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Heart-shaped mollusc has windows that work like fibre optics

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Tuesday, November 19, 2024

Heart cockles come in many colours and host photosynthetic algae inside their shellsDakota McCoy A heart-shaped mollusc has evolved tiny windows that work like fibre-optic cables, the first known example in nature. Heart cockles (Corculum cardissa) are bivalve molluscs a bit like clams that have a symbiotic relationship with photosynthetic algae that live inside them. The algae have a safe home, get light to photosynthesise and provide nutrients for their hosts. Unlike other bivalves, heart cockles don’t open their shells up wide, yet they somehow funnel light to their interior even while staying shut. Now, Dakota McCoy at the University of Chicago and her colleagues have found that there are transparent calcium carbonate crystal structures in the heart cockle shells that function like fibre-optic bundles, letting light inside to bathe the algae. “If you don’t have to open and can just have a transparent window, that’s a very safe way to irradiate your algae,” says McCoy. The researchers examined fragments of different heart cockle shells and the transparent structures within them, as well as the intensity and colour of light that gets through. They found that the windows were made from long, thin fibres of a mineral called aragonite – a form of calcium carbonate – which lets twice as much of the photosynthetically useful light through as it does harmful ultraviolet light. “We put on sunblock because UV causes mutations and cancer. The heart cockles are using these windows as a sunblock,” says McCoy. Heart cockle shells illuminated from within to show the transparent windows in their shells, which can be little triangles (left) or stripes (right)Dakota McCoy While the aragonite threads look similar to manufactured fibre optics, they lack a protective, insulating sheath, called cladding, yet transmit light just as effectively. This could serve as an inspiration for cladding-free fibre-optic cables, which would be cheaper to manufacture. The natural, UV-blocking properties of the shells could also be used to help protect corals, which, like the cockles, host photosynthetic algae inside them, but are more susceptible to environmental stresses like light and heat, says McCoy.

Tiny, solid windows in the shells of heart cockles let in light for the photosynthetic algae inside them – and they could show us how to make better fibre-optic cables

Heart cockles come in many colours and host photosynthetic algae inside their shells

Dakota McCoy

A heart-shaped mollusc has evolved tiny windows that work like fibre-optic cables, the first known example in nature.

Heart cockles (Corculum cardissa) are bivalve molluscs a bit like clams that have a symbiotic relationship with photosynthetic algae that live inside them. The algae have a safe home, get light to photosynthesise and provide nutrients for their hosts.

Unlike other bivalves, heart cockles don’t open their shells up wide, yet they somehow funnel light to their interior even while staying shut.

Now, Dakota McCoy at the University of Chicago and her colleagues have found that there are transparent calcium carbonate crystal structures in the heart cockle shells that function like fibre-optic bundles, letting light inside to bathe the algae. “If you don’t have to open and can just have a transparent window, that’s a very safe way to irradiate your algae,” says McCoy.

The researchers examined fragments of different heart cockle shells and the transparent structures within them, as well as the intensity and colour of light that gets through. They found that the windows were made from long, thin fibres of a mineral called aragonite – a form of calcium carbonate – which lets twice as much of the photosynthetically useful light through as it does harmful ultraviolet light. “We put on sunblock because UV causes mutations and cancer. The heart cockles are using these windows as a sunblock,” says McCoy.

Heart cockle shells illuminated from within to show the transparent windows in their shells, which can be little triangles (left) or stripes (right)

Dakota McCoy

While the aragonite threads look similar to manufactured fibre optics, they lack a protective, insulating sheath, called cladding, yet transmit light just as effectively. This could serve as an inspiration for cladding-free fibre-optic cables, which would be cheaper to manufacture.

The natural, UV-blocking properties of the shells could also be used to help protect corals, which, like the cockles, host photosynthetic algae inside them, but are more susceptible to environmental stresses like light and heat, says McCoy.

Read the full story here.
Photos courtesy of

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To Improve Your Gut Microbiome, Spend More Time in Nature

Microbes found in green spaces can transfer into your body, increasing bacterial diversity and potentially boosting the strength of the immune system.

