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Florida fossil porcupine solves a prickly dilemma 10-million years in the making

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Florida fossil porcupine solves a prickly dilemma 10-million years in the making


There’s a longstanding debate simmering among biologists who study porcupines. There are 16 porcupine species in Central and South America, but only one in the United States and Canada. DNA evidence suggests North America’s sole porcupine belongs to a group that originated 10 million years ago, but fossils seem to tell a different story. Some paleontologists think they may have evolved just 2.5 million years ago, at the beginning of the ice ages.

A new study published in the journal Current Biology claims to have reconciled the dispute, thanks to an exceptionally rare, nearly complete porcupine skeleton discovered in Florida. The authors reached their conclusion by studying key differences in bone structure between North and South American porcupines, but getting there wasn’t easy. It took an entire class of graduate and undergraduate students and several years of careful preparation and study.

“Even for a seasoned curator with all the necessary expertise, it takes an incredible amount of time to fully study and process an entire skeleton,” said lead author Natasha Vitek. While studying as a doctoral student at the Florida Museum of Natural History, Vitek teamed up with vertebrate paleontology curator Jonathan Bloch to create a college course in which students got hands-on research experience by studying porcupine fossils.

Ancient radiation gave rise to world’s largest rodents

Porcupines are a type of rodent, and their ancestors likely originated in Africa more than 30 million years ago. Their descendants have since wandered into Asia and parts of Europe by land, but their journey to South America is a particularly defining event in the history of mammals. They crossed the Atlantic Ocean — likely by rafting — when Africa and South America were much closer together than they are today. They were the first rodents to ever set foot on the continent, where they evolved into well-known groups like guinea pigs, chinchillas, capybaras and porcupines.

Some took on giant proportions. There were lumbering, rat-like animals up to five feet long, equipped with a tiny brain that weighed less than a plum. Extinct relatives of the capybara grew to the size of cows.

Porcupines remained relatively small and evolved adaptations for life in the treetops of South America’s lush rainforests. Today, they travel through the canopy with the aid of long fingers capped with blunt, sickle-shaped claws perfectly angled for gripping branches. Many also have long, prehensile tails capable of bearing their weight, which they use while climbing and reaching for fruit.

Despite their excellent track record of getting around, South America was a dead end for many millions of years. A vast seaway with swift currents separated North and South America, and most animals were unable to cross — with a few notable exceptions.

Beginning about 5 million years ago, the Isthmus of Panama rose above sea level, cutting off the Pacific from the Atlantic. This land bridge became the ancient equivalent of a congested highway a few million years later, with traffic flowing in both directions.

Prehistoric elephants, saber-toothed cats, jaguars, llamas, peccaries, deer, skunks and bears streamed from North America to South. The reverse trek was made by four different kinds of ground sloths, oversized armadillos, terror birds, capybaras and even a marsupial.

The two groups met with radically different fates. Those mammals migrating south did fairly well; many became successfully established in their new tropical environments and survived to the present. But nearly all lineages that ventured north into colder environments have gone extinct. Today, there are only three survivors: the nine-banded armadillo, the Virginia opossum and the North American porcupine.

New fossils catch evolution in the act

Animals that traveled north had to contend with new environments that bore little resemblance to the ones they left behind. Warm, tropical forests gave way to open grasslands, deserts and cold deciduous forests. For porcupines, this meant coping with brutal winters, fewer resources and coming down from the trees to walk on land. They still haven’t quite gotten the hang of the latter; North American porcupines have a maximum ground speed of about 2 mph.

South American porcupines are equipped with a menacing coat of hollow, overlapping quills, which offer a substantial amount of protection but do little to regulate body temperature. North American porcupines replaced these with a mix of insulating fur and long, needle-like quills that can be raised when they feel threatened. They also had to modify their diet, which changed the shape of their jaw.

“In winter, when their favorite foods are not around, they will bite into tree bark to get at the softer tissue underneath. It’s not great food, but it’s better than nothing,” Vitek said. “We think this type of feeding selected for a particular jaw structure that makes them better at grinding.”

