that contained interconnected campsites, villages, towns and monumental centers thrived in the Amazon rainforest more than 600 years ago.
In what is now Bolivia, members of the Casarabe culture built an urban system that included straight, raised causeways running for several kilometers, canals and reservoirs, researchers report May 25 in Nature.
Such low-density urban sprawl from pre-Columbian times was previously unknown in the Amazon or anywhere else in South America, say archaeologist Heiko Prümers of the German Archaeological Institute in Bonn and colleagues. Rather than constructing huge cities densely packed with people, a substantial Casarabe population spread out in a network of small to medium-sized settlements that incorporated plenty of open space for farming, the scientists conclude. Airborne lasers peered through dense trees and ground cover to identify structures from that low-density urban network that have long eluded land-based archaeologists.
Earlier excavations indicated that Casarabe maize farmers, fishers and hunters inhabited an area of 4,500 square kilometers. For about a century, researchers have known that Casarabe people fashioned elaborate pottery and constructed large earthen mounds, causeways and ponds. But these finds were located at isolated forest sites that are difficult to excavate, leaving the reasons for mound building and the nature of Casarabe society, which existed from about the year 500 to 1400, a mystery.
Prümers’ team opted to look through the Amazon’s lush cover from above, aiming to find relics of human activity that typically remain hidden even after careful ground surveys. The scientists used a helicopter carrying special equipment to fire laser pulses at the Amazon forest as well as stretches of grassland. Those laser pulses reflect data from the Earth’s surface. This technique, called light detection and ranging, or lidar for short, enables researchers to map the contours of now-obscured structures.
Looking at the new lidar images, “it is obvious that the mounds are platforms and pyramids standing on artificial terraces at the center of well-planned settlements,” Prümers says.
Prümers’ team conducted lidar surveys over six parts of ancient Casarabe territory. The lidar data revealed 26 sites, 11 of them previously unknown.
Two sites, Cotoca and Landívar, are much larger than the rest. Both settlements feature rectangular and U-shaped platform mounds and cone-shaped earthen pyramids atop artificial terraces. Curved moats and defensive walls border each site. Causeways radiate out from Cotoca and Landívar in all directions, connecting those primary sites to smaller sites with fewer platform mounds that then link up to what were probably small campsites or areas for specialized activities, such as butchering prey.
The Casarabe society’s network of settlements joins other ancient and present-day examples of low-density urban sprawl around the world, says archaeologist Roland Fletcher of the University of Sydney. These sites raise questions about whether only places with centralized governments that ruled over people who were packed into neighborhoods on narrow streets, such as 6,000-year-old Mesopotamian metropolises, can be defined as cities.
Some past urban settlements organized around crop growing spanned up to 1,000 square kilometers or more in tropical regions. These include locales such as Southeast Asia’s Greater Angkor roughly 700 to 800 years ago and interconnected Maya sites in Central America dating to at least 2,300 years ago (SN: 4/29/16; SN: 9/27/18). Today, extended areas outside large cities, especially in Southeast Asia, mix industrial and agricultural activities over tens of thousands of kilometers.
Clusters of interconnected Casarabe settlements ranged in area from 100 square kilometers to more than 500 square kilometers. Spread-out settlements of comparable area include 6,000-year-old sites from Eastern Europe’s Trypillia culture (SN: 2/19/20).
Tropical forests that have gone largely unexplored, such as Central Africa’s Congo Basin, probably hosted other early forms of low-density urban development, Fletcher predicts.
Only further excavations guided by lidar evidence can begin to untangle the size of the Casarabe population, Prümers says. Whether primary Casarabe sites represented seats of power in states with upper and lower classes also remains unknown, he adds.
Casarabe culture’s urban sprawl must have encompassed a considerable number of people in the centuries before the Spanish arrived and Indigenous population numbers plummeted, largely due to diseases, forced labor and slavery, says archaeologist John Walker of the University of Central Florida in Orlando.
Whatever Casarabe honchos had in mind as their tropical settlement network spread, he says, “we may have to set aside some of our strongly held ideas about what the Amazon is, and what a city is, to better understand what happened.”
