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A century from now, when biologists are playing games of clones and engineers are playing games of drones, physicists will still pledge their loyalty to the Kingdoms of Substance and Force.

Physicists know the subjects of these kingdoms as fermions and bosons. Fermions are the fundamental particles of matter; bosons transmit forces that govern the behavior of the matter particles. The math describing these particles and their relationships forms the “standard model” of particle physics. Or as Nobel laureate Frank Wilczek calls it, “The Core Theory.”
Wilczek’s core theory differs from the usual notion of standard model. His core includes gravity, as described by Einstein’s general theory of relativity. General relativity is an exquisite theory of gravity, but it doesn’t fit in with the math for the standard model’s three forces (the strong and weak nuclear forces and electromagnetism). But maybe someday it will. Perhaps even by 100 years from now.

At least, that’s among the many predictions that Wilczek has made for the century ahead. In a recent paper titled “Physics in 100 Years,” he offers a forecast for future discoveries and inventions that science writers of the future will be salivating over. (The paper is based on a talk celebrating the 250th anniversary of Brown University. He was asked to make predictions for 250 years from now, but regarded 100 as more reasonable.)

Wilczek does not claim that his forecast will be accurate. He considers it more an exercise in imagination, anchored in thorough knowledge of today’s major questions and the latest advances in scientific techniques and capabilities. Where those two factors meet, Wilczek sees the potential for premonition. His ruminations result in a vision of the future suitable for a trilogy or two of science fiction films. They would involve the unification of the kingdoms of physics and a more intimate relationship between them and the human mind.

Among Wilczek’s prognostications is the discovery of supersymmetric particles, heavyweight partners to the matter and force particles of the Core Theory. Such partner particles would reveal a deep symmetry underlying matter and force, thereby combining the kingdoms and further promoting the idea of unification as a key path to truth about nature. Wilczek also foresees the discovery of proton decay, even though exhaustive searches for it have so far failed to find it. If protons disintegrate (after, on average, trillions upon trillions of years), matter as we know it has a limited lease on life. On the other hand, lack of finding proton decay has been a barrier to figuring out a theory that successfully unifies the math for all of nature’s particles and forces. And Wilczek predicts that:

The unification of gravity with the other forces will become more intimate, and have observable consequences.

He also anticipates that gravity waves will be observed and used to probe the physics of the distant (and early) universe; that the laws of physics, rather than emphasizing energy, will someday be rewritten in terms of “information and its transformations”; and that “biological memory, cognitive processing, motivation, and emotion will be understood at the molecular level.”

And all that’s just the beginning. He then assesses the implications of future advances in computing. Part of the coming computation revolution, he foresees, will focus on its use for doing science:

Calculation will increasingly replace experimentation in design of useful materials, catalysts, and drugs, leading to much greater efficiency and new opportunities for creativity.

Advanced calculational power will also be applied to understanding the atomic nucleus more precisely, conferring the ability…

to manipulate atomic nuclei dexterously … enabling (for example) ultradense energy storage and ultrahigh energy lasers.

Even more dramatically, computing power will be employed to enhance itself:

Capable three-dimensional, fault-tolerant, self-repairing computers will be developed.… Self-assembling, self-reproducing, and autonomously creative machines will be developed.

And those achievements will imply that:

Bootstrap engineering projects wherein machines, starting from crude raw materials, and with minimal human supervision, build other sophisticated machines (notably including titanic computers) will be underway.

Ultimately, such sophisticated computing machines will enable artificial intelligence that would even impress Harold Finch on Person of Interest (which is probably Edward Snowden’s favorite TV show).

Imagine, for instance, the ways that superpowerful computing could enhance the human senses. Aided by electronic prosthetics, people could experience the full continuous range of colors in the visible part of the electromagnetic spectrum, not just those accessible to the tricolor-sensitive human eye. Perhaps the beauty that physicists and mathematicians “see” in their equations can be transformed into works of art beamed directly into the brain.

Artificial intelligence endowed with such power would enable many other futuristic fantasies. As Wilczek notes, the “life of mind” could be altered in strange new ways. For one thing, computationally precise knowledge of a state of mind would permit new possibilities for manipulating it. “An entity capable of accurately recording its state could purposefully enter loops, to re-live especially enjoyable episodes,” Wilczek points out.

And if all that doesn’t sound weird enough, we haven’t even invoked quantum mechanics yet. Wilczek forecasts that large-scale quantum computers will be realized, in turn leading to “quantum artificial intelligence.”