They also lost their prehensile tails. Although North American porcupines still like climbing, it’s not their forte. Museum specimens often show evidence of healed bone fractures, likely caused by falling from trees.

Many of these traits can be observed in fossils. The problem is there aren’t many fossils to go around. According to Vitek, most are either individual teeth or jaw fragments, and researchers often lump them in with South American porcupines. Those that are considered to belong to the North American group lack the critical features that would provide paleontologists with clues to how they evolved.

So when Florida Museum paleontologist Art Poyer found an exquisitely preserved porcupine skeleton in a Florida limestone quarry, they were well aware of its significance.

“When they first brought it in, I was amazed,” said Bloch, senior author of the study. “It is so rare to get fossil skeletons like this with not only a skull and jaws, but many associated bones from the rest of the body. It allows for a much more complete picture of how this extinct mammal would have interacted with its environment. Right away we noticed that it was different from modern North American porcupines in having a specialized tail for grasping branches.”

By comparing the fossil skeleton with bones from modern porcupines, Bloch and Vitek were confident they could determine its identity. But the amount of work this would require was more than one person could do on their own in a short amount of time. So they co-created a paleontology college course, in which the only assignment for the entire semester was studying porcupine bones.

“It’s the kind of thing that could only be taught at a place like the Florida Museum, where you have both collections and enough students to study them,” Vitek said. “We focused on details of the jaw, limbs, feet and tails. It required a very detailed series of comparisons that you might not even notice on the first pass.”

The results were surprising. The fossil lacked the reinforced bark-gnawing jaws and possessed a prehensile tail, making it appear more closely related to South American porcupines. But, Vitek said, other traits bore a stronger similarity to North American porcupines, including the shape of the middle ear bone as well as the shapes of the lower front and back teeth.

With all the data combined, analyses consistently provided the same answer. The fossils belonged to an extinct species of North American porcupine, meaning this group has a long history that likely began before the Isthmus of Panama had formed. But questions remain as to how many species once existed in this group or why they went extinct.

“One thing that isn’t resolved by our study is whether these extinct species are direct ancestors of the North American porcupine that is alive today,” Vitek said. “It’s also possible porcupines got into temperate regions twice, once along the Gulf Coast and once out west. We’re not there yet.”

Jennifer Hoeflich, Isaac Magallanes, Sean Moran, Rachel Narducci, Victor Perez, Jeanette Pirlo, Mitchell Riegler, Molly Selba, María Vallejo-Pareja, Michael Ziegler, Michael Granatosky and Richard Hulbert of the Florida Museum of Natural History are also authors on the paper.



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Prying open the AI black box

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Prying open the AI black box


Artificial intelligence continues to squirm its way into many aspects of our lives. But what about biology, the study of life itself? AI can sift through hundreds of thousands of genome data points to identify potential new therapeutic targets. While these genomic insights may appear helpful, scientists aren’t sure how today’s AI models come to their conclusions in the first place. Now, a new system named SQUID arrives on the scene armed to pry open AI’s black box of murky internal logic.

SQUID, short for Surrogate Quantitative Interpretability for Deepnets, is a computational tool created by Cold Spring Harbor Laboratory (CSHL) scientists. It’s designed to help interpret how AI models analyze the genome. Compared with other analysis tools, SQUID is more consistent, reduces background noise, and can lead to more accurate predictions about the effects of genetic mutations.

How does it work so much better? The key, CSHL Assistant Professor Peter Koo says, lies in SQUID’s specialized training.

“The tools that people use to try to understand these models have been largely coming from other fields like computer vision or natural language processing. While they can be useful, they’re not optimal for genomics. What we did with SQUID was leverage decades of quantitative genetics knowledge to help us understand what these deep neural networks are learning,” explains Koo.

