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Healthy oceans need healthy soundscapes

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Healthy oceans need healthy soundscapes

Rain falls lightly on the ocean’s surface. Marine mammals chirp and squeal as they swim along. The pounding of surf along a distant shoreline heaves and thumps with metronomic regularity. These are the sounds that most of us associate with the marine environment. But the soundtrack of the healthy ocean no longer reflects the acoustic environment of today’s ocean, plagued with human-created noise.

A global team of researchers set out to understand how human-made noise affects wildlife, from invertebrates to whales, in the oceans, and found overwhelming evidence that marine fauna, and their ecosystems, are negatively impacted by noise. This noise disrupts their behavior, physiology, reproduction and, in extreme cases, causes mortality. The researchers call for human-induced noise to be considered a prevalent stressor at the global scale and for policy to be developed to mitigate its effects.

The research, led by Professor Carlos M. Duarte, distinguished professor at King Abdullah University of Science and Technology (KAUST), and published in the journal Science, is eye opening to the global prevalence and intensity of the impacts of ocean noise. Since the Industrial Revolution, humans have made the planet, the oceans in particular, noisier through fishing, shipping, infrastructure development and more, while also silencing the sounds from marine animals that dominated the pristine ocean.

“The landscape of sound — or soundscape — is such a powerful indicator of the health of an environment,” noted Ben Halpern, a coauthor on the study and director of the National Center for Ecological Analysis and Synthesis at UC Santa Barbara. “Like we have done in our cities on land, we have replaced the sounds of nature throughout the ocean with those of humans.”

The deterioration of habitats, such as coral reefs, seagrass meadows and kelp beds with overfishing, coastal development, climate change and other human pressures, have further silenced the characteristic sound that guides the larvae of fish and other animals drifting at sea into finding and settling on their habitats. The call home is no longer audible for many ecosystems and regions.

The Anthropocene marine environment, according to the researchers, is polluted by human-made sound and should be restored along sonic dimensions, and along those more traditional chemical and climatic. Yet, current frameworks to improve ocean health ignore the need to mitigate noise as a pre-requisite for a healthy ocean.

Sound travels far, and quickly, underwater. And marine animals are sensitive to sound, which they use as a prominent sensorial signal guiding all aspects of their behavior and ecology. “This makes the ocean soundscape one of the most important, and perhaps under-appreciated, aspects of the marine environment,” the study states. The authors’ hope is that the evidence presented in the paper will “prompt management actions … to reduce noise levels in the ocean, thereby allowing marine animals to re-establish their use of ocean sound.”

“We all know that no one really wants to live right next to a freeway because of the constant noise,” commented Halpern. “For animals in the ocean, it’s like having a mega-freeway in your backyard.”

The team set out to document the impact of noise on marine animals and on marine ecosystems around the world. They assessed the evidence contained across more than 10,000 papers to consolidate compelling evidence that human-made noise impacts marine life from invertebrates to whales across multiple levels, from behavior to physiology.

“This unprecedented effort, involving a major tour de force, has shown the overwhelming evidence for the prevalence of impacts from human-induced noise on marine animals, to the point that the urgency of taking action can no longer be ignored,” KAUST Ph.D. student Michelle Havlik said. The research involved scientists from Saudi Arabia, Denmark, the U.S. and the U.K., Australia, New Zealand, the Netherlands, Germany, Spain, Norway and Canada.

“The deep, dark ocean is conceived as a distant, remote ecosystem, even by marine scientists,” Duarte said. “However, as I was listening, years ago, to a hydrophone recording acquired off the U.S. West Coast, I was surprised to hear the clear sound of rain falling on the surface as the dominant sound in the deep-sea ocean environment. I then realized how acoustically connected the ocean surface, where most human noise is generated, is to the deep sea; just 1,000 m, less than 1 second apart!”

The takeaway of the review is that “mitigating the impacts of noise from human activities on marine life is key to achieving a healthier ocean.” The KAUST-led study identifies a number of actions that may come at a cost but are relatively easy to implement to improve the ocean soundscape and, in so doing, enable the recovery of marine life and the goal of sustainable use of the ocean. For example, simple technological innovations are already reducing propeller noise from ships, and policy could accelerate their use in the shipping industry and spawn new innovations.