Microbes in our gut can have a profound impact on our health, but research is showing that those surrounding us in our environment—what’s known as the natural environmental microbiome—can have a big impact too. This suggests that we should all spend a lot more time interacting with nature, both outdoors and indoors.I was first introduced to this emerging area of science by Professor Gretchen Daily from Stanford University. She mentioned a Finnish research project that showed how letting kindergarten-aged children play in a yard that contained “dirt” from the forest floor resulted in a significant positive impact on their gut microbiome. Seventy-nine young children took part, all living in urban environments and spending the majority of their days at different daycare centers around Finland. The only difference between them was that these daycare centers had three different types of outdoor spaces.The first type was a fairly standard outdoor play area, comprised of concrete, gravel, and some plastic matting. The second was the type typically found in daycare environments that are already nature-orientated, with grass, soil, and planted areas for the children to play in. These two acted as a control against which to compare the third experimental space, where the concrete and gravel were covered with segments of forest floor and soil from the local coniferous forest.The children were encouraged to play in only one of the three types of yard each day over the 28 days of the experiment (note that some kindergartens have multiple play areas). Before and after periods of play, the children’s skin and gut microbiota were measured using genetic sequencing of bacteria taken from skin swabs and stool samples, along with changes to T cells and cytokines in their blood. These cells and proteins play a critical role in preventing autoimmunity and autoimmune diseases; their levels are often used as an indication of how well the immune system is functioning.Science NewsletterYour weekly roundup of the best stories on health care, the climate crisis, new scientific discoveries, and more. Delivered on Wednesdays.Remarkable results emerged. The children who played in the experimental yard showed a large increase in the diversity of microbiota on their skin and in their gut in comparison to the children playing in the urban and nature-orientated areas. Importantly, these were the “good” types of microbiota—those associated with health benefits. There was also a significant increase in the children’s immunity markers, indicative of them having gained enhanced immunoregulatory pathways—which is indicative of a reduced risk of immune-mediated diseases such as inflammatory bowel disease and rheumatoid arthritis.The importance of this study cannot be overstated. It implies that even short-term exposure to nature’s microbial diversity has the potential to radically alter the diversity of microbiota on our skin and in our gut. In addition, it suggests that the altered gut microbiota can modulate the function of our immune system.A Healthy Microbiome Is Made, Not BornEveryone has a distinctive community of microbes in their gut—a person’s ethnicity, the food they consume, antibiotic use, body size, and the amount they exercise all leave a clear signature on their gut microbial diversity. The role of these microbiota communities is significant. Our organs can only synthesize 11 of the 20 essential amino acids that we need, so the rest, along with 13 essential vitamins, are retrieved and synthesized by our gut microbes.And these microbial communities don’t just help our gut extract nutrients from food. Microbes also produce some of the most important compounds for our health, including immuno-suppressants, anti-cancer, and anti-inflammatory compounds. They appear to be associated with the functioning of our immune system, central nervous system, and associated health outcomes, so much so that clear correlations have been found between particular gut microbiota—so called “sick” microbiomes—and certain illnesses. Those with a distinctive gut microbial signature include irritable bowel syndrome, inflammatory bowel disease, celiac disease, and colorectal cancer as well as nonintestinal disorders such as obesity and type 2 diabetes.

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Canyon De Chelly in Arizona Will Become Latest National Park Unit to Ban Commercial Air Tours

Commercial air tours will soon be prohibited over Canyon de Chelly National Monument in northeastern Arizona under a plan approved this week by the Federal Aviation Administration and the National Park Service

CANYON DE CHELLY NATIONAL MONUMENT, Ariz. (AP) — Commercial air tours will soon be prohibited over Canyon de Chelly National Monument in northeastern Arizona under a plan approved this week by the Federal Aviation Administration and the National Park Service.The park service said in a statement that the plan was was signed Thursday and will take effect in 180 days, barring any legal challenges. It will ban the tours over the park and within a half mile (800 meters) outside its boundary.“Prohibiting commercial air tours protects these lands’ cultural and spiritual significance to the Navajo Nation,” said park Superintendent Lyn Carranza. “Canyon de Chelly National Monument’s Air Tour Management Plan honors the unique nation-to-nation relationship regarding decisions affecting the park and helps to preserve one of the most important archeological landscapes in the southwest.” What is Canyon de Chelly National Monument? The park lies within the Four Corners region inside the Navajo Nation and is among the most visited national monuments in the United States. It's known for its soaring sandstone cliffs and 800-foot (244-meter) high Spider Rock spire. Prehistoric rock art is found throughout the area, which has been home to Native Americans for millennia. What's the history of air tours at U.S. national parks and monuments? The sightseeing flights reportedly date back to the 1930s, when crews building the Hoover Dam on the Arizona-Nevada border asked helicopter pilots working on the project to give flyovers to their families.The tours offering a unique overhead view of spectacular landscapes have long been popular at Grand Canyon National Park in Arizona. Some of the nation’s busiest spots for tour operators have included Hawaii Volcanoes National Park, which is home to one of the world’s most active volcanoes, and Haleakala National Park. What are some objections to to the tours? Supporters of the tours say they offer an exciting experience to tourists and allow older people and those with disabilities to see and enjoy the parks. Critics say the flights are an unnecessarily dangerous way to view some of the most stunning public lands in the United States. Rules designating routes and minimum altitudes were set in 1986 after two tour aircraft collided over the Grand Canyon, killing 25 people. Still, there are currently numerous options for helicopter tours to the Grand Canyon, departing from places including Las Vegas and Sedona, Arizona. Critics also complain that the buzz of helicopters drowns out the sounds of nature, disrupting the experiences of visitors on the ground and tribal members who call the land around the parks home. What regulations exist to manage the tours? The park service works with the FAA to implement the National Park Air Tour Management Act of 2000, which requires tour operators who want to conduct such commercial air tours to get FAA approval. The law also requires the FAA, in conjunction with the park service, to establish management plans for air tours for those parks and nearby tribal lands where applications are made. What other parks have air tour regulations? Canyon de Chelly is the last of roughly two dozen national park units where the group Public Employees for Environmental Responsibility had fought for flyover restrictions. Other national parks where such commercial flyovers essentially are or will be banned in coming years include Badlands National Park and Mount Rushmore National Memorial in South Dakota, Glacier National Park in Montana, and Bandelier National Monument in New Mexico. Only two air tours per year are allowed at Death Valley National Park along the California-Nevada border.Copyright 2024 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.Photos You Should See - Sept. 2024