SQUID works by first generating a library of over 100,000 variant DNA sequences. It then analyzes the library of mutations and their effects using a program called MAVE-NN (Multiplex Assays of Variant Effects Neural Network). This tool allows scientists to perform thousands of virtual experiments simultaneously. In effect, they can “fish out” the algorithms behind a given AI’s most accurate predictions. Their computational “catch” could set the stage for experiments that are more grounded in reality.

“In silico [virtual] experiments are no replacement for actual laboratory experiments. Nevertheless, they can be very informative. They can help scientists form hypotheses for how a particular region of the genome works or how a mutation might have a clinically relevant effect,” explains CSHL Associate Professor Justin Kinney, a co-author of the study.

There are tons of AI models in the sea. More enter the waters each day. Koo, Kinney, and colleagues hope that SQUID will help scientists grab hold of those that best meet their specialized needs.

Though mapped, the human genome remains an incredibly challenging terrain. SQUID could help biologists navigate the field more effectively, bringing them closer to their findings’ true medical implications.



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Iron meteorites hint that our infant solar system was more doughnut than dartboard

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Iron meteorites hint that our infant solar system was more doughnut than dartboard


Four and a half billion years ago, our solar system was a cloud of gas and dust swirling around the sun, until gas began to condense and accrete along with dust to form asteroids and planets. What did this cosmic nursery, known as a protoplanetary disk, look like, and how was it structured? Astronomers can use telescopes to “see” protoplanetary disks far away from our much more mature solar system, but it is impossible to observe what ours might have looked like in its infancy — only an alien billions of light years away would be able to see it as it once was.

Fortunately, space has dropped a few clues — fragments of objects that formed early in solar system history and plunged through Earth’s atmosphere, called meteorites. The composition of meteorites tells stories of the solar system’s birth, but these stories often raise more questions than answers.

In a paper published in Proceedings of the National Academy of Sciences, a team of planetary scientists from UCLA and Johns Hopkins University Applied Physics Laboratory reports that refractory metals, which condense at high temperatures, such as iridium and platinum, were more abundant in meteorites formed in the outer disk, which was cold and far away from the sun. These metals should have formed close to the sun, where the temperature was much higher. Was there a pathway that moved these metals from the inner disk to the outer?

Most meteorites formed within the first few million years of solar system history. Some meteorites, called chondrites, are unmelted conglomerations of grains and dust left over from planet formation. Other meteorites experienced enough heat to melt while their parent asteroids were forming. When these asteroids melted, the silicate part and the metallic part separated due to their difference in density, similar to how water and oil don’t mix.

Today, most asteroids are located in a thick belt between Mars and Jupiter. Scientists think that Jupiter’s gravity disrupted the course of these asteroids, causing many of them to smash into each other and break apart. When pieces of these asteroids fall to Earth and are recovered, they are called meteorites.

Iron meteorites are from the metallic cores of the earliest asteroids, older than any other rocks or celestial objects in our solar system. The irons contain molybdenum isotopes that point toward many different locations across the protoplanetary disk in which these meteorites formed. That allows scientists to learn what the chemical composition of the disk was like in its infancy.

Previous research using the Atacama Large Millimeter/submillimeter Array in Chile has found many disks around other stars that resemble concentric rings, like a dartboard. The rings of these planetary disks, such as HL Tau, are separated by physical gaps, so this kind of disk could not provide a route to transport these refractory metals from the inner disk to the outer.

The new paper holds that our solar disk likely didn’t have a ring structure at the very beginning. Instead, our planetary disk looked more like a doughnut, and asteroids with metal grains rich in iridium and platinum metals migrated to the outer disk as it rapidly expanded.

But that confronted the researchers with another puzzle. After the disk expansion, gravity should have pulled these metals back into the sun. But that did not happen.

“Once Jupiter formed, it very likely opened a physical gap that trapped the iridium and platinum metals in the outer disk and prevented them from falling into the sun,” said first author Bidong Zhang, a UCLA planetary scientist. “These metals were later incorporated into asteroids that formed in the outer disk. This explains why meteorites formed in the outer disk — carbonaceous chondrites and carbonaceous-type iron meteorites — have much higher iridium and platinum contents than their inner-disk peers.”

