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Birdsong and human voice built from same genetic blueprint

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Birdsong and human voice built from same genetic blueprint


Humans have been long fascinated by bird song and the cacophony of other avian sounds — from coos and honks to quacks and peeps. But little is known about how the unique vocal organ of birds — the syrinx — varies from species to species or its deeper evolutionary origins.

A trio of recent studies led by researchers from The University of Texas at Austin is changing that.

The studies include high-resolution anatomical scans of syrinxes from hummingbirds and ostriches — the world’s smallest and largest bird species — and the discovery that the syrinx and larynx, the vocal organ of reptiles and mammals, including humans, share the same developmental programming.

According to Julia Clarke, a professor at UT’s Jackson School of Geosciences, this genetic connection between the vocal organs is an exciting new example of “deep homology,” a term that describes how different tissues or organs can share a common genetic link.

“To me, this is as big as the flippers-to-limbs transition,” said Clarke, who co-led or co-authored the studies. “In some ways, it’s even bigger because the syrinx is not a modified organ with a new function but a completely new one with an ancient and common function.”

The three studies are built on a foundation of collaborative and interdisciplinary syrinx research with physiologists and developmental biologists that Clarke has been leading for over a decade. The research got its start in 2013 when Clarke, a paleontologist, discovered a syrinx in a fossil of a duck-like bird that lived in what is now Antarctica during the Late Cretaceous. The specimen is the oldest syrinx to be discovered. But when she tried to compare the fossil syrinx to the syrinxes of modern birds, she found the scientific literature lacking. Many of the studies dated back to the 19th century, before the advent of modern scientific imaging, or cited claims from those older studies made without double-checking them.

This set Clarke on a mission to modernize — and maximize — syrinx data collection.

“We had this new three-dimensional structure, but we had nothing to compare it to,” said Clarke, describing CT imaging data of the fossil syrinx. “So, we started generating data that did not previously exist on syrinx structure across many different groups of birds.”

Over the years, Clarke and members of her lab have developed new methods for dissecting, preserving and CT-scanning syrinxes that have helped reveal the syrinx in more detail. These enhanced views of the ostrich and hummingbird vocal organ have shown that bird behavior may be just as important as the syrinx when it comes to the repertoire of sounds these birds produce.

For example, in the study of the ostrich syrinx, the researchers found no significant differences in syrinx anatomy between adult male and female birds (previous studies focused only on male ostriches.) However, even though both sexes have the same vocal equipment, male ostriches tended to make a wider variety of sounds than female ostriches, with the sounds often associated with aggressive behaviors between rowdy males. On a visit to a Texas ostrich farm, the researchers recorded 11 types of calls, ranging from high frequency peeps and gurgles in baby ostriches to low frequency boos and booms in adult males. These included a few call types that had never been recorded before. The only sounds definitively recorded from adult female ostriches were hisses. What the females lacked in range, they made up for in attitude said Michael Chiappone, who became involved with the ostrich research as an undergraduate student at the Jackson School and is the lead author of the study.

“They were quite prolific hissers,” said Chiappone, who is now a doctoral student at the University of Minnesota.

For the hummingbird study, the researchers compared the hummingbird syrinx to the syrinx of swifts and nightjars, two close relatives, and found that all three birds have similar vocal folds in their syrinx despite having different ways of learning their calls. Swifts and nightjars work with a limited repertoire of instinctive calls while hummingbirds are able to elaborate on calls by learning complex songs from each other, a trait called vocal learning.

According to Lucas Legendre, a Jackson School research associate who led the hummingbird research, the findings suggest that the common ancestor of all three birds also had a similar vocal fold structure — and that it may have helped lay the groundwork for the evolution in vocal learning in hummingbirds.

“Having all of the [vocal fold] structures already present before vocal learning was acquired by hummingbirds probably made it easier for them to acquire vocal production learning,” he said.

Before the study, it was uncertain if swifts even had vocal folds. As part of the research, Legendre created a 3D digital model of the swift vocal track that takes viewers down the windpipe to the syrinx and to the vocal folds that rest near the top of each branch of the syrinx. The model — dubbed the “magical mystery voyage” by Clarke — shows the advances in anatomical knowledge of syrinx that her lab is leading.

“This is a structure that wasn’t known to exist outside of hummingbirds, but our CT scans revealed that swifts have these vocal folds in the same position,” Clarke said. “This is the kind of voyage we needed to go on to get these answers.”

At the same time Clarke and her team were developing methods to preserve and capture syrinx anatomy across bird species, they were collaborating with Clifford Tabin, a developmental biologist at Harvard University, on investigating the evolutionary origins of the syrinx by tracking the gene expression that accompanied vocal organ development in the embryos of birds, mammals and reptiles.

The research published in Current Biology is a culmination of that collaboration. The study details how scientists discovered the deep connection between the larynx and the syrinx tissues by observing that the same genes were controlling the development of the vocal organs in mice and chicken embryos, respectively, even though the organs arose from different embryological layers.

“They form under the influence of the same genetic pathways, ultimately giving the vocal tissue similar cellular structure and vibratory properties in birds and mammals,” said Tabin, a co-lead on the study.

The study also analyzed syrinx development across bird species — which involved observing gene expression in embryos from 14 different species, from penguins to budgies — and found that the common ancestor of modern birds probably had a syrinx with two sound sources, or two independently functioning vocal folds. This trait is found in songbirds today, allowing many to create two distinct sounds at the same time. The research suggests that that the common ancestor of birds may have been making similarly diverse calls.

These results may shed light on the syrinx’s origins but it’s still unknown when the syrinx first developed and whether non-avian dinosaurs — the ancestors of today’s birds — had the vocal organ, said Clarke. No one has yet found a fossil syrinx from a non-avian dinosaur.

According to Clarke, the best way to understand the possibilities for ancient dinosaur sounds is to continue studying vocalization as it exists today in birds, the dinosaurs that are still with us, and other reptile cousins.

“We can’t start talking about sound production in dinosaurs until we truly understand the system in living species,” she said.

This research was supported by the Gordon and Betty Moore Foundation, Howard Hughes Medical InstituteProfessors Program and the Jackson School of Geosciences. Chad Eliason, a senior research scientist at the Field Museum of Natural History and former postdoctoral scholar at the Jackson School, was also a major contributor to these syrinx projects and others.



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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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