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Aren’t we all? This article is scheduled to go live soon. Please check back shortly! The post Work In Progress appeared first on Bay Nature.

Aren’t we all? This article is scheduled to go live soon. Please check back shortly! About the Author Tanvi Dutta Gupta is a 2024-2025 editorial fellow at Bay Nature focusing on Wild Billions, Bay Nature's project tracking federal money for nature. She graduated in June 2024 from Stanford with an assortment of degrees including earth systems, ecology, and science communication. Before reaching California, she grew up across Singapore, London, Hong Kong, and India. She enjoys unraveling the intersections of people, nature, and politics; cool animal facts; long runs; and new scone flavors. Every story from Bay Nature magazine is the product of a team dedicated to connecting our readers to the world around them and increasing environmental literacy. Please help us keep this unique regional magazine thriving, and support the ecosystem we’ve built around it, by subscribing today—you’ll get Bay Nature four times a year in your mailbox! Read This Next December 18, 2024 Baynature.org November 27, 2024 Baynature.org November 19, 2024 Baynature.org November 19, 2024 Magazine

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Ecologists find computer vision models’ blind spots in retrieving wildlife images

Biodiversity researchers tested vision systems on how well they could retrieve relevant nature images. More advanced models performed well on simple queries but struggled with more research-specific prompts.