“A quantum mind could experience a superposition of ‘mutually contradictory’ states, or allow different parts of its wave function to explore vastly different scenarios in parallel,” Wilczek points out. “Being based on reversible computation, such a mind could revisit the past at will, and could be equipped to superpose past and present.”

And with quantum artificial intelligence at its disposal, the human mind’s sensory tentacles will not merely be enhanced but also dispersed. With quantum communication, humans can be linked by quantum messaging to sensory devices at vast distances from their bodies. “An immersive experience of ‘being there’ will not necessarily involve being there, physically,” Wilczek writes. “This will be an important element of the expansion of human culture beyond Earth.”

In other words, it will be a web of intelligence, rather than a network of physical settlements, that will expand human culture throughout the cosmos. Such “expanded identities” will be able to comprehend the kingdoms of substance and force on their own quantum terms, as the mind itself merges with space and time.

Wilczek’s visions imply a future existence in which nature is viewed from a vastly different perspective, conditioned by a radical reorientation of the human mind to its world. And perhaps messing with the mind so drastically should be worrisome. But let’s not forget that the century gone by has also messed with the mind and its perspectives in profound ways — with television, for instance, talk radio, the Internet, smartphones and blogs. A little quantum computer mind manipulation is unlikely to make things any worse.

Pocket gophers certainly don’t qualify as card-carrying 4-H members, but the rodents might be farming roots in the open air of their moist, nutrient-rich tunnels.

The gophers subsist mostly on roots encountered in the tunnels that the rodents excavate. But the local terrain doesn’t always provide enough roots to sustain gophers, two researchers report in the July 11 Current Biology. To make up the deficit, the gophers practice a simple type of agriculture by creating conditions that promote more root growth, suggest ecologist Jack Putz of the University of Florida in Gainesville and his former zoology undergraduate student Veronica Selden.
But some scientists think it’s a stretch to call the rodents’ activity farming. Gophers aren’t actively working the soil, these researchers say, but inadvertently altering the environment as the rodents eat and poop their way around — much like all animals do.

Tunnel digging takes a lot of energy — up to 3,400 times as much as walking along the surface for gophers. To see how the critters were getting all this energy, Selden and Putz in 2021 began investigating the tunnels of southeastern pocket gophers (Geomys pinetis) in an area being restored to longleaf pine savanna in Florida that Putz partially owns.

The pair took root samples from soil adjacent to 12 gopher tunnels and extrapolated how much root mass a gopher would encounter as it excavated a meter of tunnel. Then the researchers calculated the amount of energy that those roots would provide.

“We were able to compare energy cost versus gain, and found that on average there is a deficit, with about half the cost of digging being unaccounted for,” Selden says.

Upon examining some tunnels, Selden and Putz saw gopher feces spread through the interior along with signs of little bites taken out of roots and churning of the soil.

The gophers, the researchers conclude, provide conditions that favor root growth by spreading their own waste as fertilizer, aerating the soil and repeatedly nibbling on roots to encourage new sprouting.
“All of these activities encourage root growth, and once the roots grow into the tunnels, the gophers crop the roots,” Selden says. She and Putz say that this amounts to a rudimentary form of farming. If so, gophers would be the first nonhuman mammals to be recognized as farmers, Putz says. Other organisms, such as some insects, also farm food and started doing so much earlier than humans (SN: 4/23/20).

But the study has its skeptics. “I don’t really think you can call it farming per the human definition. All herbivores eat plants, and everybody poops,” says J.T. Pynne, a wildlife biologist at the Georgia Wildlife Federation in Covington who studies southeastern pocket gophers. So the root nibbling and tunnel feces might not be signs of agriculture, just gophers doing what all animals do.

Evolutionary biologist Ulrich Mueller agrees. “If we accept the tenuous evidence presented in the Selden article as evidence for farming … then most mammals and most birds are farmers because each of them accidentally have also some beneficial effects on some plants that these mammals or birds also feed on,” he says.

Not only that, but the study is also dangerous, says Mueller, of the University of Texas at Austin. The public will see through “the shallowness of the data,” he says, and will conclude that science is “just a bunch of storytelling, eroding general trust in science.”

For her part, Selden says she understands that because gophers don’t plant their crops, not everyone is comfortable calling them farmers. Still, she argues that “what qualifies the gophers as farmers and sets them apart from, say, cattle, which incidentally fertilize the grass they eat with their wastes, is that gophers cultivate and maintain this ideal environment for roots to grow into.”