Deploying these mitigation actions is a low hanging fruit as, unlike other forms of human pollution such as emissions of chemical pollutants and greenhouse gases, the effects of noise pollution cease upon reducing the noise, so the benefits are immediate. The study points to the quick response of marine animals to the human lockdown under COVID-19 as evidence for the potential rapid recovery from noise pollution.

Using sounds gathered from around the globe, multimedia artist and study coauthor Jana Winderen created a six-minute audio track that demonstrates both the peaceful calm, and the devastatingly jarring, acoustic aspects of life for marine animals. The research is truly eye opening, or rather ear opening, both in its groundbreaking scale as well as in its immediacy.

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Simple test for flu could improve diagnosis and surveillance

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Healthy oceans need healthy soundscapes


Fewer than one percent of people who get the flu every year get tested, in part because most tests require trained personnel and expensive equipment. Now researchers have developed a low-cost paper strip test that could allow more patients to find out which type of flu they have and get the right treatment.

The test, developed by a team from the Broad Institute of MIT and Harvard and Princeton University, and supported by the US Centers for Disease Control and Prevention, uses CRISPR to distinguish between the two main types of seasonal flu, influenza A and B, as well as seasonal flu subtypes H1N1 and H3N2. It can also identify strains that resist antiviral treatment, and with further work, could potentially detect swine and avian flu strains, including H5N1, which is currently infecting cattle.

Appearing in The Journal of Molecular Diagnostics, the results could help improve outbreak response and clinical care by bringing tests that are accurate, low-cost, and fast to doctors’ offices and labs across the US and in other countries.

“Ultimately, we hope these tests will be as simple as rapid antigen tests, and they’ll still have the specificity and performance of a nucleic acid test that would normally be done in a laboratory setting,” said Cameron Myhrvold, co-senior author on the study along with Pardis Sabeti, an institute member at the Broad and a professor at Harvard University and the Harvard T.H. Chan School of Public Health, as well as a Howard Hughes Medical Institute investigator. Myhrvold, who is currently an assistant professor at Princeton University, was a postdoctoral researcher in Sabeti’s lab when the study began.

SHINE a light

The test is based on a technology called SHINE, which was developed by Sabeti’s lab in 2020 and uses CRISPR enzymes to identify specific sequences of viral RNA in samples. The researchers first used SHINE to test for SARS-CoV-2, and later to distinguish between the Delta and Omicron variants. Then, in 2022, they began adapting the assay to detect other viruses they knew were always circulating: influenzas. They wanted to create tests that could be used in the field or in clinics rather than hospitals or diagnostic labs with expensive equipment.

“Using a paper strip readout instead of expensive fluorescence machinery is a big advancement, not only in terms of clinical care but also for epidemiological surveillance purposes,” said Ben Zhang, co-first author on the study, a medical student at Harvard Medical School and an undergraduate researcher in Sabeti’s lab when the study began.

Typical diagnostic approaches such as polymerase chain reaction (PCR) require lengthy processing times, trained personnel, specialized equipment, and freezers to store reagents at -80°C, whereas SHINE can be conducted at room temperature in about 90 minutes. Currently, the assay only requires an inexpensive heat block to warm the reaction, and the researchers are working to streamline the process with the goal of returning results in 15 minutes.

The researchers also adapted SHINE to distinguish between different flu strains. In the future, they say the assay could be adapted to detect two different viruses with similar symptoms, such as influenza and SARS-CoV-2.

“Being able to tease apart what strain or subtype of influenza is infecting a patient has repercussions both for treating them and public health interventions,” said Jon Arizti-Sanz, a postdoctoral researcher in Sabeti’s lab and co-first author on the study.

For example, the tests could help clinicians decide whether to use Oseltamivir, a common antiviral that is effective for only some strains, Arizti-Sanz added. In the field, rapid testing could also help scientists collect samples more strategically during an outbreak to better monitor how the virus is spreading.

Next, the researchers are adapting SHINE to test for both avian and swine influenza strains. “With SARS-CoV-2 and now flu, we’ve shown that we can easily adapt SHINE to detect new or evolving viruses,” Arizti-Sanz said. “We’re excited to apply it to H5N1.”



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Prying open the AI black box

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Healthy oceans need healthy soundscapes


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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Healthy oceans need healthy soundscapes


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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