Try taking a picture of each of North America's roughly 11,000 tree species, and you’ll have a mere fraction of the millions of photos within nature image datasets. These massive collections of snapshots — ranging from butterflies to humpback whales — are a great research tool for ecologists because they provide evidence of organisms’ unique behaviors, rare conditions, migration patterns, and responses to pollution and other forms of climate change.While comprehensive, nature image datasets aren’t yet as useful as they could be. It’s time-consuming to search these databases and retrieve the images most relevant to your hypothesis. You’d be better off with an automated research assistant — or perhaps artificial intelligence systems called multimodal vision language models (VLMs). They’re trained on both text and images, making it easier for them to pinpoint finer details, like the specific trees in the background of a photo.But just how well can VLMs assist nature researchers with image retrieval? A team from MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL), University College London, iNaturalist, and elsewhere designed a performance test to find out. Each VLM’s task: locate and reorganize the most relevant results within the team’s “INQUIRE” dataset, composed of 5 million wildlife pictures and 250 search prompts from ecologists and other biodiversity experts. Looking for that special frogIn these evaluations, the researchers found that larger, more advanced VLMs, which are trained on far more data, can sometimes get researchers the results they want to see. The models performed reasonably well on straightforward queries about visual content, like identifying debris on a reef, but struggled significantly with queries requiring expert knowledge, like identifying specific biological conditions or behaviors. For example, VLMs somewhat easily uncovered examples of jellyfish on the beach, but struggled with more technical prompts like “axanthism in a green frog,” a condition that limits their ability to make their skin yellow.Their findings indicate that the models need much more domain-specific training data to process difficult queries. MIT PhD student Edward Vendrow, a CSAIL affiliate who co-led work on the dataset in a new paper, believes that by familiarizing with more informative data, the VLMs could one day be great research assistants. “We want to build retrieval systems that find the exact results scientists seek when monitoring biodiversity and analyzing climate change,” says Vendrow. “Multimodal models don’t quite understand more complex scientific language yet, but we believe that INQUIRE will be an important benchmark for tracking how they improve in comprehending scientific terminology and ultimately helping researchers automatically find the exact images they need.”The team’s experiments illustrated that larger models tended to be more effective for both simpler and more intricate searches due to their expansive training data. They first used the INQUIRE dataset to test if VLMs could narrow a pool of 5 million images to the top 100 most-relevant results (also known as “ranking”). For straightforward search queries like “a reef with manmade structures and debris,” relatively large models like “SigLIP” found matching images, while smaller-sized CLIP models struggled. According to Vendrow, larger VLMs are “only starting to be useful” at ranking tougher queries.Vendrow and his colleagues also evaluated how well multimodal models could re-rank those 100 results, reorganizing which images were most pertinent to a search. In these tests, even huge LLMs trained on more curated data, like GPT-4o, struggled: Its precision score was only 59.6 percent, the highest score achieved by any model.The researchers presented these results at the Conference on Neural Information Processing Systems (NeurIPS) earlier this month.Inquiring for INQUIREThe INQUIRE dataset includes search queries based on discussions with ecologists, biologists, oceanographers, and other experts about the types of images they’d look for, including animals’ unique physical conditions and behaviors. A team of annotators then spent 180 hours searching the iNaturalist dataset with these prompts, carefully combing through roughly 200,000 results to label 33,000 matches that fit the prompts.For instance, the annotators used queries like “a hermit crab using plastic waste as its shell” and “a California condor tagged with a green ‘26’” to identify the subsets of the larger image dataset that depict these specific, rare events.Then, the researchers used the same search queries to see how well VLMs could retrieve iNaturalist images. The annotators’ labels revealed when the models struggled to understand scientists’ keywords, as their results included images previously tagged as irrelevant to the search. For example, VLMs’ results for “redwood trees with fire scars” sometimes included images of trees without any markings.“This is careful curation of data, with a focus on capturing real examples of scientific inquiries across research areas in ecology and environmental science,” says Sara Beery, the Homer A. Burnell Career Development Assistant Professor at MIT, CSAIL principal investigator, and co-senior author of the work. “It’s proved vital to expanding our understanding of the current capabilities of VLMs in these potentially impactful scientific settings. It has also outlined gaps in current research that we can now work to address, particularly for complex compositional queries, technical terminology, and the fine-grained, subtle differences that delineate categories of interest for our collaborators.”“Our findings imply that some vision models are already precise enough to aid wildlife scientists with retrieving some images, but many tasks are still too difficult for even the largest, best-performing models,” says Vendrow. “Although INQUIRE is focused on ecology and biodiversity monitoring, the wide variety of its queries means that VLMs that perform well on INQUIRE are likely to excel at analyzing large image collections in other observation-intensive fields.”Inquiring minds want to seeTaking their project further, the researchers are working with iNaturalist to develop a query system to better help scientists and other curious minds find the images they actually want to see. Their working demo allows users to filter searches by species, enabling quicker discovery of relevant results like, say, the diverse eye colors of cats. Vendrow and co-lead author Omiros Pantazis, who recently received his PhD from University College London, also aim to improve the re-ranking system by augmenting current models to provide better results.University of Pittsburgh Associate Professor Justin Kitzes highlights INQUIRE’s ability to uncover secondary data. “Biodiversity datasets are rapidly becoming too large for any individual scientist to review,” says Kitzes, who wasn’t involved in the research. “This paper draws attention to a difficult and unsolved problem, which is how to effectively search through such data with questions that go beyond simply ‘who is here’ to ask instead about individual characteristics, behavior, and species interactions. Being able to efficiently and accurately uncover these more complex phenomena in biodiversity image data will be critical to fundamental science and real-world impacts in ecology and conservation.”Vendrow, Pantazis, and Beery wrote the paper with iNaturalist software engineer Alexander Shepard, University College London professors Gabriel Brostow and Kate Jones, University of Edinburgh associate professor and co-senior author Oisin Mac Aodha, and University of Massachusetts at Amherst Assistant Professor Grant Van Horn, who served as co-senior author. Their work was supported, in part, by the Generative AI Laboratory at the University of Edinburgh, the U.S. National Science Foundation/Natural Sciences and Engineering Research Council of Canada Global Center on AI and Biodiversity Change, a Royal Society Research Grant, and the Biome Health Project funded by the World Wildlife Fund United Kingdom.

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Butterflies fed with Q-tips, Hollywood moments on the trail, bird battles, beetles, and the Bay Naturiest story of 2024. (It was a competitive field.) The post Bay Nature Staff Picks of 2024 appeared first on Bay Nature.

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