Zhang and his collaborators previously used iron meteorites to reconstruct how water was distributed in the protoplanetary disk.

“Iron meteorites are hidden gems. The more we learn about iron meteorites, the more they unravel the mystery of our solar system’s birth,” Zhang said.



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Supermassive black hole appears to grow like a baby star

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Supermassive black hole appears to grow like a baby star


Supermassive black holes pose unanswered questions for astronomers around the world, not least “How do they grow so big?” Now, an international team of astronomers, including researchers from Chalmers University of Technology in Sweden, has discovered a powerful rotating, magnetic wind that they believe is helping a galaxy’s central supermassive black hole to grow. The swirling wind, revealed with the help of the ALMA telescope in nearby galaxy ESO320-G030, suggests that similar processes are involved both in black hole growth and the birth of stars.

Most galaxies, including our own Milky Way have a supermassive black hole at their centre. How these mind-bogglingly massive objects grow to weigh as much as millions or billions of stars is a long-standing question for astronomers.

In search of clues to this mystery, a team of scientists led by Mark Gorski (Northwestern University and Chalmers) and Susanne Aalto (Chalmers) chose to study the relatively nearby galaxy ESO320-G030, only 120 million light years distant. It’s a very active galaxy, forming stars ten times as fast as in our own galaxy.

“Since this galaxy is very luminous in the infrared, telescopes can resolve striking details in its centre. We wanted to measure light from molecules carried by winds from the galaxy’s core, hoping to trace how the winds are launched by a growing, or soon to be growing, supermassive black hole. By using ALMA, we were able to study light from behind thick layers of dust and gas,” says Susanne Aalto, Professor of Radio Astronomy at Chalmers University of Technology.

To zero in on dense gas from as close as possible to the central black hole, the scientists studied light from molecules of hydrogen cyanide (HCN). Thanks to ALMA’s ability to image fine details and trace movements in the gas — using the Doppler effect — they discovered patterns that suggest the presence of a magnetised, rotating wind.

While other winds and jets in the centre of galaxies push material away from the supermassive black hole, the newly discovered wind adds another process, that can instead feed the black hole and help it grow.

“We can see how the winds form a spiralling structure, billowing out from the galaxy’s centre. When we measured the rotation, mass, and velocity of the material flowing outwards, we were surprised to find that we could rule out many explanations for the power of the wind, star formation for example. Instead, the flow outwards may be powered by the inflow of gas and seems to be held together by magnetic fields,” says Susanne Aalto.

The scientists think that the rotating magnetic wind helps the black hole to grow.

Material travels around the black hole before it can fall in — like water around a drain. Matter that approaches the black hole collects in a chaotic, spinning disk. There, magnetic fields develop and get stronger. The magnetic fields help lift matter away from the galaxy, creating the spiralling wind. Losing matter to this wind also slows the spinning disk — that means that matter can flow more easily into the black hole, turning a trickle into a stream.

For Mark Gorski, the way this happens is strikingly reminiscent of a much smaller-scale environment in space: the swirls of gas and dust that lead up to the birth of new stars and planets.

“It is well-established that stars in the first stages of their evolution grow with the help of rotating winds — accelerated by magnetic fields, just like the wind in this galaxy. Our observations show that supermassive black holes and tiny stars can grow by similar processes, but on very different scales,” says Mark Gorski.

Could this discovery be a clue to solving the mystery of how supermassive black holes grow? In the future, Mark Gorski, Susanne Aalto and their colleagues want to study other galaxies which may harbour hidden spiralling outflows in their centres.

“Far from all questions about this process are answered. In our observations we see clear evidence of a rotating wind that helps regulate the growth of the galaxy’s central black hole. Now that we know what to look for, the next step is to find out how common a phenomenon this is. And if this is a stage which all galaxies with supermassive black holes go through, what happens to them next?,” asks Mark Gorski.



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