At the very least, Putz says, he hopes their research makes people kinder toward the rodents. “If you go to the web and put in ‘pocket gopher,’ you’ll see more ways to kill them than you can count.”

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.”

Some mosquito-borne viruses turn mice into alluring mosquito bait.

Mice infected with dengue or Zika viruses — and people infected with dengue — emit a flowery, orange-smelling chemical that tempts hungry mosquitoes, researchers report June 30 in Cell. In mice, the infections spur the growth of skin-inhabiting bacteria that make the chemical, drawing in bloodsucking Aedes aegypti mosquitoes that could then transmit the viruses to new hosts, including humans.

Previous studies showed that other mosquito species prefer to feed on animals carrying the parasite that causes malaria (SN: 2/9/17). But it was unknown whether the same was true for viruses such as dengue or Zika, says Gong Cheng, a microbiologist at Tsinghua University in Beijing.

The chemical acetophenone — which to humans smells like orange blossom — may be that lure. Mice infected with dengue or Zika viruses give off approximately 10 times more acetophenone and attract more mosquitoes than uninfected animals, Cheng and colleagues found. People infected with dengue similarly release more of the chemical than healthy people. Samples of odors taken from the armpits of infected people also created potent mosquito magnets when smeared on filter paper attached to a volunteer’s palm.
Acetophenone typically comes from bacteria. Researchers found that Bacillus bacteria on mice were the likely culprits producing the chemical. An infection stops mice from making an antimicrobial protein called RELMα, allowing the acetophenone-emitting microbes to flourish.

But a component of some acne medications can bring back RELMα in mice, the team found. Infected animals fed a derivative of vitamin A called isotretinoin produced less acetophenone and become less attractive mosquito targets.

It’s possible that giving people isotretinoin could help reduce virus transmission among people by hiding infected people from the bloodsucking insects, Cheng says. He and colleagues are planning to test the strategy in Malaysia, where dengue circulates.

Bees that land on short, wide flowers can fly away with an upset stomach.

Common eastern bumblebees (Bombus impatiens) are more likely to catch a diarrhea-inducing gut parasite from purple coneflowers, black-eyed Susans and other similarly shaped flora than other flowers, researchers report in the July Ecology. Because parasites and diseases contribute to bee decline, the finding could help researchers create seed mixes that are more bee-friendly and inform gardeners’ and land managers’ decisions about which flower types to plant.
The parasite (Crithidia bombi) is transmitted when the insects accidentally ingest contaminated bee feces, which “tends to make the bees dopey and lethargic,” says Rebecca Irwin, a community and evolutionary ecologist at North Carolina State University in Raleigh. “It isn’t the number one bee killer out there,” but bees sickened with it can struggle with foraging.

In laboratory experiments involving caged bees and 16 plant species, Irwin and her colleagues studied how different floral attributes affected transmission of the gut parasite. They focused on three factors of transmission: the amount of poop landing on flowers when bees fly and forage, how long the parasite survives on the plants and how easily the parasite is transmitted to new bees. Multiplied together, these three factors show the overall transmission rate.

Compared with plants with long, narrow flowers like phlox and bluebeards, short, wide flowers had more feces land on them and transmitted the parasite more easily to the pollinators, increasing the overall parasite transmission rate for these flowers. However, parasite survival times were reduced on these blooms. This is probably due to the open floral shapes increased exposure to ultraviolet light, speeding the drying out of parasite-laden “fecal droplets,” Irwin says.

The findings confirm a new theory suggesting that traits, such as flower shape, are better predictors of disease transmission than individual species of plants, says Scott McArt, an entomologist focusing on pollinator health at Cornell University who wasn’t involved with the study. Therefore, “you don’t need to know everything about every plant species when designing your pollinator-friendly garden or habitat restoration project.”

Instead, to limit disease transmission among bees, it’s best to choose plants that have narrower, longer flowers, he says. “Wider and shorter flowers are analogous to the small, poorly ventilated rooms where COVID is efficiently transmitted among humans.”

If ripping out coneflowers or black-eyed Susans isn’t palatable, don’t fret. Irwin recommends continuing to plant a diversity of flower types. This helps if one type of flower is “a high transmitting species,” she notes. In the future, she plans to conduct field experiments examining other factors that could influence parasite transmission, such as whether bees are driven to visit certain types of flowers more often in nature.

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.”